McKay: "Elizabeth?"
Computer Voice: "Rodney."
Sheppard: "Is it just me, or does 'Elizabeth' sound a little different?"

McKay: "Are you Elizabeth Weir?"
Computer Voice: "Yes, Rodney. It's me."
McKay: "It's the best I can do."
Computer Voice: "I'm sorry to cause all this trouble. Who's there with you? Is... is John Sheppard there?"
Sheppard: "Hi." (His face!)
Computer Voice: "It's so good to hear your voice again."
Sheppard: "We, uh... thought you were... dead."
Computer Voice: "I suppose I am -- my... my physical body, anyway, but my consciousness is still intact."
Sheppard: "Right. So, um, what happened?"
Computer Voice: "Do you remember the day I ordered you to leave me behind?"
Sheppard: "Yeah. Yeah, I remember."

Fran/Weir: "I'm Elizabeth Weir."
McKay: "Obviously she was in a hurry. She just used the previous Replicator template that was already in the machine... which was FRAN."
Fran/Weir: "John, I'm not a threat to you."
Sheppard: "Well, whatever you are, I'd say building a Replicator body's a pretty big threat."

Fran/Weir: "A child?! Oh, Teyla!" - "I'm so happy for you." - "Is it a boy or a...?"
Teyla: "Boy."
Fran/Weir: "What's his name?"
Teyla: "Torren John Emmagan."
Fran/Weir: "Torren, for your father. And John... Colonel Sheppard."
Teyla: "Yes."
Fran/Weir: "Wait, you're not saying John Sheppard is..."
*giggles* she was worried, wasn't she?
Teyla: "No. No."

Sheppard: "Um, look, we all wanna believe you are who you say you are..."
Fran/Weir: "I understand. You have to be cautious. But it really is me, John. You just have to give me time. You'll see that..."

Sheppard: "Once these human bodies are made and they're downloaded into them, what happens then?"
Woolsey: "Well, seeing as they'll be just like any other human beings, I see no reason not to let them go. They could become valuable allies."
Sheppard: "Well, what if one of them decides to stay?"
Richard looks at him, knowing which one he's referring to.
Woolsey: "Let's cross one bridge at a time, all right?"
Poor John, he so wants to keep Elizabeth, no matter in what form.

Fran/Weir: "John, stay back. Let me handle this."
Sheppard: "Haven't you done enough already?"
Fran/Weir: "I'm trying to help you."
Sheppard: "By what? Escaping?"
Fran/Weir: "I didn't know that Koracen would do this."
Koracen: "Of course she knew." - "Elizabeth has been a willing participant in our goals from the very beginning. It was her idea to come here in the first place."
Sheppard: "You said you broke off from them, that they couldn't track you."
Koracen: "Track her? She was the one who alerted us when the time was right to come. We were only following her commands."
Fran/Weir: "John, listen to me. I had to bring them here. It was our only chance, our only way out. I didn't think that Koracen would cause this kind of trouble." - "I didn't think that anyone would get hurt."
Sheppard: "What did you think we were gonna do: just give you a bunch of Replicator bodies and send you on your way?"
Fran/Weir: "I truly believed that we were no threat to you."
Sheppard: "You may still think that you're Elizabeth, but you're not."
Fran/Elizabeth looks at him, hurt. As she bows her head in pain, the lights come on. Taking advantage of the distraction, Koracen charges at John, pulls his rifle out of his hand and hurls him hard against the wall. As John slumps to the floor, Fran/Elizabeth races over and grabs Koracen, slamming him angrily back against the wall. Before he can react, she pushes her fingers into his forehead and concentrates. John looks up from the floor in confusion. She pulls her fingers out again and Koracen disintegrates into tiny pieces.
Way to go, Elizabeth. Nobody threatens her John.

Fran/Elizabeth turns around and looks at John. She smiles at him. John looks like he doesn't know what to feel. Fran/Elizabeth steps through the Gate, leading the Replicators to their death.
McKay: "They were sent to a space Gate." - "I guess that answers the question as to whether it was really Elizabeth."
John remains where he is, staring at the Gate in grief, maybe because he believes now it was Elizabeth.
On the other side of the Gate, Fran/Elizabeth floats helplessly in space. Gradually her eyes close and she ceases to function. Her body slowly drifts into the void.
Oh dear. John is heartbroken by her sacrifice. So am I.

John is standing in Elizabeth's office. Rodney comes in.
McKay: "Any word on how she's doing?"
Sheppard: "She's still in the OR. No real news yet." John looks like he's under a lot of pressure having to make so many decisions without Elizabeth at his side. Rodney looks like he feels his pain.

Sheppard: "Is she okay?"
Keller: "She's alive, but she's in bad shape. She's got six broken ribs, one of which punctured a lung. Amazingly, she doesn't have any spinal damage, but her head got knocked around pretty good. She's suffering from cerebral edema, which may have caused substantial brain damage."
Sheppard: "What does all that mean?"
Keller: "Well, it's too early to know for sure but, if she survives, and I gotta stress the if, she'll never be the same Elizabeth again. I'm sorry."
John looks utterly shocked. He is close to tears but fights not to cry.

Sheppard: "You wanna do what?"
McKay: "Reactivate Weir's nanites."
Sheppard: "That is a terrible, terrible idea."
McKay: "What? I'd reprogram them."
Sheppard: "No."
McKay: "John, we are losing her here. Keller and her team have done everything they can. If I can reprogram the nanites to help repair her body without trying to take over her brain, then..."
Sheppard: "Well, that's a big if, isn't it?"
McKay: "I'm fairly confident I can reprogram them to do only what we want."
Sheppard: "Fairly confident? What if they come back online and start communicating with the other replicators? The last thing we need right now is a bunch of robot warships showing up."
McKay: "Are you listening? Look, I said, I can reprogram them to be completely harmless."
Sheppard: "I am not having this conversation until you're sure. I wanna save Elizabeth as much as anyone, (John pauses, and takes a deep breath), but she wouldn't want us risking the city, not even for her."

McKay: "She'd be part Replicator for the rest of her life."
Keller: "Yeah, Sheppard's not gonna go for that." You think! Well, Elizabeth's welfare is always about Sheppard, isn't it?

Sheppard: "What were you doing in there?"
McKay: "Look, she was dying, okay?"
Sheppard: "Rodney?"
McKay: "Look, her heart was weak, her nervous system was fried."
Sheppard: "What did you do?"
McKay: "I reactivated the nanites."
Sheppard: "DAMMIT, McKay!"
McKay: "Look, you were busy! It was life or death! If I didn't act..."
Sheppard: "Yes, she would have died, I know!"
McKay: "Okay, I know what you're thinking, but helping Elizabeth is not putting us at risk."
Sheppard: "You just reactivated the Replicator nanites."
McKay: "They're harmless! Look, I am a 100% certain they're not gonna try to take her over, or contact the others."
Sheppard: "No, no, you can't know that for sure."
McKay: "Yes. Yes I can."
Sheppard: "Shut it down."
McKay: "But... that would kill her."
Sheppard: "What do you think Elizabeth would want? Do you think she'd want this?"
McKay: "Yes, she would! She'd sure as hell do the same for you."
Sheppard: "Then you obviously didn't know her very well."
McKay: "Oh, maybe not, but do you know what? Give it some time, you can ask her yourself."
Sheppard: "NO! It's too dangerous. Shut it down. Right now."
McKay: "No. No, I'm not going to."
Sheppard: "Meyers. Bring an EMP generator to the OR."
McKay: "Would you please just listen to me?"
Nurse: "Doctor Keller!"
The doors to the O.R. open. John and Rodney walk in, followed by Jennifer and Ronon. The nurse is nervously backing towards the wall as the sound of loud and shaky breathing can be heard from the bed. Everyone stares as Elizabeth sits up in bed.
Weir: "John?" - "Rodney."
Breathing shakily, she reaches up to the bandage around her head and pulls it off. Her hair has grown back to its full length. "What's going on?"
John is a true leader. The city comes first. Sadly he is right. Elizabeth would agree with him - she says so to Teyla later.

Sheppard: "I ordered Rodney to write a kill switch into the nanites' code. If we trigger the program, it'll neutralise them."
Weir: "Neutralise them. You mean shut them off?"
McKay: "Yes."
Weir: "And you said the nanites are all that are keeping me alive."
Sheppard: "They are. If we shut them off, it will... kill you." He pauses, then whispers: "But that's not gonna happen, all right?" He continues in a normal voice. "I've ordered Rodney to keep an eye on the little bastards, make sure they behave."

Rodney, Ronon and Teyla leave the room. John walks closer to Elizabeth as the doors close. She tries to meet his gaze but then lowers her head in distress.
Sheppard: "You're gonna be okay, Elizabeth."
Weir: "Still, I would like all of you to keep a very close eye on me, and the first sign of any suspicious behaviour, do not hesitate with that kill-switch."
Sheppard: "Okay, but that's not gonna happen..."
Weir: "John, I mean it."
They gaze at each other for a moment, then Elizabeth nods her head fractionally. Reluctantly, John nods back.

Sheppard: "How you feeling, Elizabeth?"
Weir: "Very strange."

McKay: "Yes... but there's a problem. Look, I can reprogram the nanites in your brain and use that link to upload the changes, but we'll need to wait for the next merge to affect all the Replicators at once, and we have no idea when that could be. Not only that, but the instant it happens, they'll know you're there. They'll take immediate steps to assimilate you."
Sheppard: "Then we're not doing it."
Weir: "John, you know what this could mean. If the Replicators go to war with the Wraith?"
Sheppard: "Forget about it. It's not happening."
Weir: "That's not your call."
Sheppard: "The hell it isn't!"

Sheppard: "Don't worry about it. You're not coming with us. Neither is Elizabeth."

Sheppard: "I need you to stay here, Rodney."
McKay: "Why?!"
Sheppard: "Rodney!"
Weir: "To keep an eye on me. You may need to activate the kill switch on the nanites. You'll be able to keep a closer eye on me if we both stay here in the Jumper."
McKay: "All right."

Weir: "Hurry, John, they're coming, and there's 100s of them." His welfare is still more important than her own.

Sheppard: "Elizabeth, this is Sheppard, do you copy?" - "Elizabeth. Respond."
Dex: "If they capture her..."
Sheppard: "I know. I know."
McKay: "So, what do we do now?"
Dex: "She said to hit the kill switch on the nanites if she did anything suspicious."
McKay: "I know, but..."
Dex: "Sheppard." - "Make the call."
Sheppard: "Do it." John's face is a mask of pain and sorrow.

Elizabeth holds off Oberoth by messing with his mind, to save John, the team and Atlantis, sacrificing herself in the end.

John is not willing to leave without Elizabeth. He'll find her he says.

Sheppard: "Elizabeth."
Weir: "Get to the Jumper!"
Sheppard: "You're coming with us."
Weir: "I can't keep them frozen much longer!"
Sheppard: "We're not leaving you behind!"
Weir: "If you don't leave right now, none of us will get out of here, so go! THAT'S AN ORDER!"
Dex: "Come on!"
Sheppard: "Elizabeth!"
Weir: "Go!"

Sheppard: "Colonel, we lost Dr. Weir on the Replicator planet. Can you lock on her locator beacon, and beam her up?"
Carter: "I'm not picking up any signal."
Sheppard: "Copy that."

Carter: "General Landry sends his condolences. He was deeply saddened to hear about Dr. Weir. We all were."
Sheppard: "We haven't given up hope. If there's a chance she's still alive, I'll find her." John says I will find her and not we!
Carter: "I know."

Sheppard: "You know, for most of us, this thing with Elizabeth isn't over yet. She's still out there."
Carter: "You really believe there's a chance she's still alive?"
Sheppard: "There's only one way to know for sure."
Carter: "You're suggesting we go back."
Sheppard: "We should have done it sooner, but the IOA's been stonewalling me. Now that you're in charge, maybe you can give me the green light."
Carter: "I'm sorry, but it's too dangerous."
Sheppard: "It's no more dangerous than the last time we went in."
Carter: "Circumstances were different. Plus, you had an advantage then that you don't have now."
Sheppard: "Well, she's the one who gave us that advantage. The only reason we're here is because of what she did."
Carter: "Believe me. I know. And I don't like the idea of leaving someone behind anymore than you do. But I am not about to send you or anyone else on a suicide mission. Now, you come to me with a plan that has even an outside chance of succeeding, and I'll consider it. Short of that, John, I'm sorry. There's nothing I can do."
Sheppard: "Fair enough."

John ingratiates himself to Colonel Carter to get her permission for a rescue mission to find Elizabeth. He gives her a fruit basket as a welcome present (which he stole from Rodney!), he comes out to the balcony and talks to her nicely, and then he makes his move. Ha. Besides that he tried to convince the IOA to give him permission.

Sheppard: "Maybe there's a way to... I don't know, reason with it."
Carter: "Being in Doctor Weir's old office made you think of that, didn't it?"
Sheppard: "Normally I just shoot the bad guys."

John is still sounding so proud, saying "Lieutenant Colonel John Sheppard."

More or less Rodney says sorry for what happened with the replicators, Elizabeth, and the recent problem, because he's the one who changed the code. John says it was his call. Well, that's true.

Sheppard: "Oh, well, they're good at that! They'll bicker and argue, but at the end of the day they're gonna leave you holding the bag just like they did with Elizabeth."

I don't like Carter calling him John. I don't like Carter being on the balcony with him. That's only Elizabeth's privilege. At least Carter is not seeing him going offworld through the gate every time, or welcoming him back home.

The name Weir is mentioned. John looks sad.

RepliWeir: "Listen to me. You have probed our minds. You know everything there is to know about us. You should know, we will never accept this. No matter how many times you wipe our memories, we'll always figure it out."
RepliSheppard: "She's right. We're genetically pre-disposed to being... stubborn, really pesky."

RepliSheppard: "You doing okay?"
RepliWeir: "Sure, all things considered. Not bad for a dead woman."
Sheppard: "Everything'll be fine."

Sheppard: "Elizabeth!"
RepliWeir: "Hello, John."
McKay: "Elizabeth! What happened to you? How'd you get away?"
RepliWeir: "I'm not Elizabeth. Well, not the Elizabeth you knew. I have all of her memories and all of her thoughts, everything that makes her me. But I'm a duplicate. I was created by a faction of the Replicators as a means to attaining ascension."
McKay: "But you... look and sound just like her."
RepliWeir: "I'm sorry, Rodney, but it's true. This group managed to isolate themselves from the others in order to pursue their study in secrecy, but they were eventually discovered and destroyed."
Sheppard: "I... don't know what to say. This is all very, uh..." His eyes are wet. He is fighting not to cry.
RepliWeir: "Strange? Yeah, I know."

Sheppard: "We appreciate all this, but the truth is we came here for another reason. You were with the Replicators. What do you know about our Elizabeth? And are you willing to help us get her back?"

John and RepliElizabeth are walking through the forest.
Sheppard: "You think this other Keller was telling the truth?"
RepliWeir: "I don't know why she'd lie."
Sheppard: "It's kinda weird, that's all. I mean, I (not we) don't see you for all this time, and then five minutes later, I find out..."
RepliWeir: "That I'm dead. Yeah. Don't worry. The moment were I learned the truth, I knew there'd be no going back the way things were. Not for me, not for any of us."

Sheppard: "It's not like this hasn't happened before. The other Elizabeth got infected by those little nanite things, and we figured out how to stop them somehow. Maybe we can do the same for you."
RepliWeir: "So we wouldn't be a security threat?"
Sheppard: "You can contribute. Things will just be... different."
RepliWeir: "That's not really the issue, John. I guess what really bothers me is just knowing that you and the others will always consider me less than what I really am."
Sheppard: "That's not true."
RepliWeir: "Of course it is – and I don't blame you."

RepliWeir: "We'll all have a better chance this way."
Sheppard: "I don't want you doing this because you feel any less, uh..."
RepliWeir: "Human? From the beginning, we've been trying to convince ourselves that we're just like you. Now we've got a chance to prove it."
Sheppard: "All right. Let's go."

McKay: "What about you? Isn't it past your bedtime?"
Sheppard: "I'll approve the removal of her personal items tomorrow. I have everything shipped back to Earth. I would have done it sooner, but I actually thought we're gonna bring her back."
McKay: "Yeah, me too."
*sniff*

A copy of Elizabeth is alive.

Sheppard: "He's not good dealing with this sort of thing."
CloneCarson: "What sort of thing?"
Sheppard: "Oh, you know, clones, duplicates, people coming back from the dead. We went through this with Elizabeth."
CloneCarson: "Rodney told me. It must be difficult."
Sheppard: "Yeah." (only a whisper on his lips.)

Colonel Caldwell informs Elizabeth about the loss of key personal (John, Rodney, Ronon), and says how sorry he is. Elizabeth doesn't allow herself to mourn but moves on to the urgent matter of saving Earth. Shortly after she ordered to go there, leaving the fate of Atlantis in the hands of Teyla and others. On Earth she fiercely defends her decisions and doesn't care if they'll fire her. Well, she mourns.

The hive ship comes out of hyperspace.
Sheppard (via radio): "Atlantis, this is Sheppard. Come in."
Teyla: "John?"
Weir: "They made it?"
Sheppard: "We're out of food, water, and we haven't slept in days, but, yeah, we made it."
Elizabeth smiles, puts her hands over her face, and keeps smiling.
Sheppard: "So now would not be a good time to fire on us. After all, wouldn't wanna damage your new hive ship."

CONFERENCE ROOM. Elizabeth is sitting at the table, glowing with joy.
Weir: "We've all logged more than a few miles these past few weeks."
John, Rodney, Teyla and Ronon are sitting around the table across from her.
Weir: "I'd just like to say that seeing you now, sitting across from me... looking at your faces..." she pauses, gazing at John more than the others "...it makes me feel very..." she pauses again, then looks away, on the brink of tears and unable to continue.
Sheppard: "You don't have to say it."
Teyla: "We feel the same way you do."
McKay: "Oh, she feels hungry too, hmm?"
Elizabeth smiles at his joke. Rodney turns to her, smiling too, knowing that he has managed to defuse one awkward moment.

John defends Elizabeth's decisions in a conversation with Woolsey, calling her Elizabeth.

John walks into Elizabeth's office where she is sitting at her desk.
Sheppard: "Just out of a political curiosity, how much trouble is it gonna cause you if I knock this Woolsey guy in the head?"
Weir: "May I ask why you'd like to do that?"
Sheppard: "It's just an impulse I had, really, one I suspect I'm gonna have again next time I see him. He may not even have to say anything."
Weir: "I've never seen you like this. What did Woolsey say to you?"
Sheppard: "Besides judging every damn decision you've ever made?"
Weir: "John Sheppard, are you defending my honour?!"
John hesitates for a moment before continuing. "And judging me for agreeing with you."
Weir: "Well, don't be too hard on him. I think of all the circling wolves, he's the least likely to actually bite. In fact, he might even convince the others to leave us alone."
Sheppard: "All right, so... no head knocking."
Weir: "It's the thought that counts." She smiles.

Weir: "Are you feeling all right?"
Carson: "What do you mean?"
Sheppard: "It's just, you're acting a little..."
Weir: "Smitten?"
Sheppard: "I had another word in mind."

Lucius turns to Elizabeth and cups her face with his hand. "Beautiful and brilliant. The two B's." Elizabeth whimpers.
Unnoticed, John has come into the room. He glares at the way that Elizabeth is behaving.
Sheppard: "Doctor Weir." Oh, not a good sign.
Weir: "Oh, hi, John. We were just discussing the gate-harvesting program."
Sheppard: "Yeah, I heard."
Weir: "And Lucius knows of an excellent planet we should investigate."
Sheppard: "I heard that too. We got Intel that the Wraith recently set up a major outpost there. An alliance of three hives."
Lucius: "No. Really?"
Weir: "Has your Intel been verified?"
Sheppard: "We haven't put boots on the ground, no, but our contacts are trustworthy. Not gonna send a team down there when there's still plenty of gates to scout."
Weir: "John, you are way behind Rodney's quota."
Sheppard: "Forget Rodney's quota. I am not sending a team into harm's way."
Lucius: "You know what? Colonel Sheppard is right. Don't get me wrong. With all your advanced weapons you could easily dispose of a tiny Wraith outpost, if there even is an outpost, but ultimately, is it worth the risk, no matter how small that risk may be? I mean, sure, people may label you a coward..."
Sheppard: "Will you knock it off?!"
Weir: "Colonel. I think it's worth investigating."
Sheppard: "No. I won't allow it."
Weir: "John, are you questioning my authority?"
Sheppard: "When it comes to the security of this base, you're damn right I am. From now on, no one goes through that gate... without my authorisation."

In John's absence Elizabeth calls John a really good man.

Sheppard: "Where's Elizabeth?"
Lucius: "She's out making me something to eat."
Sheppard: "What?" His tone. Hilarious! He just can't believe it.

Sheppard: "So everyone here, uh, back to normal?"
Weir: "We're still fine, John."
Sheppard: "No lingering desires? Secret longings for his touch?"
Carson: "It's embarrassing enough without you constantly reminding us, thank you."
Sheppard: "All right, all right." Oh, the way John smirks at Elizabeth.

Elizabeth attends the mission without telling anybody. John looks torn between excitement and worry, plus he says, she's the boss.

John makes a sarcastic comment. Elizabeth smiles.

They all head for the Gate. Elizabeth pauses as the others run into the event horizon, looking around the Gateroom as a marine ushers the last of the evacuees into the Gate. Up in the Control Room, John runs over to the balcony and looks down at her. "We're losing power! Get through the Gate!"
Elizabeth backs towards the Gate, reluctant to leave, but then turns and runs towards it, glancing back one last time just as she enters the event horizon.

Niam turns and looks at Elizabeth for a moment, then reaches out and grabs her around the throat with both hands. Ronon jumps up and grabs one of his arms, trying to pull him away from her. Teyla runs and pulls on Niam's other arm as Elizabeth chokes. John jumps up and charges at Niam, knocking him to the floor in the rear compartment. As Ronon draws his blaster and aims it, John punches the button that closes the bulkhead doors. John turns, thinking for a second, then races to the controls and slaps a button. In the rear compartment, Niam -- just getting up onto his hands and knees -- looks up in horror as the rear hatch blows out. A moment later, he is blown out into space. In the front compartment, Elizabeth sits down, coughing, as Teyla tends to her. She nods reassuringly to Teyla as she continues to cough. John, now back in the pilot's seat, looks round at Elizabeth. "You okay?"
Elizabeth, still a little breathless but recovering, looks at him and nods. "Yeah."

They share a moment on the balcony, gazing up into a moonlit night sky.

Elizabeth is on the brink of losing the battle against the nanites. John is worried sick. She sees his shadow haunting her in the fantasy world the nanites have created.

John waits until he's alone with Elizabeth, then turns to her.
"You know, if Carson's right and you can hear me, I suppose I should say something profound. Okay, I'm not so good at profound, but you should know we're doing everything we can to get you through this. These, these nanites, I don't know what they're putting you through, I don't know what they're doing to you, but... don't let them get to you. We're doing everything we can to bring you back, but you've got to do your part. You've gotta fight this."

Lying in bed, Elizabeth wakes up at the sound of John's voice. "Elizabeth." A male figure is silhouetted in the open doorway. Elizabeth gasps. "What do you want?" The figure turns and walks away.

Sheppard: "You're not alone, Elizabeth. We're right here with you. You have to fight this. Fight this. Fight this.
Elizabeth sees his shape again and starts fighting, running after him.
Sheppard: "Elizabeth! Don't listen to them. This way." He walks on. She follows him.

Beckett: "They've begun to spread faster. We're losing her."
Sheppard: "Not yet we're not." Before anyone can stop him, he moves to the isolation tent and unzips it.
McKay: "What're you doing?"
John hurries over to the bed and puts both hands on Elizabeth's arm.
McKay: "What, are you crazy? She could infect you!"

Sheppard: "Elizabeth!"
Weir: "John!"
Sheppard: "You've been infected by nanites. They're trying to take control of your mind and body. Don't let them do it. You have to fight them. So fight. You know which way you have to go. Run."
Elizabeth runs towards him.

Carson pulls John away from Elizabeth. Shortly after Elizabeth wakes up all thanks to him.

NIGHT TIME. John walks into the Control Room and goes over to Elizabeth, who is standing with her back to him on the balcony facing the Gateroom, holding something in her hands.
Sheppard: "Still up, huh?"
Weir: "Oh, hey. Yeah, I wasn't all that keen to go back to sleep just yet."
Sheppard: "Understandable."
Weir: "I'm glad to see you've been released from quarantine."
Sheppard: "Yeah. Well, I guess the nanites were too focused on you... to spread to me."
Weir: "I now realise just how insidious they really are. I mean, if such a small number of them could do that to me..."
Sheppard: "Let's just take it as a win right now."
Weir: "All right. Still... I can't believe I was only out for five hours."
Sheppard: "Felt longer, huh?"
Weir: "Yes. A lifetime."
Sheppard: "Well, it's good to have you back in the real world. At least, I think it's the real world. I could be infected right now, which makes me the one--"
Weir: "John. Don't."
Sheppard: "Sorry."

John vanishes. Elizabeth is concerned.

Elizabeth demands to speak to John. Kolya orders to remove the gag in John's mouth.
Sheppard: "On my command authority, whatever he asks, don't do it--" He is gagged again.
Kolya laughs. Shortly after Elizabeth has to watch how a Wraith is feeding on John. 2 times she pleads, "Don't do this", then she screams, "Stop! Stop!"

Dex: "I say we turn him over and let them fight it out."
McKay: "We can't do that."
Dex: "Why not?"
McKay: "Because. Well, can we?"
Teyla: "Colonel Sheppard has already ordered us not to."
Weir: "At this point, it's not his decision."

Rodney looks up to Elizabeth who is standing on the balcony.
Weir: "Just bring him back."

Kolya: "I think you underestimate the sympathetic nature of Dr. Weir."
Sheppard: "Well, then you underestimate Elizabeth."

Weir: "It was John Sheppard's last order that we do not submit to Kolya's demands. And it is my own country's policy to never yield to terrorists. Those are the reasons you're still here, Mr. Radim. Because believe me, if it was simply my choice--" Her voice breaks.

The Wraith feeds on John again. Elizabeth looks like breaking apart.

Elizabeth seizes the railing of the balcony, waiting, desperate.

McKay: "None of us are saying what we're all thinking here." That John is dead.
Weir: "No, Rodney, we're not."

Weir: "If you do find Kolya--"
Dex: "No promises."
Weir: "Exactly."

Elizabeth and John are walking down the stairs to the gate.
Weir: "Has he talked about his sister with you?"
Sheppard: "Once or twice in passing. Usually like, come on, even my sister can do it. You know, that type of thing."
Elizabeth chuckles.

They watch the two McKays, smiling at each other.

They have to make a tough decision concerning the safety of Atlantis.
Sheppard: "I don't see that we have a choice."
Weir: "All right. Do it."

Sheppard and his team are once again missing without having any contact to them und Elizabeth is worried sick.

Soldier: "Can it hurt us?"
McKay: "No, it's doubtful, apart from the obvious sterility issues."
Soldier: "W-What?"
Sheppard: "He's kidding. You're kidding right?" That's the second time John is thinking about having a child someday.

Elizabeth is unhappy because the Ancients made them leave Atlantis and John is unhappy because Elizabeth is.

General O'Neill gives Sheppard and order, and he looks at Elizabeth first, before he obeys.

He comes to her quarters.

Weir: "Colonel."
Sheppard: "Doctor." OMG! Hilarious.

They go to dinner with Rodney and Carson.
Weir: "You know what? It's getting late."
Sheppard: "Since when do you sleep?"
Weir: "Since I got back. I've had a lot of catching up to do. But it's... it's been lovely seeing all of you again. Thank you for getting me out."
Sheppard: "No, we should thank you. You're taking us to dinner, right?"
Weir: "Cheeky!"

Beckett: "I just bought some wee baby turtles and no one knows to feed them."
Weir: "Well, turtles are pretty hardy. I'm sure they'll be fine."
Sheppard: "And they make good soup."
Elizabeth smirks just a bit.

General Landry threatens to end John's career in the military if he doesn't turn around. Elizabeth looks deeply concerned.

Sheppard: "I'll be damned if I let a bunch of Replicators take our home away from us."
Oh, the way Elizabeth looks at him for saying this. So much love in her eyes.

Weir: "Remember the plan?"
McKay: "Of course I remember the plan. It's my plan."
Sheppard: "Uh, actually, using Niam was Elizabeth's plan."
Weir: "Thank you."

Sheppard: "Good to be back home, huh?"
Weir: "Hmph. There's no place like it."

Weir: "If we keep this up, there won't be much of a city left to save."
Sheppard: "I'll try to run the drones into your least favourite buildings."

Elizabeth and John are comfortably amused talking to Rodney.

Sheppard: "Oh, crap."
Weir: "John, what's going on there?"
Sheppard: "Rodney's passed out. His ears are bleeding. We gotta get out of the water."
Weir: "Medical team to Jumper bay. John, are you all right? John!"
Sheppard: "We're out of the water. Rodney's in trouble. Have a medical team ready."
Weir: "Already done."

Elizabeth faints and drops to the floor. John carries Elizabeth into the Infirmary and lays her on a bed. He looks deeply concerned.

Weir: "What are the chances it could make him more pleasant?"
McKay: "Oh, thank you."
Sheppard: "I'll keep an eye on him."
Weir: "Thank you." She smiles at John.

John and Elizabeth discuss the powers Rodney received and Elizabeth knows what John's wish is.
Sheppard: "I'm just saying--"
Weir: "Yes, you can be next."
Sheppard: "Thank you!"
Weir: "Hm." She shakes her head. Boys!

John comes to the office. Elizabeth is reading.
Sheppard: "Well, how's it coming?"
Weir: "Actually, I think I'm just getting to the good bit."
Sheppard: "Don't you hate it when people interrupt right when things are getting good?"
Weir: "Mm." She looks at him. He doesn't notice that he's doing that right now. He even stays, sits down and starts talking to her. Eventually he figures McKay is in danger.
Sheppard: "What does this mean for McKay?"
Weir: "Like I said, just getting to the good bit."
Sheppard: Then I'll leave you to it." Aw. He got it know. He walks away.
Weir: "John, wait! We need to talk to Rodney right away." She goes with him.

Elizabeth and John have lunch together. She asks him to take care of Rodney. Of course John can't say no to her.

McKay: "So why am I here?"
Sheppard: "Elizabeth made me."
McKay: "Oh, yeah? Me too."

McKay: "Now, is Sheppard still bugging you to let him use the ascension device to turn himself into some kind of a superhero?"
Weir: "Oh, yes."
McKay: "Hmm. Despite the fact that the Ancient database states that its effects on people are wildly unpredictable and that I'm just lucky I wasn't instantly melted down into a pool of protoplasm."
Weir: "Yes."
McKay: "Huh. Well, maybe you should let him."
Weir: "I think not."

McKay: "That flag's similar to the one I designed in our game."
Sheppard: "It's exactly like the one you designed in our game."
Weir: "What game?"
Sheppard: "The game Rodney and I play."
McKay: "We didn't tell you about the game?"
Sheppard: "We've been playing for a while now."
McKay: "Yeah, off and on in our spare time, at night, between missions. I could've sworn we told you about it."
Weir: "What game?" She glares at John. You didn't tell me? You're hiding something from me?
John looks uncomfortable with her being angry with him. He looks at Rodney then.
McKay: "It started a while ago."

John and Rodney learn that the game they have played is real and caused a war between two countries. First Elizabeth let them feel how displeased she is with their actions, particularly because she wasn't informed about the game earlier. John actually squirms in her presence. When the situation turns more serious Elizabeth is pissed. She even shouts at the two men constantly arguing. John looks unhappy now because he knows how disappointed she is in him. He tries everything to correct his mistake.

Sheppard: "Weir will send a team as soon as she doesn't hear from us which should be... any minute." Definitely knowing how often you screw up.

Sheppard: "Well, Weir will send a rescue team." Oh, John reassuring yourself much? - Besides, whenever did you go back to call her Weir instead of Elizabeth? Did you two have a fight? Are you on a break? Is it because of the events in 'THE GAME', because you didn't tell her about what you were doing with Rodney in secret? *snorts*

Weir: "Colonel Sheppard, do you read me?" Well, she just waited a little more than an hour, and she addresses him with his rank instead of John. Oops. There's trouble in paradise.
Sheppard: "Loud and clear and your timing is perfect. Now... get Beckett here with a rescue team and some cutting equipment ASAP."
Weir: "Do it." - "What's happened?"
Sheppard: "We've got ourselves in a damaged moon base in a decaying orbit cut off from each other and we lost the Jumper. That happened. Well, there's more to it than that but you get the idea."
Weir: "Help is on his way. What else can we do?"
Dex: "Hurry."

Weir: "And I assume you have come to the Infirmary in order to have your head examined?"
Sheppard: "Hey, I pulled it off, didn't I?"

A man named Mike talks Elizabeth into having lunch with him. She's having a nice time chatting with him, but as he kisses her out of the blue she backs off immediately, saying: "This was a mistake. I can't." She doesn't even knew the guy before. Is he crazy to just kissing her after a few hours? Didn't he listen when she mentioned she likes the movie 'Harry met Sally', which is the most infamous movie about Friends to Lovers ever? Idiot. She also mentions that she doesn't want to get involved with anyone she works with. Damn. Where does that leave you, John?

Ronon asks John if he's dating anyone. John denies, saying there isn't really anyone here he is interested in. He smiles mysteriously saying that. Ronon mentions Teyla and John is truly surprised, so, there are obviously no romantic feelings on his side. So, what's the secret? Who is he thinking about? The leader of Atlantis? The unreachable Elizabeth who doesn't want to get involved with the man she works with. So, John thinks, if he can't have her, he doesn't want anyone else.

Weir: "Well, we have a lot of exploring to do."
Sheppard: "We?"
Weir: "Until Rodney delivers the preliminary status report, I'm all yours. Put me to work, Colonel."
Sheppard: "All right, let's make up some time. Break into teams. Ronon, you're with Teyla. Elizabeth, you're with me, or I'm with you, however you wanna put it."
Weir: "Either [ee-ther] way... or either [eye-ther] way."

John and Elizabeth explore the underwater station together.

Sheppard: "You and Elizabeth go back to the control room. Ronon and I will check on Teyla."
Weir: "Be careful."

Weir: "I'm sending in backup."
Sheppard: "We can handle it."
Weir: "I know you can, but I'd rather be safe than sorry. I'll send a team of Marines to assist you."
Sheppard: "All right. If you feel the need."
Weir: "I feel the need. Weir out."

Sheppard: "Hey."
Weir: "Hey."
Sheppard: "Colonel Ellis has asked me to join the mission."
Weir: "I know."
Sheppard: "I was gonna stay behind in a cloaked Jumper after they launch the warheads; do some battle damage assessment."
Weir: "I know that too."
Sheppard: "He told me that you called Woolsey and General O'Neill and tried to get the whole thing called off."
Weir: "Yes, I did."
Sheppard: "They didn't bite?"
Weir: "They did not."
Sheppard: "Look, I know you think we're doing the wrong thing here, but, uh..."
Weir: "John." She stops walking and looks at him. "Good luck." She walks away. (Oh oh... she is pissed and...)
John looks unhappy.

The minute John is back he's looking for Elizabeth to tell her about the outcome.
Weir: "Welcome back."
Sheppard: "Thanks."
Weir: "I hear congratulations are in order."
Sheppard: "Yeah, you heard right." (... he knows it.)

Elizabeth subtly dresses down Colonel Ellis and leaves. John shrugs and makes an apologetic face. What can I say? That's my woman.

Sheppard: "I'm sorry, sir, but I can't help to think that we're somehow responsible for this."
Ellis: "Why, because Weir said so?"
Sheppard: "No, sir."

Ellis: "You should be running Atlantis, not Dr. Weir."
Sheppard: "Well, then I'd be The Man, and who would I have to rage against?"

Elizabeth calls John and Rodney's idea to save the city ingenious. John smiles about the praise.

The power beam strikes the city before McKay is able to raise the shield up again.
John manages to fly the city into hyperspace.
Sheppard: "We did it. McKay? Elizabeth?"
Voice via radio: "I need a medical team to the control room stat. Multiple injuries."
John races to the control room. Elizabeth is just put on a stretcher by Dr. Keller.
Sheppard: "Elizabeth. Is she gonna be okay?"
At the moment Dr. Keller is not sure about Elizabeth's condition.

*sniff*

She thinks he is dead. She looks devastated.

Sheppard: "Atlantis, this is Sheppard."
Weir: "John?"
Sheppard: "What other Sheppards do you know?"

Sheppard: "Atlantis, this is Sheppard. Come in. Atlantis. Elizabeth. I repeat, this is Sheppard. What is your status?"
Zelenka: "The explosions must have disrupted radio signals."
Weir: "Well, we're still here. That's our status."
Sheppard: "Don't scare me like that."
Weir: "Sorry."

Colonel Caldwell mentions how anxious John is to get back to Atlantis.

The Hug

Sheppard: "Well, I'm home."
Weir comes down the stairs to greet him. She leans in and hugs him. John finally returns the hug and puts a hand on her back. Elizabeth pulls back, keeping her hands on his arms and looks at him.
Weir: "Yes, you are. I truly thought you..."
Sheppard: "Yeah, yeah. I thought the same thing about you a minute ago. We gotta stop that."
Weir: "I'd like that."
Sheppard: "So, uh, where are we?"

Sheppard: "We should make it home before they do."
Weir: "I hope so. We'll keep the porch light on for you."

He's unhappy because of what happened to Ford, she tries to comfort him and fails.

Space. Daedalus. Elizabeth Weir is on board. She is alone in a room and sits looking out of the windscreen as she drinks from a mug. After a while, John Sheppard strolls in.
Weir: "Hey, what are you doing up so late?"
Sheppard: "Couldn't sleep." He goes to a coffee pot and pours himself a drink. "Must be the, uh, burden of command -- you know, ever since I was promoted to Lieutenant Colonel." He sits down opposite to Elizabeth.
Weir: "All right, John, it's been almost a month. When are you gonna stop trying to bring that up in every single conversation?"
Sheppard: "You gotta understand, there's a lot of people in the Air Force who never thought I'd make it past captain."
Weir: "Well, obviously the people whose opinions matter the most thought otherwise."
Sheppard: "What about you? What are you still doing up?"
Weir: "I think I got used to falling asleep to the sound of the ocean."
Sheppard: "Well, McKay says we're already at the edge of the Pegasus galaxy. You'll be fine once we get back to Atlantis. You know, it's funny. I spent the past year wondering if I'd ever see Earth again, and as soon as I got there..."
Weir: "I know how you feel. Kind of was extremely convenient to be able to step through the Gate and be at Stargate Command in an instant, and now this feels extremely inconvenient having to spend eighteen days cooped up in this ship to get back."
Sheppard: "Well, until we find another Z.P.M. to power the Earth Gate, that's just the way it's gonna have to be."

Elizabeth argues with Caldwell, John tries not to smile.

Earth. Stargate Command. Weir defends Sheppard who isn't supposed to go back to Atlantis.
"I wanted Major Sheppard to come back with me."
"Atlantis has a military commander."
"Major Sheppard's record before he joined my team doesn't concern me. All I can tell you is that if it wasn't for him, I wouldn't be sitting here right now. And as for his rank, if that's not good enough for you, you're just gonna have to promote him."
"I shouldn't have to remind you gentlemen that I continue to have the support of the President and our foreign allies. You don't wanna fight me on this one."

Weir's boyfriend Simon breaks up with her.

John is in danger - again, of course she worries.
Weir: "Are you all right?"
Sheppard: "Yeah. Two arms, ten fingers...," he looks down, "I'll check the rest later."

He outmaneuvers another ship.
Weir: "Nice move!"
Hermiod: "Indeed."

Weir: "Well done, both of you. You had us a little worried there for a minute."
Sheppard: "Sorry about that."

Teyla addresses Sheppard by his new rank. Elizabeth smiles proudly. Sheppard to Teyla and Weir: "Thank you! Ladies." He waits for Elizabeth to reply but she even doesn't look at him. He heads off.

They address each other by their given names regularly now.

Weir: "I'm not sure it's a good idea, John."
Sheppard: "Elizabeth, you've gotta see this guy in action. He is an incredible shot; none of my guys can beat him in a fight; and he's ex-military."
Weir: "Not a military on Earth."
Sheppard: "The guy's got no place to go."
Weir: "You're not just being charitable?"
Sheppard: "No, I'm not -- and I think he'd make a great addition to my team."
Weir: "We don't know anything about him."
Sheppard: "Well, what's there to know?"
Weir: "Well, anything would be helpful. He's not very forthcoming."
Sheppard: "He's been on the run from the Wraith for the past seven years. What do you expect? Listen (He taps on her back/She turns around to face him.) -- just talk to the guy. You owe him that at least."
Weir: "Okay."

Weir: "I understand Major Sheppard extended an invitation to you to join his team."
(Yes, she really does say “Major”! What the hell?)
Dex: "Yeah, he did."
Weir: "Well, he was supposed to speak to me about that first."

Sheppard: "Uh, did you get the chance to talk to Ronon?"
Weir: "Yes, I did. Chatty fellow, isn't he?"
Sheppard: "And?"
Weir: "He would be your responsibility."
Sheppard: "I knew you'd say yes!"
Weir: "I haven't said yes."
Sheppard: "Well, you were about to."
Weir: "Yes."
Sheppard: "There you go!"
Weir: "Hmm."

Waiting for Rodney to wake up they are sitting close together.

Sheppard: "Well, Dr. Elizabeth Weir will be the one to begin official negotiations with -- That's really her thing." (Does he have to say her full name, sounding completely proud?)

Weir: "I may have to go off-world to assist Colonel Sheppard. I'd like you to assemble a team and have a Puddle Jumper ready to go." Does she have to go offworld herself just for him? Isn't there enough military staff in Atlantis to take that risk? Aw, Elizabeth.)

Sheppard: "Elizabeth, where are you?"
Weir: "We're in Jumper Two. We're cloaked, directly above you. Are you all right?" (Both are concerned for the safety of the other.)

Sheppard: "Elizabeth, I need you to keep the gate open until the last of them go through, then shut it down. Dial Atlantis."
Weir: "We can land and pick you up."
Sheppard: "Negative. Just keep the gate open. We'll take it from there." (Again the safety of the other is more important than the own.)

Discussing some exciting news they smile at each other and she asks for his agreement before she gives Rodney a go.

John wants to tell Elizabeth what they had found but Rodney sails in and tells her instead. John doesn't look amused.

Rodney to John: "Elizabeth will listen to you." (You don't say!) Well, later in the conversation with Caldwell, she actually does.

Oh, the gentle way in which Elizabeth says to Caldwell, Go to your ship already and fuck off. John can barely hide his amusement.

Weir: "I cannot afford to lose either one of you. Now tell me: can you do this?"
McKay: "Yes."
Sheppard: "Are you sure?"
McKay: "Yes."
Sheppard: "Are you sure you're sure?"
McKay: "I said yes!"
Sheppard: "Because if you're wrong..."
McKay: "I'm not!"
Sheppard: "We'll call you back after the test -- how does that sound?"
Weir: "You'd better."

Sheppard: "So it's a teenage thing. Pimples, rebellion, life-sucking."
Elizabeth smiles at his silly joke.

Beckett: "I'd like to go to the planet and check into it."
Weir: "Is that really necessary? I'm sure he (Sheppard) could get a sample and bring it back here for you to analyze?" (Elizabeth refers to John as He. That's something.)

Beckett tries to comfort Sheppard, saying it could be he's just fine. John turns to Elizabeth and says, "See?" as if she needs to be comforted about his condition and not him. Aw.

Beckett: "You'll need to check in every six hours."
Sheppard: "I can do that."
Weir: "And you should probably..."
Sheppard: "...suspend my off-world activities until we know more?"
Weir: "Thank you."

Sheppard is lying in the infirmary, being scanned. He is staring rather fixedly at the ceiling, looking grim.
Beckett: "You should talk to him. He's hiding it very well, but if I was him, I'd be scared to death."
Sheppard: "How am I doing?"
Weir goes over to Sheppard's exam bed. Sheppard looks her up and down, then frowns, but sounds like himself for this conversation.
Sheppard: "Anything that has you speechless has me concerned."
Weir: "You're gonna be fine."
Sheppard: "Wow. That's dead-man talk."
Weir: "No, it isn't."
Sheppard turns up his right arm, showing that the scaly patch has grown a bit and changed to an ickily shiny, carbuncle-looking thing.
Sheppard: "Have you seen this?"
Weir: "Beckett is gonna figure this one out."
Sheppard: "I think I already have. You know who I'm starting to feel like? Ford."
Weir: "Now, what happened to you is completely different."
Sheppard: "I know, I know. Still, I can feel it. I mean, I can feel it changing me inside... like he did."
Weir: "I don't think that's even possible. Look, you're very worried..."
Sheppard: "No, no. No, it's... uh... One of the best weeks of my life was when I got my wisdom teeth out. I was on codeine for a full seven days. This is kind of the same. I know I should be in pain, or at the very least freaked out by this, but hey I'm not... and that freaks me out more than anything."
Weir: "We're gonna beat this."
Sheppard: "'We're gonna beat this? Beckett will figure this out? You're gonna be fine'? You really suck at the whole bedside manner thing."
Weir: "I know. I'm sorry."
Sheppard: "But I appreciate the effort."

Caldwell: "You two are pretty close, aren't you?"
Weir: "Well, we've been through a lot together. Yes."

Weir enters her office. Sheppard enters through another door, followed by an armed Marine. Sheppard: "Look! I made a new friend."
Weir: "It's only protocol."
Sheppard: "That's your answer for everything."
Weir: "You look well."
Sheppard's right hand has gone crinkly and claw-like. He puts it in his pocket.
Weir: "Should you be out of bed?"
Sheppard: "I was goin' a little crazy down there, so they said I could walk around for a bit."
Weir: "That's good."
Sheppard: "Look, what I'm trying to say is that I want to go on this mission."
Weir: "Hey, you said yourself, you are not fit for any off-world activity."
Sheppard: "The inhibitor that Beckett's got me on, the one that's keeping me lucid... they keep having to up the dose."
Weir: "I know. They told me."
Sheppard: "I don't know how much time I have, but the last thing I wanna do is sit on my... mutating hands, while my team puts their lives on the line trying to find me a cure. I should be with them!"
Weir: "No. I'm sorry."
Sheppard: "What's the worst that can happen? I, I... die?"
Weir: "You could compromise the mission. They have enough things to worry about..."
Sheppard: "Oh, no no... so, what? Suddenly I'm a liability?"
Weir: "Your condition can change rapidly."
Sheppard: "I know, and I know I can do this!"
Weir: "I'm glad... you feel that way. But it would be irresponsible of me..."
Sheppard: "This is my life we're talking about."
Weir: "I know that."
Sheppard: "I'm going on that mission."
Weir: "No, John! You're not."
Sheppard: "DAMMIT!"
His face twists in rage as he turns and smashes his fist through the plate glass wall of her office. Before the glass has even shattered completely, the Marine has his sidearm out and aimed steadily at Sheppard. People come running from the control room, other weapons being drawn. Weir charges over, a restraining hand up to the Marine.
Weir: "It's okay! Put it down."
Sheppard: "I'm betting that didn't sell you?"
Weir: "No. No, not really."
Sheppard: "I should go back to the infirmary."
Weir: "Yes."
Sheppard goes quietly.

Weir: "John?"
Weir reaches for a light switch.
Sheppard: "Leave them off."
Weir: "What?"
Sheppard: "The lights. Leave the lights off."
Weir: "Okay. I thought I should come by and practice my bedside manner."
Silence.
Weir: "How are you?"
Sheppard: "My body's mutating into a bug. How are you?"
Weir: "Would you like an update on your team's progress?"
Silence.
Weir: "They found an iratus cave and they've headed in."
Sheppard: "Good."
Weir: "They should locate some eggs and be back here in no time."
Sheppard: "No time."
Weir: "Yes."
Sheppard: "Then what?"
Weir: "Honestly, I don't know."
Silence.
Weir: "Hey? Are you all right?"
Silence.
Weir: "Would you like me to call someone?"
Sheppard: "Who would you call?"
Weir: "If you need to see a doctor..."
Sheppard: "I need a bigger security detail."
Weir: "Excuse me?"
Sheppard: "At least two men, stationed at my door, sooner rather than later."
Weir: "Now, what are you talking about?"
Sheppard: "Just trust me, Elizabeth. You're gonna need it."
Weir: "Listen, John if--"
He turns sharply full face to show her that his right eye has gone all slit-pupiled and yellow-gold. The blue bruise color on his neck shows a blackened ridge crawling up from his collar line.
Weir: "Oh, my God."
Sheppard: "They need to hurry."
Weir: "You should be in the infirmary."
Sheppard: "The infirmary isn't secure. The inhibitor's only keeping me lucid, it's not slowing the retrovirus."
Weir: "Still--"
Sheppard leaps to his feet and gets right into her personal space. She doesn't flinch back... much.
Sheppard: "DON'T ARGUE WITH ME! I'm not safe to be around anymore. Get some more men at my door and get the hell out of here."
Weir: "Okay. Okay."
She leaves the room and speaks to the guard.
Weir: "Double the detail."

Weir: "John?" - "So this is when I usually ask you a stupid question, like 'How are you feeling?'" - "John? John?" - "Our team got back from the mission."
There is a thump behind her. She whirls around and there is Sheppard standing right behind her. She gasps at the sight of him.
Weir: "The nest was too well protected. We were unable to retrieve the eggs. They tried their best."
Sheppard: "Best?"
Weir: "The bugs attacked--"
Sheppard: "Try again."
Weir: "I can't do that."
Sheppard: "Why?"
Weir: "John--"
Sheppard: "No."
Weir: "I understand--"
Sheppard: "If you won't... then kill me now."
Weir: "John."
Sheppard: "It's better for the both of us." (Whatever he is insinuating with his choice of words.)
Weir: "I can't do that."
Sheppard: "Then try again."
Weir shakes her head. Sheppard suddenly surges forward, grabbing her by the throat with his right hand, pushing her backward and pinning her against the wall. Weir seizes his wrist with both hands, trying to hold him off.
Weir: "We lost Walker and Stevens. I won't send another team! I won't risk more lives!"
As she continues to struggle for breath, Sheppard glares at her for a moment, then releases her, dropping her to the floor. He walks away.

Caldwell: "All right. Four teams. Surround him and close in. I want him stopped. And, gentlemen, use whatever level force you deem necessary. Move out."
Weir: "You will only use such force as a last resort."
Caldwell: "That's not Sheppard any more, ma'am."
Weir: "You heard me."

Sheppard is shot down and brought back to the infirmary. Elizabeth is worried sick.

Teyla: "Any progress?"
Weir: "No. He's still in a coma. At least he isn't in any pain."
She can't sleep and has lost almost any hope.

John is coming out of the coma. "Did I hurt anyone?"
Weir: "No, not seriously."

Elizabeth allows John to go on the mission to save himself. (Isn't that what he was asking for the whole time?) She stays behind, and murmurs, "Good luck."

Elizabeth only gets some rest when she learns that John is going to be fine. She also lets Colonel Caldwell feel how much she wants him to go on his ship and leave Atlantis. *snorts*

Weir: "Good! Colonel Sheppard's team is ready to go."
Caldwell: "My crew can handle this."
Weir: "My team has far more experience with Ancient technology."
Caldwell: "My people will only get that kind of experience by going on this kind of a mission."
Weir: "Not this mission. We discovered it, we check it out. Your crew can cut their teeth on something else."
Caldwell: "Fine. Have Colonel Sheppard's team ready to go in an hour."
Weir: "They're ready now."
She and Caldwell enter the Bridge to find John, Rodney, Teyla and Ronon waiting for them. Elizabeth smiles proudly at them. Caldwell just looks peeved.

Sheppard: "Uh, before we break up the party, there's something I'd like to do."
He reaches down and picks up a bottle of champagne from the floor beside him. Elizabeth, to whom he must have explained his plan beforehand, picks up a tray of wine glasses and brings them over to him as he stands.
Sheppard: "It might seem a little strange, but I promised to do something when we got home."
Everyone stands and takes a glass as John opens the bottle. Elizabeth puts the tray down and picks up the last two glasses. They hold the glasses out and John pours some champagne into each. John takes his glass from Elizabeth, his hand lightly touches hers, and raises the glass.
Sheppard: "To the crew of the Aurora."
They clink their glasses together, and then drink.

Weir: "Colonel Sheppard's team, three hours overdue."
Lorne: "Wouldn't be the first time. Any radio contact?"
Weir: "None since they left."
Lorne: "Well, you know those guys."
Weir: "What do I know about those guys?"
Lorne: "Just that they tend to get all caught up in whatever it is they're doing, and sometimes they don't check in. They forget how much you worry."
Elizabeth looks at him.
Lorne: "That we worry. Collectively, I mean."
Weir: "Yes, we do."
Lorne: "Yeah. We do." - "Okay, guys, it looks like we're headin' back out."
Weir: "Thank you, Major."
Lorne: "You're welcome."

Weir: "If they were okay, they would have radioed in by now."
Lorne: "I understand that, ma'am."
Weir: "I want everyone who is cleared for off-world activity to help with the search. The Daedalus is on its way from Earth, then they'll be able to help, but until they get here, it's up to us."
Lorne: "And I know that, but I need you to understand that it is gonna take a very long time to search all the planets on our list. It... it could take months."
Weir: "We can't afford months, Major."
Lorne: "And I know that too."
Weir: "Good."

Weir: "...and thanks to several modifications, the specifics of which are encrypted in this data burst, we believe we can streamline our power consumption a further thirty percent. Also at the time of this transmission, Colonel Sheppard's team is still missing and is... is presumed... Colonel Sheppard's team is still missing. End transmission."

Rodney escapes and comes home to Atlantis. Elizabeth smiles and runs to the gate. She passes Rodney and then realizes that no one else is coming. Her disappointment about the fact that John is still missing is obvious. "Where is Colonel Sheppard," she urges Rodney on to tell her.

Elizabeth gets bad news and thinks John is dead, a second later, the Gate is dialed with his code and John, Teyla and Ronon arrive in Atlantis. Elisabeth runs down the stairs. John makes a placatory gesture to the two marines standing at either side of the Gate with their weapons raised. Elizabeth meets the three of them.
Sheppard: "Sorry we're late."
Elizabeth smiles delightedly at them, particularly at John.

Elizabeth joins the rescue mission for Sheppard. Why should one leader come along to save the second in command? If both would die that's what you call a disaster. So this is all personal, aka as an emotion called love.

Teira: "I'm glad I finally got you outside. You've been alone in your room for so long."
Sheppard: "It's called being depressed."
Teira: "Is it so terrible here?"
Sheppard: "No, you folks have been great, it's just I have responsibilities home. People I care about and who care about me. At least I thought they did."

Teira: "Your friends have come. They number five. They've come for you."
Sheppard: "They have? Are you sure? That's the best news I've heard." He gets up immediately. He'd waited so long. Hearing the beast is upon them he starts running.

John is hurt and on the ground. Elizabeth runs to him and tries to touch him. He rejects her touch, furious.
Sheppard: "What the hell took you so long?!"
Weir: "Believe it or not, you were only gone a couple of hours."
Sheppard: "Try six months!"

Teira appears to fight with John. Elizabeth looks jealous about the woman she doesn't know.

Weir: "Well, the beard is interesting."
Sheppard: "First thing to go when we get home. I never thought I'd see any of you again. Kind of even... missed you a little."

He's sitting down on the desk in her office as if he has every right to. She's unhappy about her decision which led to the almost torture of Kavanagh. He tries to cheer her up, saying that she did the right thing for a greater purpose. She doesn't agree. Neither do I. Torture is never the right thing to do. Elizabeth is truly a good person.

Weir: "You and Rodney have been bugging me for a chance at trying a Jumper as a submersible, but you sure went a hell of a long way to make me say yes."
Sheppard: "You still haven't said it yet."
Weir: "I just did."
John bounces away like an over-excited little boy.

Weir: "Look, I'm not gonna order you to go." (to Zelenka)
Sheppard: "I will!" in the harshest tone.
Elizabeth looks at him as if she is turned on by his strictness.

Sheppard walks out to the balcony. Elizabeth is already there.
Sheppard: "Got the drones, got a few Jumpers, I even got the girl."
Weir: "You got the girl?!"
Sheppard: "Well, I mean I could have got the girl. I turned her down."
Elizabeth smiles.
Weir: "What did you offer them in return for the drones and the Jumpers?"
Sheppard: "A supply of medicines and an I.D.C. if they need to reach us. We also offered to help them come up with a new way of running things when the time comes."
Weir: "They didn't offer you King?."
Sheppard: "Turned that down too."
Elizabeth smiles at him, then they both look out over the ocean.

Elizabeth enters the room. Carson calls her name. John turns around immediately. He sees Caldwell at her side and doesn't look happy about it. Elizabeth and John look at each other behind Caldwell's back.

A strong energy beam hits Elizabeth and she falls down, unconscious. Sheppard and Caldwell both reach for her.

Elizabeth lies in a hospital bed, still unconscious.
McKay: "Okay, this is not my fault." He says that to Sheppard only. Why's that, huh?
Sheppard: "We were all there. Relax."

Sheppard: "Yeah, yeah, yeah. We're all very sorry. Where's Elizabeth?"

Elizabeth asks John to do a favor for Phoebus. Of course, he can't say no.

Weir: "Ah, love is a powerful thing, Carson."
Sheppard: "You're a hopeless romantic, you know that?"
Weir: "Well, you're just as hopeless, otherwise you wouldn't have agreed."
John looks a bit embarrassed by her insight in him.

Sheppard: "You know, they were husband and wife. Anything could happen." Oh? What are you thinking about?

Phoebus/Elizabeth kisses Thalan/John. He is stunned. A few seconds later they both grab some weapons and start shooting at each other, then hunting each other, running through the city.

Sheppard: "Good morning."
Weir: "Good morning."
Sheppard: "What's-her-name sure hung in there for a while."
Weir: "W-When did she--?"
Sheppard: "Sometime in the middle of the night, kicking and screaming."
Weir: "That was the strangest feeling, no?"
Sheppard nods and smirks.
Weir: "The entire time I was shouting to everyone. But nothing I want to would come out of my mouth."
Sheppard: "I know. It was a real nightmare."

Weir: "Did they believe you were you?"
Sheppard: "To be honest, I think the only people who believe 100 percent are Beckett... you..." He looks at her. She smiles.

Caldwell: "Well, if you'll excuse me, I'm sure you'll both agree that the paperwork on this is going to be a nightmare... especially that kiss."
John and Elizabeth stare at him in horror.
Sheppard: "Yes, sir!"
Caldwell: "Well, try not to kill each other while I'm gone."
Elizabeth gives Caldwell a half-hearted thumbs-up. He turns and walks away. Elizabeth smiles ruefully at John, then looks away and slides down in the bed in embarrassment.

Weir: "I think we should consider this."
Sheppard: "Correct me if I'm wrong, but aren't you the one the Genii threatened to kill on two separate occasions?" Aw. He won't ever forget that.

Sheppard: "Dr. Weir, we have Ladon."
Weir: "What has he said?"
Sheppard: "Not much. Apparently he doesn't like me." Elizabeth makes a funny face. "Okay. Take him to my office."
Sheppard: "Your office? Really?"
Weir: "Really, Colonel. I'm on my way."

Weir: "Good thinking."
Sheppard smiles. "Could have been Mensa."

Cowen: "Dr. Weir, this is Commander Cowen, leader of the Genii."
Weir: "Were is Colonel Sheppard?" Not where are my men? Duh!

Cowen: "The Genii people need the Atlantean ships you call Jumpers. I believe you have 10 of them. You have one hour to bring them all here."
Weir: "And if I don't?"
Cowen: "We will kill one of your team every 15 minutes... until our demands are met. Oh, and we will be starting with Colonel Sheppard." Of course you will.

Cowen: "I will contact you again in 15 minutes... so you can decide whether you would like Dr. McKay to live. In the meantime, you have forfeited the life of Colonel Sheppard."
Weir: "Cowen, wait!"

John is sitting down on her desk again.
Weir: "So a nuclear explosion and the lives of an entire battalion of men don't count?"
Sheppard: "Yeah, it's all a spin. What do you think the fallout's gonna be?"
Weir: "Well, historically, most coups end up with the new government being about as bad as the old one."
Sheppard: "I don't know. He seemed pretty grateful we saved his sister."
Weir: "There's that."
Sheppard: "He did save me and my team."
Weir: "There's that too."
Sheppard: "So I say we call it a win."
Weir: "Who's spinning now?"
Sheppard: "All right. Then I say we call it a night." You're you coming, babe?
Weir: "That we can do!"

Sheppard: "Uh... I'm gonna get back there now, make sure he's (Rodney) not distracted."
Weir: "Distracted?"
Sheppard: "Well, the lead scientist, uh... she's very... um...."
Weir: "Hot?"
Sheppard: "I was gonna say 'attractive'. But McKay is acting very... uh...."
Weir: "Smitten?"
Sheppard: "I was gonna say 'pathetic'."
Weir: "Wait, I should head back with you... and begin negotiations with the Taranian leader. What's he like?"
Sheppard: "Well, you know, he's a guy. Didn't pay much attention, sorry."

So, John is smitten with some attractive scientist, Elizabeth knows that he is talking about himself, and she wants go with him to check out the males. I think, that is not much to John's liking. *snorts*

He calls her Elizabeth, thrice. She calls him John. In front of strangers.

Sheppard: "Let's just say I'm worried about my grandkids."
Elizabeth looks at him, stunned, as if she never thought that he wanted one of those, kids, grandkids, whatever.

Their first encounter. "Who is this?" Elizabeth asks.

She appears to give her speech to the team and passes by him. He smiles.

Colonel Sumner: "Don't forget who gives the orders."
Sheppard: "That would be Dr. Weir, right?"

Arrival in Atlantis. He stands on the balcony. Holding the champagne bottle she smiles up to him. He nods at her.

Sheppard: "I didn't touch anything."
Weir: "Relax, Major."

Weir: "Major, I'd like you to go along."
Sheppard: "Yes, ma'am."

Leaving Atlantis to step through the Stargate for the second time, John turns back and waves bye to her. (or McKay. Choose for yourself.)

He's back. Atlantis is crashing. She pulls him by the arm to get him out of immediate danger.

First argument on the balcony.

Weir: "I'm not sending more good people, including you, to their deaths."
Sheppard: "Okay."

She calls him John for the first time.

He calls her "Doctor".

She stands at the gate waiting for his return.

He's depressed, she cheers him up; and they talk, standing on the balcony.

She calls him John for the second time.

Weir: "Well, you are the ranking military officer now, or do you need to be reminded of that? We need to get back out there; do what we came to do."
Sheppard: "You do realise I can get us in to all sorts of trouble, right?"

Weir - Sheppard - Teyla tension

Watching football and eating popcorn

Weir: "Hey what are you guys doing?"
Sheppard: "I'm teaching Teyla how football's the corner stone of western civilization."
Weir: "And you didn't invite me?"
Sheppard: "You like football?"
Weir: "No, not really."
Sheppard: "Oh, come on. It's real, it's unpredictable, it's full of passion and beer. Hotdogs."

He's seriously injured - she's worried sick

Weir: "How's Major Sheppard?"
Sheppard: "I'm still here."
Weir: "Hang in there, Major. We're working on the problem."
Sheppard: "I know you are. Listen, uh, I'd like to say something while I still can."
Weir: "Don't! You're going to get through this."
Sheppard: "If I was... He wouldn't have let me go."
Weir: "Who wouldn't have let you go?"
Sheppard: "The Wraith... I guess he saw me as good as dead, cause he just walked away, so... what I wanted to say was..."
Weir: "Save your strength, John, and tell me in person."
Sheppard: "This is important."
Weir: "I'm listening."

Sheppard dies but Beckett is able to reanimate him. Elizabeth is visibly relieved.

Weir: "By the way, what were you going to say?"
Sheppard: "When?"
Weir: "Before, when you thought, you know..."
Sheppard: "Oh that..."
Weir: "I didn't want you to say it at the time, but now I'm curious."
Sheppard: "I was going to say, um, take care of each other."
Weir: "That's nice."
Sheppard: "Yep."
McKay: "And, indeed, we did."
Sheppard: "Yes, you did. Thank you. Again."
McKay: "You're welcome."
Teyla: "Good night."
McKay, Ford and Teyla leave.
Weir: "You weren't really going to say that, were you?"
Sheppard: "I have no idea what you're talking about."
Weir: "I didn't think so."

Serious tension and arguments because of Teyla

Sheppard: "You like us to bring back anything special?"
Weir: "Uh... no thanks..."
Sheppard: "Groceries? A new outfit? Flatware..."
Weir: "Hm... no... just yourselves... in one piece please. Dial it up." - "Be safe."

Bates: "Again with all due respect Major I believe you're putting your personal feeling in front of your..."
Sheppard: "You're dismissed."
Bates: "Yes, sir."
He walks out.
Sheppard: "What?"
Weir: "I'm the one who put him in charge of security."
Sheppard: "Yes, you did... and if you want to dismiss me. Go ahead."
Weir: "Why don't you go see how Ltd Ford is doing."
Sheppard thinks about that, and leaves.

McKay: "Hence Major Sheppard has generously offered our help to the Hoffans."
Weir: "Has he?"
Sheppard: "Look, the fact is, if they're onto something, maybe we can speed up the process."
Weir: "Okay, Major, you have a go. But if the drug really is just a pipe dream..."
Sheppard: "Our Doctor Beckett's already volunteered to help us find that out."
Weir: "Oh, he has, huh?"
Sheppard: "He will."

He calls her Doc.

He waits for her to make a decision, he doesn't move until she says yes.

Weir: "Be safe, Major."
Sheppard: "That's the plan."

Weir: "Isn't that risky?"
McKay: "I'll be fine."
Sheppard: "I think she means in terms of breaking our own Gate."

She visits him in his quarters

Weir: "It's kinda what I wanted to talk to you about. Home. Going home."
Sheppard: "Oh."
Weir: "McKay's right. If this works and we are able to establish a wormhole back to Earth..."
Sheppard: "You know, if this conversation is going where I think it's headed, you can put your mind at rest. I'm not going anywhere. I haven't read my book."
Weir: "Look, all I'm saying is that you are the person who is best qualified to brief General Hammond and the other powers-that-be about the Wraith threat."
Sheppard: "Well, maybe so, but I think I'm needed here."
Weir: "Good."
Sheppard: "But if you wanna go, I understand that too."
Weir: "What, are you saying I'm not needed here?"
Sheppard: "I said I'd understand."
Weir: "Well, thank you, but I made a commitment."
Sheppard: "Of course, in all fairness, life-sucking aliens weren't part of the brochure."
Weir: "Regardless, I'm staying."
Sheppard: "Good. Wouldn't be the same without you."

Teyla: "What is it?"
Sheppard: "I was just thinkin' again – about Doctor Weir and everyone else on Atlantis."
Teyla: "Of course. I am sure she is fine – as I am sure they are all fine."

Weir: "Rodney, be careful with that. I wanna make sure we can get back home."
McKay: "Uh, you mean Atlantis."
Sheppard: "I think that's what she meant."
McKay: "How do I know she wasn't suggesting we pull a double fake-out of our own and dial Earth?"
Sheppard: "Forget the double fake-out – get the damned crystal!"

Two times John refers to Elizabeth as She.

Weir: "I think in the future, Major, I should do the negotiating."
Sheppard: "I did say I had to ask you first."
Weir: "Aha... to terms you already agreed to."
Sheppard: "Yes."

Weir: "No. How's that for an answer?"
Sheppard: "It's pithy. I'll give you that."
Weir: "I'm sure you already agreed to this."
Sheppard: "Only because we'll get something out of it."

Weir: "You might be happy to know Sgt Bates was able to broker us a small trade agreement for food while you were gone."
Sheppard: "Oh, he did, did he?"
Weir: "Yes, he did, but it's not a competition."

Weir lies about Sheppard's whereabouts when Rodney and she are taken hostage.

Kolya: "He's (Sheppard) good."
Weir: "Yes, he is. I'd do what he says." she says proudly

Sheppard: "I'm not finished yet!"
Kolya: "Neither am I. Say goodbye to Doctor Weir." (He points his pistol at Elizabeth.)
Sheppard: "The city has a self-destruct button. You hurt her, I'll activate it. Nobody'll get Atlantis."
Kolya: "Even if it exists, Major, you need at least two senior personnel to activate it – and I'm about to take one of them out of the equation."
Sheppard: "Kolya?! - Kolya?! - I'll give you a ship! I'll fly it out of here for you myself! - KOLYA!!"

Sheppard: "Kolya!! - Kolya! Don't do this!!"

Kolya: "Weir is dead."
Sheppard: "I. am. Going. To. Kill. You."

Kolya: "Second. If and when I determine Atlantis unsalvageable Doctors Weir and McKay become obsolete."
Sheppard: "Weir's alive?!"
Kolya: "Doctor McKay was able to make a strong case for keeping her alive..."
Sheppard: "Let me talk to her."
Weir: "Sheppard! We're both here!"
Sheppard: "It's good to hear your voice."
Weir: "Yeah, it's good to hear."
Kolya: "We have less than one hour until the storm hits full force. If the power is not returned to grounding station three within the next 10 minutes Dr. Weir dies."
Sheppard: "Again you mean?"

Teyla: "Would he really kill them (Weir and McKay) because they are of no further use to them?"
Sheppard: "No, he'd kill them to punish me."

Weir: "You need to keep stalling."
McKay: "What for?"
Weir: "Major Sheppard is still out there. If you activate—"

Sheppard: "Sorry about that. I had to... you okay?
Weir: "No."
Sheppard: "You will be. Come on."

Sheppard: "You're extremely optimistic, you know that?"
Weir: "You think so?"

McKay mouths to Sheppard: Say something. If Elizabeth listens to anyone then to you.

Weir: "And it would take at least fifteen hours to send out any sort of rescue."
McKay: "We'll be fine."
Weir: "Major?"
Sheppard: "I agree with McKay."
Weir: "Of course you do! How could either of you resist exploring a crashed alien spaceship?!"
Sheppard: "Exactly."
McKay: "I assure you our interest is purely professional, Elizabeth."
Sheppard: "Seriously, the amount of Intel we could gather from their weapons system – codes, shields..."
Weir: "All right. Proceed with extreme caution, please, and check in with me in three hours."
McKay: "Three hours is hardly enough time..."
Sheppard: "Will do! Jumper One out." Well, he respects her wishes as she respected theirs.

Weir: "Lieutenant, I'd like you to put a team on standby for a rescue mission."
Ford: "Is the Major allright?"
Weir: "I'm sure he's just fine. I'd just like to have a team ready."
Ford: "So, just in case?"
Weir: "Yeah. Just in case."
Ford: "Yes, ma'am."

Elizabeth sends the second team on their way, even though the time is not up and she doesn't know if John and Rodney are in danger or not.

Sheppard: "I'm ranking military officer here."
Weir: "Yes, I'm aware of that, Major."

Weir: "You said so yourself – you are the ranking military officer. I can't chance you getting infected."
Sheppard: "I can't chance you getting infected."

Weir: "You are not in command here, Major."
Sheppard: "Well, we'll agree to disagree. Bates, open the door."
Weir: "Don't."
Sheppard: "Elizabeth, he's heading right for you."

He calls her Elizabeth for the first time.

Teyla: "You should not have undermined Doctor Weir's authority in front of Sergeant Bates."
Sheppard: "Sometimes Elizabeth makes a decision early on and gets locked into it. That's a problem."
Teyla: "She is not the only one who suffers from that affliction."
Sheppard: "Doctor Weir, this is Sheppard. Teyla and I are ready to head out. What's Peterson's location?"
Elizabeth hears him but stares at her laptop and does not reply.
Sheppard: "Elizabeth."
Weir: "He's in section E19, level three."

Sheppard: "Well, I wish we would have thought of that."
Weir: "We did think of that, Major! That entire section had to be powered up for you to open the door to Peterson. In fact, if you hadn't gone after him, he wouldn't have been able to use the transporters. Do you still feel it was a good idea?"
Sheppard: "Where did he transport to?"
Weir: "The Mess Hall. Thankfully everyone else respected the quarantine – there's only a handful of people there."
Sheppard: "All right, you made your point."

Sheppard: "What do you mean, no?"
Weir: "It's too dangerous."
Sheppard: "You'd rather lose a third of our population?" Obviously!
Weir: "We're not there yet, Major."
Sheppard: "We are there!"

Sheppard: "It's worth the risk."
Weir: "Okay. You have a go."

Weir: "Good luck."
Sheppard: "You too."

Weir: "Major Sheppard, come in. This is Weir. Please respond. Major, do you read me?"
Sheppard: "This is Sheppard. I've cleared the blast. I'm returning home."
Weir: "Glad to hear it, Major."

Weir: "Are you okay?"
Sheppard: "Yeah, just a little nuke. Nothing, really."
Weir: "The naqahdah generator plan was very clever. Good work."
Sheppard: "Thank you. Now I'm going to bed."
Weir: "We need to discuss what happened earlier."
Sheppard: "Now?"
Weir: "That can never happen again."
Sheppard: "Look, I'm sorry about..."
Weir: "I understand your expertise in military matters and I agree that I should defer to those expertise in such situations."
Sheppard: "Thank you."
Weir: "But you are not the one who decides what is and what is not a military situation. Both General O'Neill and Colonel Sumner warned me that you don't respect the proper chain of command."
Sheppard: "Sometimes I see a situation a little different than..."
Weir: "No, listen to me, John. You endangered yourself and the lives of many others."
Sheppard: "Because I thought it was the best course of action to take. And, by the way, I saved your ass."
Weir: "I know you did. But you have to trust me."
Sheppard: "I do."
Weir: "Do you?"

Weir: "Perhaps you'd like a full tour?"
Chaya: "I'd love that."
Teyla: "Major Sheppard has already promised to do so."
Weir: "Of course he has."
Sheppard: "Of course I have."

Sheppard asks Chaya to call him "John". He never made Elizabeth such an offer. Sometimes she just calls him by his given name.

John calls Dr. Weir "Elizabeth" after Chaya calls her "Dr. Weir".

Elizabeth allows John to follow Chaya with the Puddle Jumper to help her. After he's gone through the gate, she sighs unhappily.

Somehow he figures out it's her birthday and gives her a present.

Weir: "How did you find out?"
Sheppard: "Mum's the word."

Sheppard: "Your own mortality staring you right in the face. I can't imagine how you must be feeling."
Weir: "When she looks at me, it's as if she's sensing my thoughts, and I'm sensing hers. It's very unsettling."
Sheppard: "Just when you thought this place couldn't get any weirder!"

She touches his shoulder to wake him up.

Sheppard: "We're about to start our mission briefing, so..."
Weir: "I'll be right there. Actually, John. Give me a minute, will you?"
Sheppard: "Sure."

She uses his present to dispose the ashes of the "old" Elizabeth. He's glad.

Weir: "While you were offworld, a Wraith dart flew over our city."
Sheppard: "I'm sorry?"
Weir: "We lost a jumper along with Markham and Smith."
Sheppard: "We what?"
Weir: "And it scanned us."
Sheppard: "We just lost two of my men and a jumper and this is the first time I'm hearing about it?"
Weir: "I tried to reach you even you've been out of radio contact for over 12 hours."

Weir: "And we found something else... rather unsettling."
Sheppard: "I'm already unsettled."

Once more he calls her "Elizabeth".

Weir: "That's good."
Sheppard: "You know, I have my moments."

Weir: "On the off-chance you decide to take the Wraith ships on yourself, Major, I am hereby ordering you not to."
Sheppard: "Believe me, you don't have to."
Weir: "Still..."
Sheppard: "Don't take on an alien armada single-handedly. Understood!"

She looks very concerned after he has left.

John defends her at an important meeting by agreeing with her.
Sheppard to Teyla: "You snapped at Doctor Weir this morning in the Briefing Room for no good reason."

McKay argues with Weir. Sheppard orders McKay: "Will you stop."

Bates criticizes one of Elizabeth's decisions.
Sheppard: "Take it easy, Sergeant."

Alone together on the balcony - talking.

McKay: "The satellite's fifteen hours away by Puddlejumper. I recommend that we put together a small crew – say myself, Grodin and a pilot."
Sheppard: "I'll go."
Weir: "No, Miller can handle it. Major, I need you to keep searching for alternate Alpha sites, just in case this fails."

He disobeys a direct order from Colonel Everett, because he thinks Elizabeth has to be included in the decisions made on Atlantis.

He just brings her along to the briefing.

Everett: "I don't need to explain myself to you, Doctor, and I don't need your cooperation."
Sheppard: "But you could probably use mine... sir. So with all due respect please answer Dr. Weir's question."
Everett: "Is that a threat, Major?"
Sheppard: "No, sir. I understand you need to establish a clear chain of command, but if you cut Dr. Weir out of the loop, you'll only alienate the people whose trust and respect she's earned, which is everyone on the base, including me."
Everett: "Is that a fact?" - "Have a seat."

They have to bid farewell before he goes on a suicide mission.
Sheppard: "Elizabeth, wait." He starts up the stairs. She turns to him. He stops on the stairs and looks down at her.
Weir: "You can't."
Sheppard: "I have to, and you know it."
Weir: "John." - "Go."
Sheppard nods and runs up the stairs. Elizabeth looks close to tears.

McKay to Weir: "You let Sheppard fly that jumper?"