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Atlantis Season 3
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Season 2 Season 4


Episode Edit

The Real World

Transcript Edit

PrologueEdit

INT—HOSPITAL ROOM

[Weir awakens to find herself lying on a hospital bed in a stark white room. She wears white hospital scrubs. Light pours through a window. She gets up and peeks through the Venetian blinds. There is a plastic patient id around her wrist. She notices it. She heads to the door, but finds it locked. The corridor outside is empty. Weir pounds on the door with the flat of her hand.]

WEIR
  Hello?

[A nurse and Fletcher quickly move down the hall. Fletcher unlocks the door and enters.]

FLETCHER
  Good morning, Doctor Weir. I'm Doctor Adam Fletcher.

WEIR
  Where am I?

FLETCHER
  You're in the acute care unit of Willoughby State Hospital.

WEIR
  Willoughby…that's um, that's a psychiatric hospital.

FLETCHER
  Outside D.C., yes.

WEIR
  I'm on Earth?

FLETCHER
  (with humorless chuckle)
  Yes.

WEIR
  Well, when did I get back?

FLETCHER
  You mean back to Earth? Doctor Weir, you never left.

[Weir stares at Fletcher in shock.]

Episode Edit

OPENING CREDITS

INT—FLETCHER'S OFFICE

[Patients can be seen socializing in a common area by a nurse's station outside the windows of Fletcher's office. Weir and Fletcher are having a session inside the office.]

FLETCHER
  You had just begun mediating the treaty for the U.N. when you collapsed mid-speech. You've been under a tremendous amount of stress recently. The treaty negotiation was the final straw that triggered what is known as a brief reactive psychosis. I know you're confused. This type of disorder can be very frightening, but the good news is your condition is most likely transitory. These episodes usually pass within a number of days.

[While Fletcher talks, Weir looks around in confusion and alarm.]

WEIR
  I'm sorry, but…how did I get here?

FLETCHER
  You were transported by ambulance to a hospital in D.C.—

WEIR
  No, I mean from Atlantis.

[Fletcher blinks.]

WEIR
  I—I don't remember coming back.

[She shrugs.]

FLETCHER
  Atlantis?

[Weir leans back, cautious.]

WEIR
  What's your security clearance?

FLETCHER
  Did you want to talk to someone regarding the treaty?

[Weir looks at him blankly.]

FLETCHER
  The U.N. accord. Non-nuclear proliferation in North Africa. That's what you were mediating when you collapsed.

[Weir's jaw drops and she shakes her head in confusion.]

WEIR
  I negotiated that treaty well over two years ago.

FLETCHER
  No. Three days ago. Since then, you've been here in a severely depressed and near-catatonic state.

WEIR
  No. No, I was in my office, and I was reading over a mission report and…this…this can't be real.

[She stands.]

FLETCHER
  Doctor Weir, I assure you, it is real.

WEIR
  (smiles, placating)
  Okay. Okay then, yes….there is somebody I need to speak with regarding the treaty…right away.

INT—WILLOUGHBY PATIENT LOUNGE

[Weir waits as General Jack O'Neill arrives. He is dressed in his Class A uniform. She stands and smiles when she spots him.]

WEIR
  Oh thank God. General O'Neill.

O'NEILL
  (smiling)
  Doctor Weir.

WEIR
  Thank you so much for coming. Er-hopefully you'll be able to help sort out this entire mess.

O'NEILL
  Anything I can do to help.

[She gulps and smiles, relieved. He stands there awkwardly for a second then shrugs.]

O'NEILL
  Would you like me to…

WEIR
  Oh! Please.

O'NEILL
  …Sit?

[She gestures, and they sit.]

WEIR
  It is a relief just seeing a friendly face.

O'NEILL
  Yeah, I was goin' for friendly.

[Weir laughs slightly. She leans forward and glances to be certain no one else can overhear.]

WEIR
  This is all very confusing for me. The last thing I remember, I was in Atlantis, and everything was fine. And next thing I know, I wake up here.

O'NEILL
  (confused)
  Everything was…fine in…Atlantis?

WEIR
  The—the problem is my memory. I—I have no memory of coming back. I don't know if I came back through the Stargate or aboard the Daedalus, or…what?

[She finally notices his bewildered expression.]

O'NEILL
  Oh, um, Doctor Weir, I'm not quite sure I'm…qualified to be in this conversation.

WEIR
  (laughing)
  Oh, please. You ran Stargate Command. You are probably the most qualified person on this planet.

O'NEILL
  (humoring her)
  Yeah…Oh-kay.

WEIR
  (flustered)
  Why are you doing this?

O'NEILL
  What? I'm not trying to do anything.

WEIR
  If you don't know what I'm talking about, then you're not really Jack O'Neill!

O'NEILL
  Oh, I'm Jack O'Neill all right. That's the one thing in this conversation I'm sure about. I met you a few months ago, when we first approached you to help broker this non-proliferation treaty. I don't know anything about Atlantis! Except that it was a fairly mediocre "Donovan" song, not one of my favorites. Now, this Stargate program I'm supposed to have run—

[Weir sits back, stunned.]

WEIR
  It's a facility inside Cheyenne Mountain, Colorado.

O'NEILL
  (impatient)
  That would be NORAD.

WEIR
  It's underneath NORAD, yes!

O'NEILL
  And the Stargate?

WEIR
  It's a portal that allows intergalactic travel. The program has been in operation for over ten years. You started the whole thing when you first encountered—

[Weir watches O'Neill's head suddenly toss back and forth violently, like a television picture that's on the fritz. His hair briefly darkens as if another person is there. A moment later, O'Neill again looks normal and is unaware anything happened.]

O'NEILL
  What?

[Weir looks away and tries to regain control of herself. O'Neill stands.]

O'NEILL
  Look, why don't I get Doctor Fletcher in here?

[Weir stands and backs away from O'Neill.]

WEIR
  No. Just…just leave. Please.

O'NEILL
  All right. Listen, for what it's worth, I hope you get better soon. We need you.

[O'Neill walks away. Weir looks at another door to the side of the room. She looks at the muscular male orderly standing watch by the nurse's station and casually moves away, heading to the door. Another orderly suddenly steps in front of the door. Weir stops and acts like she's moving away. Instead she punches the orderly and tries to get through the door. The orderly is able to grab her and pull her away. He picks her up off her feet from behind. She kicks out at the desk and struggles.]

WEIR
  No! Let me go! Please! Let me go! Let me go!

[Both orderlies wrestle her to the ground. Fletcher arrives with a syringe.]

WEIR
  No! No! No!

[Fletcher injects her with the sedative.]

INT—WEIR'S HOSPITAL ROOM

[Weir sits in her bed, her knees to her chest, her head in her hands, backed into the corner. Fletcher enters.]

FLETCHER
  I've spoken with several people at the Pentagon. They assure me there is no such thing as the Stargate Program, no Atlantis base in another galaxy, and no department of Homeworld Security. I'm sorry.

WEIR
  (brokenly)
  So you are telling me that I dreamt up the last two years of my life?

FLETCHER
  Sometimes when a person experiences a significant emotional trauma, their mind just decides to shut down to escape the pain.

WEIR
  I have brokered dozens of treaties, many of them very stressful, yes. But none of them bad enough to cause "significant emotional trauma."

FLETCHER
  The treaty negotiation was just the trigger point. We believe the actual trauma you suffered occurred three weeks ago. You were riding in a car with a man named Simon Wallace.

[Weir starts with recognition.]

FLETCHER
  You remember Simon?

WEIR
  Yes, of course I do. We—we're no longer in a relationship, but—

FLETCHER
  You were coming home from dinner. A car ran a red light and broadsided you, impacting the driver's side door. Simon was killed instantly. You suffered only minor injuries in the crash, made a quick recovery. But in the days following Simon's funeral, several of your colleagues noticed your behavior changing. Clear signs of depression, confusion.

WEIR
  No.

FLETCHER
  It culminated in your collapse at the negotiation.

WEIR
  No. I'm sorry, I don't believe you.

FLETCHER
  Sometimes, the mind's only way to cope with tragedy is to completely erase it from memory…and on rare occasions, supplant it with something else. In this case, something—

[Weir sees a blurry dark haired figure in blue standing outside the frosted glass of the window and gasps. Fletcher breaks off and looks to the door. Nothing is there.]

FLETCHER
  You all right?

[Weir huddles in the corner.]

EXT—WILLOUGHBY GROUNDS, DAY

[Weir, dressed in her robe and scrubs, walks with Fletcher. They meet with an older woman, and Fletcher stays back as Weir approaches.]

WEIR'S MOTHER
  Hello, sweetheart.

WEIR
  Mom.

[Some time has passed and Weir and her mother are walking alone down the steps further from the Willoughby building.]

WEIR
  I don't understand what's happening to me, Mom. I feel as if…as if I'm asleep, or…or I'm in a dream.

WEIR'S MOTHER
  Look at me. Do I look like a dream, hmm? My hand…does it feel like a dream.

[Her mother caresses Weir's cheek. Weir grasps it and kisses it.]

WEIR
  No. But neither did the last two years of my life. I just…I can't believe it was all a figment of my imagination.

WEIR'S MOTHER
  Give it time. The doctors here will help you get through this. The accident….getting that phone call was the worst night of my life. We all miss Simon terribly, but…I don't know what I'd do if I lost you.

[Weir hugs her mother.]

WEIR'S MOTHER
  Oh. Oh, wait. I have something.

[She rummages in her purse and pulls out a silver pocket watch.]

WEIR'S MOTHER
  Your father's watch. I found it a few months ago. He'd always meant to give it to you.

[Weir gasps and holds the watch.]

WEIR
  I know. I mean…I mean, I took this with me…

[She walks over to a nearby bench and sits on it, then buries her head in her hands and weeps. Her mother approaches and pets her.]

WEIR'S MOTHER
  It's all right, sweetheart. You're safe now. You'll be fine. I'll make certain of it.

INT—WEIR'S WILLOUGHBY ROOM, NIGHT

[Weir sleeps restlessly. There is a noise and she awakens. She spots a dark silhouette of a man behind a white curtain in the room. Weir sits up.]

WEIR
  Hello?

[She warily gets up and approaches the curtain. The silhouette gets larger. The man's face starts to push out the curtain and a strange noise sounds. Weir screams and runs to the door, pounding on it. Fletcher is approaching from outside. He opens the door, and Weir runs into his arms.]

FLETCHER
  What's wrong? What's wrong? What's wrong?

[Weir spins around, but there is no man, and no hospital curtain. Only the chair, sink and window on that side of the room.]

INT—FLETCHER'S OFFICE

[It is now daylight. Weir sits in Fletcher's office with him. He writes on a pad.]

FLETCHER
  I'm going to prescribe some additional medications for you. A mood stabilizer, an antidepressant, and also stronger anti-psychotic medications. These should help reduce the acute symptoms you're experiencing.

WEIR
  Wipe out the last two years of my life.

FLETCHER
  I talked with your mother. She told me how, as a child, you had a brief phase where you dreamed of being an astronaut. She and your father even bought you a telescope for your twelfth birthday.

WEIR
  (smiling at the memory)
  That's true.

FLETCHER
  Sometimes childhood fantasies can offer a peaceful refuge from the harsh realities of adult life.

WEIR
  (scoffing)
  So you're saying, when Simon died, my mind shut down and went to another galaxy?

FLETCHER
  It traveled as far as it could to escape the pain.

WEIR
  And in a matter of…three days, I managed to live out an entire two years of my life?

FLETCHER
  (shrugging)
  Time is relative in the dream state. People live out entire lifetimes in the blink of an eye. Imagine you were in my position listening to your story. Traveling to another galaxy through a star gate? Leading an expedition to the lost city of Atlantis. Would you believe it?

INT—PATIENTS' LOUNGE

[Weir types at a computer. She finds a news report with a picture of Simon's car. The headline reads "Georgetown Doctor Killed in Accident." A nurse approaches with a small cup filled with pills.]

NURSE
  Doctor Weir? Your medications.

[Weir takes the cup.]

WEIR
  Thanks.

INT—BATHROOM

[Weir goes to the toilet and spits out the pills, flushing them.]

INT—PATIENTS' LOUNGE

[Fletcher leads a circle of patients in a group session. Weir is among them.]

FLETCHER
  Have you gone out to the garden today?

ENID
  No. I was going to, but they're out there, so I decided it would be better to wait.

FLETCHER
  The others?

ENID
  Yes. Four of them.

FLETCHER
  Did they see you?

ENID
  Of course. They were waiting for me.

FLETCHER
  Did you speak to them?

ENID
  Yes. I told them what you told me to say, that: "my blood isn't theirs for the taking."

FLETCHER
  Good for you, Enid. That was very brave.

WEIR
  Excuse me. What others?

ENID
  The invaders, dear. From one of the moons of Saturn? They're cold blooded, you see. So they need our warm blood for theirs. You have to be very careful. Doctor Fletcher doesn't think they're real, but I know the truth.

[Weir and Fletcher exchange looks.]

FLETCHER
  Doctor Weir, would you like to speak next? Perhaps you can tell the group about your experience in Atlantis.

[Enid's jaw drops with excitement.]

WEIR
  No.

FLETCHER
  Sometimes, when we share these experiences—

WEIR
  (firmly)
  I said, no.

INT—WEIR'S WILLOUGHBY ROOM, NIGHT

[Weir is locked into her room by an orderly. She looks around warily. Lumps start moving under the blankets of her bed. She goes and whips off the blankets, to find nothing there. She turns as the dark haired figure moves by the frosted window again. She sees the top of his head at the clear window, and the doorknob rattles.]

WEIR
  (quietly)
  No. Go away.

[The figure appears again in the frosted window, pressing his face against the window and banging. Weir backs to the wall and crouches, putting her hands over her ears.]

WEIR
  Go away!

INT—PATIENTS' LOUNGE

[Weir takes some water and swallows her medication.]

EXT—WILLOUGHBY GROUNDS, DAY

[Fletcher approaches the bench where Weir sits.]

WEIR
  Hello.

FLETCHER
  Hi.

[He gestures to the bench.]

WEIR
  Oh. Please.

[He sits beside her.]

WEIR
  Will I ever remember the accident?

FLETCHER
  I don't know. Often in cases like this, the memory of the trauma never returns. Maybe it's the mind protecting itself.

WEIR
  I suppose it's a good thing, really. I mean, there's pain enough even without remembering it.

[Fletcher nods and smiles, then looks at her.]

WEIR
  What?

FLETCHER
  It's just, you're doing great. I'm impressed. You're sleeping well?

WEIR
  Yes! I'm sleeping better than I can remember.

FLETCHER
  Good. I think you're ready.

WEIR
  Ready?

EXT—WEIR'S GEORGETOWN HOME, DAY

[Weir and Fletcher drive up to the house and get out. Weir is in casual every day clothes.]

FLETCHER
  Well, is it how you remember it?

WEIR
  (smiling)
  It's exactly how I remember it.

[The door opens, letting out her dog who comes out to greet her. She bends down to pet the dog.]

WEIR
  Oh! Sedgewick! Hey, sweetie! Hi!

[Her mother follows Sedgewick down the steps.]

WEIR'S MOTHER
  Welcome home, sweetheart.

[Weir and her mother embrace.]

EXT—WEIR'S HOME, DAY

[Weir sits outside at a table, working on a puzzle. The public sidewalk is close-by. O'Neill, dressed in casual clothing, appears just outside the gate.]

O'NEILL
  Hello, hello!

WEIR
  (smiling and standing)
  General!

O'NEILL
  Enough with the "general", okay? It's Jack.

WEIR
  Ah, but which Jack is it?

O'NEILL
  (confused)
  What?

WEIR
  I'm sorry. I'm just trying to have some fun at my own expense. Too soon, maybe.

O'NEILL
  So, you all settled back in?

WEIR
  Getting there.

O'NEILL
  So I hear you're going back to teaching.

WEIR
  Yeah, my poli-sci class at Georgetown. They're holding it open for me for the Fall.

O'NEILL
  Have you given any thought to coming back to the negotiating table? That non-proliferation treaty…you kinda left us hanging mid-sentence there. It'd sure be nice to hear the punchline someday.

[Weir bites her thumbnail and paces.]

WEIR
  And the U.N. would be okay with that?

O'NEILL
  Not just okay, they're insisting.

WEIR
  Really?

O'NEILL
  When you're the best, you're the best. Even if you've had a little…setback, so to speak…he said, awkwardly.

[O'Neill picks at the hedge awkwardly; Weir ducks her head.]

O'NEILL
  It's only if you feel you're ready to go back.

WEIR
  Well, actually, yeah. I think I am.

INT—WEIR'S BEDROOM, NIGHT

[Weir takes her medication and climbs into bed. Sedgewick follows. She pets the dog.]

WEIR
  Hey. It's good to be home.

[She lies down on top of the covers and drifts to sleep.]

INT—ATLANTIS INFIRMARY

[Weir lies unconscious, an oxygen cannulas over her nose as a green grid of light scans over her. Medical personnel in hazmat gear are near her while McKay, Beckett, and others work outside. Sheppard approaches the edge of the plastic isolation chamber and looks inside.]

SHEPPARD
  What've you got, Doc?

BECKETT
  It's gettin' worse. It's not just her brain anymore. They're spreading throughout her body. We're losing her.

[A computer scanner shows a human figure. Red dots appear throughout the body, mostly concentrated at her head and spine. Teyla and Ronon look at the display.]

TEYLA
  Those are all nanites?

BECKETT
  Aye. They've spread throughout her entire body.

RONON
  How'd they get inside her?

MCKAY
  Niam.

FLASHBACK

[In the puddle jumper, Niam turns and begins to choke Weir. The others try and pull him away.]

MCKAY
  (voiceover)
  When he attacked her in the puddle jumper.

END FLASHBACK

MCKAY
  In that one brief moment of contact, he managed to infect her with nanites that began replicating immediately. Now they're multiplying exponentially. Consuming her.

SHEPPARD
  How much time does she have?

BECKETT
  I don't think their intention's to kill her. If that were the case, they could've easily done it already. I don't think there's enough of them to survive on their own. They need Elizabeth's body as raw material.

MCKAY
  So they're attempting to assimilate her? To transform her into one of them?

BECKETT
  (nodding)
  Until they can reach sufficient numbers to form a viable independent entity, I would say so, yes.

TEYLA
  And this is how they replicate?

BECKETT
  I doubt it's their normal way. It may well be a last-ditch attempt to survive.

RONON
  How do we stop them?

SHEPPARD
  EMP. Maybe we can hit 'em with the electromagnetic pulse like we did last time.

BECKETT
  I'm afraid we're well beyond that possibility now, Colonel. Looking at her scan, the nanites have literally bonded to neurons and other cells throughout her central nervous system. If we attempt to disable them, we'll likely end up killing her along with them.

TEYLA
  Then, how do we help her?

BECKETT
  In the petri dish, her white blood cells attack individual nanites as though they were a bacterium or a virus, quite successfully. But for some reason, inside her body, there's almost no immune response whatsoever. It's as if the nanites themselves have convinced her immune system that they pose no threat.

SHEPPARD
  How do they do that?

BECKETT
  I have no idea. I've begun administering drugs to help boost her immunities.

SHEPPARD
  Doesn't seem to be working.

BECKETT
  Not yet. I've just increased the dosage. For the moment, we're losing this battle.

EXT—BUILDING, D.C., DAY

[A town car drives up to the curb and Weir gets out. She is dressed in a suit. O'Neill comes out of the door to meet her. He is in his Class A uniform.]

O'NEILL
  Hey! Right on time! You all set?

WEIR
  I think so.

O'NEILL
  Did you get some sleep?

WEIR
  Yes. But still, I've been really tired lately.

O'NEILL
  Well, maybe you've got to work yourself back into playing shape. Spend a little time doing a some short shifts before you jump up to the first line.

WEIR
  (shrugging)
  I'm sorry. I don't know a thing about football.

[She heads to the door. O'Neill follows.]

O'NEILL
  Nor hockey, apparently.
  (to man holding door)
  Thanks.

[Inside the lobby, Weir pauses.]

WEIR
  It's strange, Jack. I'm…I feel kind of numb.

O'NEILL
  You know, I feel like that all the time.

WEIR
  I'm serious.

O'NEILL
  Did you talk to Doctor Fletcher about it?

WEIR
  Yes. He says it's probably just my medications. He's gonna adjust the dosage, dial them back. See if that helps.

O'NEILL
  Probably just a matter of balance then, eh?

[They both start walking again.]

O'NEILL
  All right. Now, just to be sure we're on the same page, we're against the proliferation of nuclear weapons, right?

WEIR
  Got it.

EXT—ATLANTIS, DAY

INT—ATLANTIS INFIRMARY

[Weir continues to be scanned. Sheppard stands outside the isolation chamber as McKay and Beckett look at the latest scan results.]

SHEPPARD
  Do you think she's aware we're here?

MCKAY
  How can she be? She's unconscious.

BECKETT
  (to Sheppard)
  You may be right. You could try talking to her. Tell her to keep fighting.

MCKAY
  And that will help exactly how?

BECKETT
  In a coma, one's sense of hearing is the last thing to go and the first thing to return. There are many cases where patients were actually able to hear others talking to them in the room.

MCKAY
  And were these comas also caused by nanites invading people's bodies, hmm?

BECKETT
  No, Rodney, but there are indications that she's thinking.

SHEPPARD
  You mean dreaming.

BECKETT
  More than that. Her mind is extremely active for someone in a coma. Her EEG reads almost as if she were going about her daily life, which suggests she may well be able to hear us.

SHEPPARD
  What the hell are they doing to her?

BECKETT
  I wish I knew. The immune-boosting drugs are having no effect.

SHEPPARD
  Aggressive little bastards.

[Beckett stares at the monitor equipment, then turns away and sighs. He pauses as a look of realization crosses his face. McKay notices.]

MCKAY
  What?

BECKETT
  What?

MCKAY
  It was that look. That's the same look I get when I have a brilliant idea.

SHEPPARD
  How would you know how you looked?

MCKAY
  'Cause it's happened more than once in front of a mirror, okay? Carson, what is it?

BECKETT
  I don't know about "brilliant", but it just might…excuse me.

[Beckett leaves.]

MCKAY
  What? What are you doing?

[McKay follows. Sheppard stays by Weir's side.]

SHEPPARD
  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.

INT—WEIR'S BATHROOM

[Weir enters and opens her pill bottle. She glances up at the mirror and finds her reflection has no face. She gasps and drops the bottle, and pills scatter across the floor. She covers her face with her hands, and when she finally lowers them, she sees a normal reflection.]

INT—ATLANTIS INFIRMARY

SHEPPARD
  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 'em get to you.

INT—WEIR'S BATHROOM

[Weir calms down and starts picking up the pills.]

INT—ATLANTIS INFIRMARY

SHEPPARD
  We're doing everything we can to bring you back, but you've got to do your part. You've gotta fight this.

INT—WEIR'S BATHROOM

[Weir looks at the pills, and starts frantically grabbing them and throwing them in the toilet. She opens her other prescriptions and dumps them in the toilet as well, flushing them away.]

INT—FLETCHER'S OFFICE

[Fletcher studies a chart. Weir sits across from him.]

FLETCHER
  I'm sure this is just a result of the adjustment I made to your medications. I think I may have dialed them back too far. It's all a question of balance.

[Weir studies him.]

WEIR
  That's what General O'Neill said.

FLETCHER
  (distractedly)
  Hmm? Yes, well, then he's right. Don't worry. We'll get you back to normal.

INT—WEIR'S BEDROOM, NIGHT

[Weir lies in bed. Sedgewick sleeps by her side]

SHEPPARD
  (distorted and echoing)
  Eliz-Elizabeth.

[Weir sits up, alert. The shadow figure stands at the foot of her bed looking at her.]

WEIR
  (Frightened)
  What do you want?

[The man walks away. Weir gets out of bed and follows. She walks into the living room and to the front door, pauses, then opens it. The door opens to an active Stargate event horizon. She tries to step through, but the two Willoughby orderlies are suddenly there, holding her back.]

WEIR
  No, wait! No! Let go of me! No!

[One orderly presses a plunger in her. She looks desperately at the event horizon as she's sedated.]

INT—WEIR'S WILLOUGHBY ROOM

[Weir awakens in her hospital bed, complete with patient bracelet. O'Neill, dressed in his Class A uniform, lounges next to her.]

O'NEILL
  Hey. How're you feelin'?

WEIR
  Why am I back here?

O'NEILL
  They're worried. Frankly, so am I.

[Weir tosses her covers aside and sits up, obviously frustrated.]

O'NEILL
  Look, obviously I've been pushing you a little hard on this treaty thing—

WEIR
  No…I feel fine.

O'NEILL
  Well, you're not. You're going to be here until you get better.

[O'Neill leaves.]

INT—ATLANTIS INFIRMAY

[Beckett and McKay head to the isolation ward where Sheppard, Teyla and Ronon are already standing vigil.]

MCKAY
  Okay! We think we've found a way to uncouple the nanite cells from Elizabeth's cells.

BECKETT
  We?

TEYLA
  How?

[McKay holds up a small cylindrical device and looks smug.]

MCKAY
  We create a distraction.

[Beckett carefully plucks the device from McKay's hand and gently sets it on a counter.]

BECKETT
  It finally occurred to me why I wasn't having any success.

MCKAY
  What were the nanites originally designed to do?

RONON
  Fight the Wraith.

MCKAY
  Exactly. So, that's what we'll get them to do now.

BECKETT
  We think by implanting a small amount of Wraith tissue into Doctor Weir's body—

[McKay pats the cylinder.]

MCKAY
  (interrupting)
  It's like a tumor.

BECKETT
  Aye. A small tumor, yes. The nanite cells will essentially—

MCKAY
  (interrupting, excited)
  Will attack it, they have to! It's what they are programmed to do, which will draw them away from Elizabeth's cells, effectively unbinding them.

BECKETT
  It will only last a few seconds or so, mind you before the nanites attack the Wraith tissue and return their focus to Doctor Weir's cells.

MCKAY
  But that's all we need! Momentary distraction to draw them away from her, so we can zap 'em with the impulse.

[The rest of the team stare at the two for a moment.]

SHEPPARD
  Okay. Let's do it.

MCKAY
  (excited)
  Hmm!

[McKay snatches the cylinder and heads toward Weir. Beckett nervously follows.]

BECKETT
  Huh! Rodney, give me that…

INT—WILLOUGHBY PATIENT LOUNGE

[Weir sits alone at a table playing solitaire with cards. She reshuffles the deck and starts to set out the cards. The first card is a Stargate glyph. She peeks at the next, but it is only the six of spades. She sets it down and continues to set up the game. The next face up card is another glyph. She keeps putting up cards, finding all the face up cards are either black or red glyphs. The final, eighth card is Earth's point of origin glyph. She stares at the cards, her hands on her head.]

INT—ATLANTIS INFIRMARY

[Beckett, in hazmat gear, injects Weir with the Wraith tissue. Sheppard watches McKay set up the EM pulse emitter.]

SHEPPARD
  Wait a minute. Aren't we supposed to turn off all Earth-based equipment in the room before we do this?

MCKAY
  The EM pulse will be directed through the scanner, so the other equipment should be fine.

[Sheppard bites his lip and watches.]

INT—FLETCHER'S OFFICE

[Weir draws glyphs on a paper to show to Fletcher. O'Neill stands nearby.]

WEIR
  I keep seeing these symbols. Eight of them.

FLETCHER
  Do they mean something to you?

WEIR
  This is the dialing sequence for the Stargate—from Earth to Atlantis.

O'NEILL
  Dialing sequence…? Like a…phone number?

[Weir stands.]

WEIR
  Look, I know you think I'm delusional. But I can't shake the overpowering feeling that something…or—or someone is trying to communicate with me.

FLETCHER
  And what are they trying to say?

WEIR
  That Atlantis is real. And that I have to get back there.

O'NEILL
  (skeptical)
  And so, we're the fantasy?

[He gestures between himself and Fletcher.]

WEIR
  (taking a deep breath)
  Yes.

O'NEILL
  You know…I don't mind being fantasized about occasionally. But come on. We're right here.

[Fletcher touches the pad where the glyphs are written.]

FLETCHER
  How would you get there?

WEIR
  Go to Stargate Command.

O'NEILL
  So now you just want to waltz into NORAD. Is that it—

WEIR
  (angry)
  I know what you told me! But I also know what I feel. Atlantis is real, and I will get back there.

INT—ATLANTIS INFIRMARY

[Beckett is outside the isolation chamber now, studying the scanner. Ronon is behind him.]

BECKETT
  And it's working!

[Sheppard joins the pair to see the nanites concentrating on Weir's right leg below the knee, where the Wraith tissue was injected.]

RONON
  They're moving fast.

BECKETT
  Aye. Get ready with the EM pulse.

MCKAY
  We're ready on your mark.

BECKETT
  And…now!

[McKay activates the EM pulse. It goes through the scanner and covers Weir. The monitor showing the nanites shuts down.]

SHEPPARD
  I thought you said that-that…

[The monitor comes back online. No nanites are visible.]

TEYLA
  It worked!

MCKAY
  (elated)
  Carson, you might be an absolute—

BECKETT
  (crestfallen)
  Oh no. We didn't get them all.

[He is studying a three dimensional image of the brain, showing some nanites still there.]

TEYLA
  How is that possible?

BECKETT
  I don't bloody know.

[Beckett storms over to the EM pulse equipment.]

MCKAY
  They've been using organic material to replicate, which has rendered them immune to the EM pulse.

RONON
  So now what?

BECKETT
  They've started replicating again.

INT—WILLOUGHBY CORRIDOR

[Weir comes out of the ladies' rest room to find Fletcher and an orderly waiting for her.]

FLETCHER
  You spit out your pills again, didn't you?

[Weir spins, but finds the other orderly blocking her path.]

FLETCHER
  You disappoint me, Elizabeth.

WEIR
  The pills are not going to help me.

FLETCHER
  Not if you won't let them. You leave me no other choice.

[The orderlies grab her by the arms and drag her away.]

WEIR
  What-what are you doing?

INT—WILLOUGHBY EXAM ROOM

[The orderlies strap Weir down onto a gurney.]

WEIR
  No!

[She struggles as she is strapped down by the wrists and ankles, but cannot break free. Fletcher hovers.]

WEIR
  Don't do this.

[A nurse prepares an electric shock application and Fletcher takes it from her.]

FLETCHER
  This will hurt.

INT—ATLANTIS INFIRMARY

TEYLA
  What do we do now?

SHEPPARD
  Zap her again. Keep it up 'till they're gone.

BECKETT
  A significant number of nanites have migrated into the arteries that supply blood flow to the higher functions of her brain.

RONON
  You're telling us they can kill her if they want to?

BECKETT
  Nurse, switch her over to 100% oxygen, stat! And start her on norepinephrine, five mics per minute.
  (to team)
  Reducing blood flow to those parts of her brain will place her in a state of cerebral hypoxia.

TEYLA
  What will that do?

MCKAY
  Render her essentially brain dead, which makes no sense.

SHEPPARD
  Unless she's fighting it.
  (everyone looks at him)
  It's the only thing that makes sense. The replicators see us as organic machines. They're trying to take control of the machine they're in—

BECKETT
  You mean replace Elizabeth's consciousness?

SHEPPARD
  Maybe when we zapped her with the EMP, we killed enough of them to even out the odds, and gave her a fighting chance at stopping them.

MCKAY
  Uh, reality check? There are microscopic robots in her brain! How does she fight that?

SHEPPARD
  (to Beckett)
  You said her mind was active, like she was thinking, reacting, living her life? What if this was the only way they could get to her? What if they were trying to force her to give up?

TEYLA
  A battle of wills.

SHEPPARD
  Exactly.

BECKETT
  Her neural activity supports Colonel Sheppard's hypothesis, Rodney.

MCKAY
  So, what, we can't do anything?

BECKETT
  I can increase the oxygen levels in her blood. Give her a little more time. But, yes…she's on her own.

SHEPPARD
  No, she's not.

[He approaches the isolation tent.]

SHEPPARD
  You're not alone, Elizabeth. We're right here with you. You have to fight this!

INT—WILLOUGHBY EXAM ROOM

[The blurred image appears through the frosted glass window.]

SHEPPARD
  (voice echoing)
  Fight this!

[Weir breaks free of the restraints, and kicks the orderly aside. She runs out of the room and spots the man (Sheppard) at the end of the hallway. She runs toward him. He walks into an open elevator. She pauses outside it, afraid. She looks back to see the orderlies and Fletcher chasing her. She gets in the empty elevator and closes the door before her pursuers arrive.]

INT—SGC CORRIDOR

[Weir steps out of the elevator into Stargate Command. She runs down different hallways. Behind her, O'Neill appears, wearing his Class A uniform.]

O'NEILL
  Doctor Weir? It's okay. You're safe now.

WEIR
  Where am I?

O'NEILL
  Stargate Command. It's okay. Follow me.

[Weir sighs, relieved and starts to follow.]

SHEPPARD
  Elizabeth!

[She pauses and turns. The man is at the far end of the corridor.]

SHEPPARD
  Don't listen to them.

O'NEILL
  What's wrong?

SHEPPARD
  This way.

O'NEILL
  (cautious)
  I'm not going to hurt you.

WEIR
  The hell you aren't.

[She runs away from O'Neill, following where the man has gone.]

[She runs into another corridor to find two guards taking aim with rifles. She turns back, but two more guards are behind her, also raising their weapons.]

INT—ATLANTIS INFIRMARY

BECKETT
  They've begun to spread faster. We're losing her.

SHEPPARD
  Not yet, we're not.

MCKAY
  What're you doing?

[Sheppard unzips the isolation tent and steps inside.]

MCKAY
  What are you crazy? She can infect you!

[Sheppard clasps both hands over Weir's left arm.]

INT—SGC CORRIDOR

SHEPPARD
  Elizabeth?

[Weir turns to find, Sheppard, now close enough to be clearly visible, standing directly behind the two guards.]

WEIR
  John!

SHEPPARD
  You've been infected by nanites.

INT—ATLANTIS INFIRMARY

[Weir lies still.]

SHEPPARD
  They're trying to take control of your mind and body.

INT—SGC CORRIDOR

SHEPPARD
  Don't let them do it. You have to fight 'em. So fight.

[O'Neill approaches from the other direction.]

O'NEILL
  Elizabeth!

[Weir turns.]

O'NEILL
  You have to come with us. I'm sorry.

SHEPPARD
  You know which way you have to go…Run.

[Weir looks back and forth, then turns in Sheppard's direction. He's disappeared, but she runs. The guards open fire to no effect. She knocks them aside as she runs past.]

INT—ATLANTIS INFIRMARY

[Personnel in hazmat wrestle Sheppard away from Weir.]

BECKETT
  Get him out of there. Put him into isolation and run a scan immediately.

[Beckett zips the tent closed again.]

INT—SGC CONTROL ROOM

[Weir enters and dials the Stargate.]

INT—SGC GATE ROOM

[The wormhole activates. Weir runs up the ramp. O'Neill blocks her path.]

O'NEILL
  I can't let you go.

WEIR
  You're not General O'Neill.

[O'Neill morphs into Fletcher.]

FLETCHER
  Elizabeth, listen to me.

WEIR
  (pointing behind him)
  You see that? That's the Stargate. And yes, leaving is exactly what I plan to do.

FLETCHER
  I won't let you go.

WEIR
  You can't stop me.

[Fletcher morphs into Niam.]

NIAM
  On the contrary, I already have. I've made your friend disappear, haven't I?
  (Weir hesitates)
  That's right. He can't help you now. And you can't possibly get past me. So you see…you've lost.

[Weir walks forward, passing through the illusory Niam and into the event horizon.]

INT—ATLANTIS INFIRMARY

[Weir regains consciousness.]

WEIR
  Where am I?

[Everyone outside the isolation tent are happy.]

TEYLA
  The infirmary. How are you feeling?

[Weir smiles.]

WEIR
  I'm back in Atlantis?

BECKETT
  You never left.

INT—ATLANTIS CONTROL ROOM

[Sheppard approaches Weir, who stands at the balcony with 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 realize 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
  (warning)
  John…? Don't.

SHEPPARD
  (sheepish)
  Sorry.

[He leaves. Weir nods and looks down. She holds her father's watch in her hands.]

FADE OUT

END CREDITS


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