ATLANTIS. Rodney McKay, Aidan Ford, Doctor Zelenka and another man 
called Hays are checking out one of the piers of Atlantis after the 
flooding caused by the hurricane. The corridors in that area are 
quite dark, so they all have torches.
ZELENKA: Seven thousand, five hundred forty-nine.
McKAY (sarcastically): Oh, *please*. Prime. Four thousand and 
twenty-one.
ZELENKA: Ah, nice try! Uh, not prime. OK – Lieutenant Ford:
five 
hundred ninety-nine.
FORD: I don't *care* if it's a prime number or not.
ZELENKA: Oh, come on. Yes or no?
FORD (clearly guessing): No.
ZELENKA (to Rodney): Ha! It's incredible! Ten for ten!
McKAY: He is terrible.
FORD: So I suck at Prime/Not Prime. Somehow I'm going to sleep 
tonight.
ZELENKA: At this point it's gone way beyond you not knowing your 
prime numbers.
McKAY: It's a true/false game. Statistically, just by guessing,
you 
should be getting at least half of these right. Look: nine ninety-
three.
FORD (guessing): Prime.
McKAY: Oh, come on, that's an easy one! You hearing this, Hays?
HAYS (bored): Not really. Guess I've been too busy doing my job.
McKAY: We've already been through this section of Atlantis,
Doctor 
Killjoy. It's structurally sound.
ZELENKA: Lieutenant Ford, would you mind being a subject of research 
paper on statistical probabilities? (He giggles.)
(Aidan, fed up and embarrassed, rounds on Zelenka.)
FORD: This is some sort of pay-back for guys like me beating up guys 
like you in high school, right? (He glares at Zelenka for a moment, 
then turns and stomps off. Zelenka stands there, startled, for a 
moment, then follows the others down the corridor to meet up with 
various other groups of personnel who have been investigating the 
area. At around that time, Elizabeth Weir contacts Rodney by radio 
from the Control Room.) [Note: in this episode a lot of people are 
wearing earpiece/microphone combinations rather than speaking into 
hand-held radios, so a comment of "(over radio)" doesn't
mean that 
the person lifts a radio and speaks into it.]
WEIR: So, Rodney, what's it like out there in the suburbs today?
McKAY: Essentially, with the exception of the upper level Storage 
Room, which the lovely and talented Dumais informs me is in no 
immediate danger, this pier's in relatively good shape. 
(Dumais and her team are just returning to the rendezvous point at 
that moment.)
WEIR: Even after all the flooding from the storm?
McKAY: Well, it's dark, it's damp and it smells terrible, but
from an 
engineering standpoint we're good.
WEIR: Head back.
McKAY: Heading back. (He turns to face the group of people around 
him.) Alright, you clowns, listen up! I don't often get a
chance to 
say this, so savour it: good work, boys and girls! Let's go home.
ZELENKA (looking around): Wait, wait, wait. We're missing
Johnson 
and Wagner.
(Rodney sighs irritably and activates his radio.)
McKAY: Wagner, Johnson, what's your position?
(There's a long silence, then Wagner's voice comes over the
radio. 
He sounds terrified.)
WAGNER: We need back-up! They're coming at us!
McKAY: What?!
FORD: (to Zelenka): Where are they?
(Zelenka checks his lifesigns detector.)
ZELENKA (indicating the way): Down this corridor.
McKAY (into radio): We're on our way.
(Everybody rushes down the corridor until they reach Wagner and 
Johnson. Wagner is lying on the floor. Johnson is sitting on the 
floor against a wall with her legs drawn up and her head down on her 
knees. Rodney rushes over to her.)
McKAY: Johnson, Johnson, you OK?
(Aidan goes to Wagner and checks his pulse.)
FORD: McKay. (Rodney looks over to him.) He's dead!
McKAY: Johnson, what happened here?
JOHNSON (crying, without looking up): They got him.
McKAY: *Who* got him?
(Johnson looks up and stares in terror over Rodney's shoulder
before 
scrambling to her feet and starting to back away.)
McKAY: Calm down. There's nothing here.
(Johnson continues backing away, now flailing at something only she 
can see.)
JOHNSON: Can't you see them? They're everywhere!
McKAY (into radio): Beckett, I need a medical team down here, stat!
(Johnson is still trying to fight off whatever she can see. Zelenka 
and Hays rush to hold her, trying to calm her down. After a moment, 
her legs buckle under her. As Zelenka and Hays lower her carefully 
to the ground, she clutches at her head, then screams in anguish for 
several seconds before going limp. Zelenka brushes her hair away 
from her face and puts his fingers to her neck. We see that there is 
blood coming from her nose and mouth. Zelenka looks up at Rodney, 
bewildered.)
ZELENKA: It's no use. She's gone.

MEDICAL LAB. Carson Beckett replies to Rodney.
BECKETT (into comms): McKay, this is Doctor Beckett. What exactly is 
the nature of the emergency?
(Back in the corridor, Wagner's and Johnson's bodies are
being 
covered over.)
McKAY (into radio): It's too late. They're gone.
BECKETT: Who's gone? How?
McKAY: Wagner and Johnson. I need a containment team here.
BECKETT: I'm sorry?
FORD (to Rodney): A containment team? Why?
McKAY: People don't just see things and drop dead, Lieutenant. 
We 
spent the last hour surveying unexplored areas of this city. I think 
Wagner and Johnson were exposed to something.
FORD: Yeah, but ...
McKAY: And if they were infected, there's a very good chance that
we 
were too.
ZELENKA: I recommend a Level Four quarantine until we know what
we're 
dealing with.
McKAY: Agreed. (Into radio) Carson, you hear all that?
BECKETT: Aye. We'll get to the hazmat gear and head down. Sit 
tight. I'll make sure Doctor Weir's briefed.
McKAY: Thank you very much.
BECKETT (to his staff): OK, you heard the man. Follow me, ladies and 
gentlemen.

CORRIDOR.
PETERSON: So, wait, what, we're just gonna stay here?
McKAY: That's the plan, yes.
PETERSON: May I say it's a terrible one?
McKAY: No, you may not.
PETERSON: I think we should get the hell out of here.
ZELENKA: If it is an airborne agent, we may already be infected. 
Heading back to the city would only endanger the rest of the 
population.
PETERSON: What if we're not infected yet?
McKAY: Well, there's no way of knowing.
PETERSON: But I feel fine. I feel perfectly fine!
McKAY: End of discussion. Peterson, we're staying here. 
Actually – 
wait a second ... (He snaps his fingers several times as he 
formulates an idea.) Everyone follow me. (He heads off and 
gradually all the others follow him. Peterson hangs back and turns 
as if to go in another direction but finds two marines standing 
behind him. One of them smiles at him mock-sweetly. Peterson 
reluctantly turns again and follows the others.)

ELIZABETH'S OFFICE. Peter Grodin is bringing Elizabeth up to
date 
with developments.
GRODIN: They've begun to institute a Level Four quarantine.
WEIR: It can't really be a biological infection, can it?
GRODIN: I have no idea *what* it is, but I agree we should play it 
safe and initiate self-regulated quarantine in all populated sections 
of the city.
WEIR: That's pretty severe.
GRODIN: We've known for some time that the Ancients suffered from
a 
plague. If McKay and his team have somehow stumbled upon it and 
become infected, we'll need to take every precaution to prevent
an 
outbreak.
WEIR: Alright. We will suspend any and all Gate activity and keep 
everyone where they are. Again, just until we have a clearer picture 
of exactly what it is that killed Wagner and Johnson.

GYM. (Or a room that has been designated the gym.) John is twirling 
two Athosian fighting sticks. Opposite him, Teyla stands with two 
sticks in one hand. She looks very relaxed, while John is 
concentrating hard. He runs forward and strikes at her with both of 
his sticks but she easily fends them off with just one hand and –
to 
add insult to injury (or rather, injury to insult) – steps
casually 
past him and smacks him none too gently on the backside with her 
sticks. John grimaces and limps round to face her again. Again he 
attacks her and again she easily meets every move he attempts. This 
continues for a minute or two until finally Teyla tires of playing 
with him, smacks one stick out of his hand, hits him in the back of 
the knees to make him fall and drop the other stick, then stands 
behind him and holds him tightly across the neck with her sticks.
TEYLA (sternly): You have not been practising.
SHEPPARD: Yes I have.
TEYLA: If this was really a fight ...
SHEPPARD: If this was really a fight, I would have *shot* you by 
now. (Exasperated, Teyla releases her grip around his neck and 
shoves him to the floor.) Y'know, no matter how many hours I put 
into this, you're still gonna kick my ass.
TEYLA: It is not for the winning that we practise.
SHEPPARD: Well, what's the point?
(They go over to a bench, collect their bags and walk towards the 
exit. Just then, there is a beeping noise and then Elizabeth's
voice 
comes over the comms.)
WEIR: May I have everyone's attention please? We have run into a 
questionable medical situation and at Doctor Beckett's suggestion
we 
have decided to put the city into a self-regulated quarantine. For 
at least the next couple of hours, I need everyone to stay where they 
are, and report anyone moving freely through the halls. I hope 
you'll understand. Thank you.
SHEPPARD: What the hell is this? (He rummages through his bag but 
can't find what he wants. He turns to Teyla.) Did you bring
your 
radio?

CORRIDORS. Rodney and the others are walking through the corridors.
FORD: Isn't this the same section Johnson and Wagner were
exploring?
McKAY: Yes.
FORD: So we're retracing their steps.
McKAY: That's right. Don't worry, my motivations are based
entirely 
on self-preservation.
PETERSON: Wait, wait, wait! Wait! Ford's right. Doesn't
this 
increase our chances of getting infected?
(Rodney stops walking and turns to face everyone else.)
McKAY: Alright, let me spell this out for you, OK? If there is a 
bacterial agent and it is not airborne, then it should be relatively 
safe for us to look around as long as we take the proper 
precautions. However, if it *is* an airborne agent, then there's
a 
very good chance we've already been infected.
FORD: Well, shouldn't we wait for Doctor Beckett to decide that?
McKAY: Those men were only down there for twelve hours. Even if they 
were infected right away, that's an alarmingly short incubation 
period. Now, if anyone else is infected – as in, I don't
know, maybe 
*us* – seconds are gonna count, Lieutenant. Alright. (He holds
out 
his hand.) Light. (Zelenka hands him a torch.) Let's go. (He 
heads off again.)

LATER. The team come to a partially open doorway. Peering inside, 
Rodney sees that it's a lab of some kind.
McKAY: Right, everybody stay here. Ford ...
FORD (who was already turning away): You just told me to ...
McKAY: Everybody except *Ford* stay here. You think I'm going in 
there by myself? Uh-uh. (He and Aidan squeeze through the doorway 
and go inside the lab. Their feet crunch through broken glass.) 
Don't touch anything. (They go over to some large glass jars on
a 
central table. Several of them are broken.) This is not good.

GYM. Teyla obviously did have her radio because John is now arguing 
with Elizabeth, who is still in the Control Room. She has Sergeant 
Bates with her.
SHEPPARD: I'm ranking military officer here.
WEIR: Yes, I'm aware of that, Major. You were off radio and we
had 
to act quickly. Now, this is all protocol that was put into place 
long before this expedition began. Bates is here with me and we 
agreed this was the best plan of action.
SHEPPARD: Alright, alright. Teyla and I are coming up to join you.
WEIR: We're in a self-regulated quarantine, Major. Everyone
stays 
where they are.
SHEPPARD: We're nearly a mile away on the east pier. D'you
really 
think I'm in any sort of danger walking from here to the Control
Room?
WEIR: At this point we don't know where they contracted the
virus. 
This is a medical situation, John. Only authorised personnel in 
hazmat suits are allowed to roam freely – those rules apply to 
everyone, including you.
SHEPPARD (slowly, as if explaining it to an idiot): Well, then, get 
someone to bring me a hazmat suit.
WEIR (starting to get angry): Everyone in hazmat is busy configuring 
the lab to deal with a possible outbreak. Now *if* an opportunity 
arises, I will send somebody to come get you, but in the meantime, 
radio contact will have to do.
SHEPPARD (frustrated): Alright. Just ... keep us in the loop.
WEIR: Will do.
(Irritated, John walks back to the bench and tosses his bag down. 
Teyla rolls her eyes slightly.)

ANCIENT LAB. The rest of Rodney's team have now come in and are 
looking at the damage. Some of them have set up laptops.
ZELENKA: Any number of these smashed and open containers could have 
released the virus that killed Johnson and Wagner.
FORD: And how would something like that survive for all these years?
DUMAIS: Viruses can remain dormant for long periods.
ZELENKA: I'm hoping the answer will be found in the database. 
(He 
walks over to a console, where Rodney is already working.) OK, I 
think that we ...
McKAY (holding up his hand): Yes, yes, yes, yes, yes. It doesn't 
appear to be networked in with the rest of the Ancient systems. In 
fact, if you look, it only contains information about the experiments 
that took place in this room. (He realises something and slaps his 
radio to activate it.) Weir, it's McKay.
WEIR: Go ahead, Rodney.
McKAY: Where's Beckett?
WEIR: He's on his way. It takes some time to load a whole
medical 
team into suits.
McKAY: Well, we seem to have stumbled across something that I 
find ... a little troubling.
WEIR: That's not what I wanted to hear.
McKAY: I think we may have found an Ancient viral lab. Wagner and 
Johnson must have been exposed here. Now, it'll take weeks to
sift 
through all this data, and there's no way of knowing whether the 
Ancients were just studying the viruses or actively creating them. 
(Behind him, Dumais looks up from her laptop, suddenly terrified.) 
Either way, the storm's done quite a number on this place and
I've 
got ... (Dumais starts whimpering in terror, staring at something 
only she can see. Rodney hears her and turns around.) Dumais. 
Dumais? (She holds up her hands to try to prevent whatever it is 
from getting to her.) Dumais!
(Dumais turns to look at Peterson standing beside her. She rushes 
towards him.)
DUMAIS: It's all over you! (She starts flailing at him, trying
to 
brush something off him.)
PETERSON: Dumais? Dumais! (He tries to fend her off.)
DUMAIS: They're all over you! They're all over you!
(Rodney rushes over and tries to pull her off Peterson. Zelenka 
comes over to help. Dumais screams and clutches her head, just like 
Johnson did, then grunts and starts to convulse.)
(Nearby, Peterson is watching what's happening, then glances away
and 
stares terrified at a wispy, Wraith-like apparition – except this 
looks a lot darker and scarier than the Wraith `ghosts'. He
flinches 
away as it rushes towards him ... and then it disappears.)
(Meanwhile, Dumais is alternating between grunting in pain and 
screaming. With everybody distracted by her, Peterson turns and 
quietly slips away.)
(McKay and Zelenka lower Dumais to the floor. There is blood coming 
from her nose, mouth and ears. Zelenka checks her pulse, then looks 
up at Rodney and shakes his head. Nobody except the viewers hears 
Peterson's footsteps receding as he runs away.)
McKAY (into radio): Tell Beckett to pick up the pace – I've
just lost 
another member of my team!
(Aidan stares in disbelief at the scene before him, then looks 
around.)
FORD: Where's Peterson?
McKAY: What?
FORD: Peterson!

LATER. Some distance away, Peterson is hurrying along a corridor. 
In the Control Room, Elizabeth and Sergeant Bates are looking at a 
screen which shows lifesigns movements in the corridors. 
WEIR: Yes, OK, I think we have him. He's trying to make his way 
back. It should be OK – Grodin is locking all the doors in the 
hallway and killing power to the entire section.
McKAY: You need to send someone to stop him.
WEIR: It's under control, Rodney.
McKAY: No, Elizabeth, it's not under control. He knows almost as 
much about Ancient technology as I do. At the very most, what
you're 
doing will just slow him down.
(Peterson has reached a sealed doorway. He has opened the door panel 
and is tinkering with the crystals inside. Moments later, the door 
opens a little. Painfully, he squeezes through the gap and continues 
on.)
(In the Control Room, Weir and Bates watch as Peterson's signal
moves 
on.)
WEIR: Where does that hallway lead?
GRODIN: Straight here.

Peterson reaches another sealed doorway and prises the cover off the 
door panel. He jumps as Elizabeth's voice comes over the comm
system.
WEIR: Peterson? This is Elizabeth Weir. Can you hear me? I
can't 
imagine how frightening this whole ordeal must be, but Doctor Beckett 
has reached the rest of your team and begun to treat them. (Peterson 
carries on working on the door panel.) Now, I think the best thing 
for you to do is to head back. If Beckett gives you a clean bill of 
health, we'll make sure you get back to the city as soon as 
possible. (Peterson succeeds in getting the door to open a little. 
He squeezes through the gap. In the Control Room, Weir sees his 
signal move on. She turns to Peter.) Are you sure he can hear me?
GRODIN: Positive.
WEIR: Can you do *anything* to make it harder to get through those 
doors?
GRODIN: I can try. (He starts working on his console as Elizabeth 
and Bates anxiously watch Peterson's signal getting closer to the 
Control Room.)

ANCIENT LAB. Beckett's team has indeed arrived, each of them
wearing 
hazmat suits. They are checking various people out. Carson is 
taking Rodney's blood pressure.
BECKETT: Well, you seem perfectly fine.
McKAY: Well, Dumais seemed fine, right up to the point where she 
wasn't.
BECKETT: I've had them set up a small field station down the 
corridor. We've already started the autopsies.
McKAY: Any ideas?
BECKETT: From what we can tell, you're all in good shape, so I 
wouldn't jump to any conclusions.
McKAY (irritably): Stop trying to convince me I'm fine, Carson. 
I 
think we all know better.
BECKETT: I was just trying to ...
McKAY: Are we done here?
BECKETT: Yes.
(Rodney pulls the blood pressure cuff off his arm.)
McKAY: I'm gonna see what I can get from the database. Let me
know 
what the autopsy shows up.
BECKETT: Alright.
McKAY: Oh – and tell your pathologists to start with their heads.
(Carson nods and walks away. Rodney walks over to the Ancient 
console, but then stops and turns around slowly. He can see 
something flitting around the room. (We don't see what it is,
but 
Rodney's head and eye movements indicate that he's watching 
something.) Nearby, one of the medical team has put a thermometer in 
Zelenka's ear. Zelenka sees what Rodney is doing and pulls his
head 
away from the medic, looking at Rodney in concern. After a moment, 
Rodney stops seeing whatever it was and turns back to the console, 
but then turns back and looks nervously around the room before 
getting back to work.)

GYM. John and Teyla are sitting on the bench.
SHEPPARD (into radio): Someone has to do something.
WEIR: We *are* doing something. (In the Control Room, Peter is 
moving small glass plates on a console into different positions.) 
Grodin's working on a plan to limit the door controls ...
SHEPPARD (interrupting): That's not good enough. Someone has to
go 
out there and stop him. Teyla and I are ready.
WEIR: Major, we've been ...
SHEPPARD (interrupting again): Peterson obviously isn't thinking 
straight and he's endangering the entire population of the city.
WEIR: We don't yet know the nature of the virus we're dealing
with. 
This is still a *medical* situation.
SHEPPARD: Oh, we don't have time for this. I'm heading out. 
(He 
stands up.)
WEIR: Grodin, seal the gym. 
(Peter presses buttons on his console. As John walks towards the 
doors of the gym, they close just before he can reach them.)
SHEPPARD: What the hell is this?
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. Bates?
BATES: Yes, sir.
SHEPPARD: Unlock the gym.
BATES: Yes, sir. (He walks towards the console.)
WEIR: Stand down, Bates. (Into comms) You are not in command here, 
Major.
SHEPPARD: Well, we'll agree to disagree. Bates, open the door.
(Bates looks at Elizabeth for a moment, then steps forward again.)
WEIR (firmly): Don't.
(Bates stops again.)
SHEPPARD: Elizabeth, he's heading right for you.
WEIR: So we'll stop him. We'll talk him down, we'll
block his way, 
we'll ...
SHEPPARD: Sergeant Bates, I am ordering you to open up the doors 
between the gym and the med lab right now.
(In the Control Room, Elizabeth and Bates commence a stare-down. 
Bates' expression is resolute; Elizabeth is trying to look firm
but 
she's clearly afraid that he is going to disobey her in favour of
his 
commanding officer.)
(In the gym, a few seconds later the doors slide open.)
SHEPPARD: We're heading out. (He runs off. Teyla grabs her bag
and 
follows.)
(In the Control Room, Bates is unsuccessfully trying to hide his smug 
expression.)
BATES: I'm sorry, ma'am.
WEIR: Doesn't really matter now, does it?

FIELD STATION. Behind protective plastic sheeting, Doctor Biro is 
preparing to start her final autopsy. Just outside, the other two 
bodies are in body bags.
BIRO (into radio): Doctor Beckett, I have the preliminary autopsy 
results from the first two victims, sir.
BECKETT: Anything of interest?
BIRO: They both died of a ruptured sacular brain aneurysm –
which, in 
itself, isn't all that remarkable. I mean, sure, the chances of
two 
people standing next to each other and dying of it is statistically 
improbable, yes, but it's not the smoking gun we were hoping for,
cos 
I know *you* said ...
BECKETT (interrupting): Get to the good part, Doctor Biro.
BIRO: Yeah, sorry, sir. (Standing next to Carson, Rodney twirls his 
hand in a `get on with it' gesture.) What is truly
interesting is 
that both ruptures happened in exactly the same place, right above 
the visual cortex.
BECKETT: And the third one, Dumais?
BIRO: Just getting to her now, sir. (She starts up a high-pitched 
drill.) I'll let you know.
McKAY: She did say brain aneurysm, right?
BECKETT: That's right.
McKAY: That's the best news I've heard all day. Let me show
you 
something.

MEDICAL LAB. John and Teyla are getting into hazmat suits.
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.
(John looks at her, then rolls his eyes before activating his radio.)
SHEPPARD: Doctor Weir, this is Sheppard. Teyla and I are ready to 
head out. What's Peterson's location?
(In the Control Room, Elizabeth hears him but stares at a laptop and 
does not reply.)
SHEPPARD: Elizabeth.
(Elizabeth pauses for a moment longer, then speaks, her voice flat 
and emotionless.)
WEIR: He's in section E19, level three.
(John puts his hazmat helmet on and looks at Teyla.)
SHEPPARD: Let's head out.

SECTION E19, LEVEL 3. Peterson is working on another door panel. 
The door opens a fraction and Peterson struggles to push it open wide 
enough to be able to squeeze through. After a second, however, he 
stops pushing and turns around, terrified, as a dark, misty, ghostly 
figure rushes towards him. There's a hint of a skeletal face in
the 
mist. The ghost is emitting a high-pitched screech. Peterson 
screams and tries to fend it off. A moment later, however, he stops 
screaming and looks around nervously – the ghost is gone. He
gets 
back to forcing the door open and squeezes through. He looks back 
briefly into the hallway he just left to see if the ghost is still 
around but there's no sign of it. He runs off.

ANCIENT LAB. Rodney opens a laptop and shows the screen to Carson.
McKAY: I've read the entire entries – it's incredibly
long, but this 
looks like our guy. Six hour hibernation, reoccurring visions, and 
best of all, so I've left it til last, brain haemorrhage, or 
aneurysms.
BECKETT: That definitely sounds familiar.
McKAY: Maybe there's something in here about how to ... (He
trails 
off and looks up, afraid. The dark ghostly mist comes out of the 
wall behind Carson. Rodney screams and ducks down. Everybody turns 
round to look at him. Rodney straightens up again, looking around 
the room, but there's no sign of the ghost. His voice is a
whimper 
as he speaks.) Sorry.
BECKETT: Rodney?
McKAY (reluctantly): I've been seeing things.
BECKETT: Since when?
McKAY: About an hour. First you think it's just your eyes
playing 
tricks on you but eventually ...
(Hays, recognising what Rodney is describing, steps forward.)
HAYS: ... they get worse.
McKAY: You too?
(Hays nods and looks at Carson.)
HAYS: They come right at you.
McKAY: It's like a ghost.
ZELENKA: I've been going over the survey schedule. Johnson and 
Wagner started off on their own, but then crossed paths with Dumais 
an hour later.
BECKETT: Dumais died almost exactly an hour after Johnson and 
Wagner. Who did they meet up with next?
ZELENKA: My greater concern is who *Dumais* met up with next.
BECKETT: Dumais? Who'd *she* run into?
(Zelenka lowers his head for a moment, then looks at Rodney.)
McKAY: Me. She ran into Hays ... and me. We're next.

CORRIDOR. Peterson gets another door open. As he walks through, 
John and Teyla are waiting on the other side. Both of them are 
armed. 
SHEPPARD: Doctor Peterson, I presume.
PETERSON (raising his hands): I'm not going back there.
SHEPPARD: You don't have much of a choice. (Peterson starts to
back 
away, looking back the way he came for an escape route.) Easy.
PETERSON: I go back there, I get infected, that's murder.
TEYLA: Once we ensure that you are *not* infected, you will be 
allowed back into the city. Until then, you are a threat to the rest 
of the population.
PETERSON: You won't shoot a member of your own team. (He lowers
his 
hands and starts to walk towards John and Teyla.)
SHEPPARD: Peterson. (He raises his P90. Peterson stops and raises 
his hands again.) You will *not* be allowed to go back to the city.
PETERSON: OK, wait, wait, *wait* a second. Take me back to the 
medlab, just quarantine me there. I'll go voluntarily – just
please 
don't make me go back there. (He indicates the direction he just 
came from.)
(John and Teyla look at each other.)
PETERSON: Really, I'm-I'm fine. (He lowers his hands and
tries to 
look calm.) I'm fine. I feel perfectly fine.
SHEPPARD (into radio): Doctor Weir, this is Sheppard. Peterson has 
agreed to go back to the medlab until we can get this situation 
resolved. 
(While he's talking, Peterson looks around and sees a transporter 
room just feet away, and the door is open. He runs towards it.)
SHEPPARD: Stop!
(As Peterson hurls himself into the transporter room, John fires 
several short bursts from his P90 at the transporter doors to try to 
stop them from closing but to no avail. At least one of the bullets 
hits Peterson in the arm, who cries out and collapses to the floor 
just as the doors finish closing.)
(The transporter doors open again and Peterson hauls himself 
painfully to his feet and stumbles out ... into the Mess Hall. 
Clutching his injured arm, he staggers up some steps, groaning, then 
collapses to the floor. Everybody rushes over to him.)
MAN 1: My God, is he alright?
WOMAN 1: Oh, my God!
MAN 2: He's been shot!
WOMAN 2: What's going on?
(There is general hubbub as they carefully turn him over onto his 
back. Suddenly an alarm starts sounding over the comm system.)
(Back in the corridor, John and Teyla rush into the transporter room 
but just as John reaches for the control panel, a hatch closes over 
it. The alarm continues to sound.)
(In the Mess Hall, a similar hatch closes over the transporter room 
control panel and the doors close. All the exit doors start to 
close.)
(In the Control Room, the doors are closing on all levels as the 
alarm continues.)
WEIR: What's going on?
GRODIN (trying to work his console): Ancient controls are 
unresponsive.
BATES: I'm getting reports that Peterson transported into the
Mess 
Hall.
SHEPPARD (from the transporter room): For some reason, we can't 
follow him.
GRODIN: The city has taken over – put us into a lockdown.
WEIR: Override it.
GRODIN: I can't! Atlantis must be designed to respond to
outbreaks 
automatically. The city initiated a lockdown when Peterson 
transported out of the east side.
WEIR: Why now? Why not when Johnson and Wagner became infected?
GRODIN: The city's detection systems might have been affected by
the 
flooding in those areas. Once Peterson entered the Mess Hall, the 
pathogen was almost instantly detected by automated systems and the 
city protected itself.
WEIR: Alright, what are my options?
GRODIN: Limited. As of now, we're completely locked out of the 
mainframe.

ANCIENT LAB. Rodney and Hays are being hooked up to heart and blood 
pressure monitors.
McKAY: Is this really necessary? I am about to die of a brain 
aneurysm – how does being attached to a heart monitor help?
BECKETT: If you die like the others, we'll have a better idea of 
how. (He smiles sarcastically.)
McKAY: At that point, I will cease to care.
FORD: There are a lot of *other* people that live in the city, man.
McKAY: Yes, the *living*.

CORRIDORS. John and Teyla are walking along. As they walk past a 
door, it opens automatically.
SHEPPARD: Thought we were in a lockdown? Why'd that open up for
us? 
(Into radio) Weir, this is Sheppard. Were you able to get the 
transporters online or not?
(Elizabeth looks round at Peter, who shakes his head.)
WEIR: Doesn't look promising. Atlantis itself seems to have
somehow 
sensed a threat and taken over most of the controls.
SHEPPARD: So it shut down the transporters?
WEIR: That's right.
SHEPPARD: Well, I wish *we* would've thought of that.
WEIR (furiously): 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. D'you still feel it was a good idea?
SHEPPARD: Where'd he transport to?
WEIR: The Mess Hall. Thankfully everyone else respected the 
quarantine – there's only a handful of people there.
SHEPPARD: Alright, you've made your point.
WEIR: Make your way back to the city. Wait in Beckett's lab for 
further instructions.

FIELD STATION. Doctor Biro has finished her autopsy of Dumais.
BIRO (into radio): Doctor Beckett.
BECKETT (over radio): Any progress, Doctor Biro?
BIRO: Just finished Dumais' autopsy. Would it surprise you to
learn 
she died of a ruptured brain aneurysm above the visual cortex, sir?
BECKETT: No, it wouldn't. Thank you, Doctor.
BIRO: Didn't think so.
BECKETT (to Rodney): You know, the position of the rupture could 
explain your visions. Swelling in that area before the breakage 
could absolutely account for the hallucinations.
McKAY: I'm no MD but wouldn't brain swelling on the visual
cortex 
just mean that we experience washes of colour or weird visual 
anomalies?
BECKETT: It would depend on the person.
McKAY: Yeah, that's my *point*. All of our visions are so
similar. 
If they're the result of arterial swelling, wouldn't the
visions we 
experience be more random?
BECKETT: Most likely, yeah.
McKAY: Well, the things we're seeing are pretty damn identical!
(Behind them, the beep rate on Hays' heart monitor begins to
speed 
up.)
BECKETT: And you think it might have something to do with the 
nature ...
McKAY: There's a good chance ...
HAYS: No! Noooo! (He starts slapping at himself, trying to get 
something off him. A couple of medics try to restrain him.)
McKAY: Hey! It's not real, remember? It's not real!
HAYS: No! No! (He continues to flail at the unseen ghosts. His 
heart rate increases drastically.) They're coming right at us! 
Can't you see them?! (He struggles with the medics who are
trying to 
restrain him. He starts to fall to the floor.)
BECKETT: [Transcriber's note: Sorry, but I really cannot work out 
what he says here!]
McKAY: Don't say fine – he's not fine! *Do* something!
BECKETT: There's nothing to do!
(Abruptly, Hays' rapid heartbeat stops altogether and the monitor 
emits a single long tone. Carson rushes over to Hays and starts to 
administer CPR as a medic puts an airbag over Hays' nose and
mouth.)
BECKETT (counting chest compressions): One, two, three, four, five. 
(He stops, and the medic pumps air into Hays' lungs. Carson
starts 
compressions again.) One, two, three, four, five.
McKAY (angrily): Stop! It's not his heart. Just ... (his voice 
fades into grief) stop.
(Carson and his team stop their work. The medic lifts away the 
airbag from Hays' face and we see that he too has blood coming
out of 
his mouth and nose. Carson stands up and turns to face Rodney, whose 
expression is one of resignation combined with fear. A medic turns 
off Hays' heart monitor. Nearby, members of Rodney's team
are 
clustered together for comfort. One of the women is in tears. Aidan 
looks at Rodney.)
FORD: How are you feeling?
McKAY: I'm ... I'm ... Listen, I have a sister. We're
not close – I 
don't even know how you'd find her.
FORD: Don't talk like that.
McKAY: She's the only family I really have, so someone should
tell 
her what happened. And, uh, make it sound good, OK? (He allows 
himself a small smile for a moment.) Tell her I ... I died saving 
someone ... kids! I died saving kids – a bunch of them. Nelenka
... 
(Zelenka shrugs at Rodney getting his name wrong again, but says 
nothing.) I've got some theories on looping the power on the
Gate to 
charge a dummy ZedPM. It probably won't work but-but you should
have 
someone look at it cos it might lead somewhere else.
ZELENKA: We'll look at it together.
McKAY (angry, but also on the verge of tears): Look, you *seriously* 
have to stop interrupting my last thoughts. I mean, this is 
important stuff you need to hear. (He looks round and sees that he 
has got everybody's attention. Zelenka nods at him to continue.)

Now – if you're here for more than a year, I've left some
notes on 
how to roll blackouts to effectively maintain your power requirements 
and-and, oh, tell everyone that I was, I was inches away from a 
Theory of Unification but uh, uh, the notes, they were lost when I 
died saving the ...
ZELENKA: ... kids.
McKAY: Yeah. (He pauses and looks around the room, expecting the 
ghostly visions to start. He turns around slowly and stares towards 
the ceiling, but still the ghosts don't come. After a long 
moment ...) OK. I should be dead now.
(Carson walks over to him.)
BECKETT: You ran into Dumais at the same time?
McKAY: *Exactly* the same time.
BECKETT: Then, yes, you *should* be dead.
McKAY (looking around as he realises that he isn't dead): Oh,
God! 
(He looks round at Ford and Zelenka.) I'm still here! (He
smiles in 
disbelieving delight.)
FORD: Yes you are.
ZELENKA: Interesting.
McKAY: "*Interesting*"?!
BECKETT: Don't take this the wrong way, but ...
ZELENKA: ... *why*?
BECKETT: Exactly.
McKAY: Well, I don't care. (He turns to Carson and smiles in 
relief.) I mean, I *really* don't care!
(Carson smiles and pats him on the arm.)

CONTROL ROOM. The place is a hive of activity as various technicians 
use laptops to try to hack back into the mainframe. Elizabeth is 
watching all the hubbub as John reports in over the radio.
SHEPPARD: Doctor Weir?
WEIR: Yes, Major?
SHEPPARD: We've reached the city, but we haven't hit the
city's 
quarantine. Are you sure it's locked you out?
WEIR: Pretty sure. I can't even get into my office.
SHEPPARD: Hasn't given us any trouble yet.
GRODIN (suddenly realising something): Hazmat suits – they're 
protected.
WEIR: What?
GRODIN: The city must be capable of sensing they're in no danger
of 
infection. It makes sense, actually – this way, Atlantis allows 
protected personnel to assist the infected.
TEYLA: If that is the case, we should make our way to the Mess Hall. 
I imagine everyone there will be very scared and confused.
WEIR: I agree. Get to the Mess Hall and report back.

FIELD STATION. Doctor Biro and her team are conducting an autopsy on 
Hays. Carson and Rodney stand nearby.
BECKETT: Are you certain you really wanna see this, Rodney?
McKAY: It's too accurate. How could something organic be that 
efficient?
BECKETT: Again, we're in the middle of another galaxy. Just
because 
it's out of the ordinary for us doesn't mean it's not
commonplace 
here.
McKAY: No, no, no, I don't buy that. Most of the habitable
planets 
we've encountered thus far are-are-are carbon copies of Earth in 
terms of environmental conditions. (Carson nods his agreement. 
Rodney is then struck by a thought and snaps his fingers a couple of 
times.) Unless ... (He rushes off.)
BECKETT (to the autopsy team): I'll be back. (He hurries off
after 
Rodney.) Wait up, Rodney!

ANCIENT LAB. Rodney has led Carson back to the lab.
McKAY: Incubation to completion is exactly six hours. The visions 
are identical for all the infected, and the location of the aneurysm 
is the same for every single deceased. (He opens up a laptop and 
shows Carson a display. Carson stares at it in dread.)
BECKETT: Is that what I think it is?
McKAY: It's a nanovirus. One manufactured to kill humans.

LATER. Rodney is reporting to Elizabeth via radio.
WEIR: A nanovirus.
McKAY: That's right.
WEIR: OK, let's pretend I don't know exactly what that is.
McKAY: Nanotechnology – it's, uh, technology that operates on
a 
nanite scale. It's around, uh, around a billionth of a
millimetre.
BECKETT: Basically, they're microscopic machines that are able to 
carry out very specific tasks suited for their size.
McKAY: It's the whole idea of being able to swallow a pill and
having 
a million little robots go to work and cure whatever ails you.
WEIR: You're all infected with microscopic machines?
McKAY: Yeah, they're no bigger than a single-celled organism
– 
although instead of having a sole purpose of curing a disease or 
mending a blood vessel ...
BECKETT: ... the virus is programmed to terrorise its victims by 
tapping into their visual cortex and then rupturing an artery in 
their brain ...
McKAY: ... infecting others along the way as they can.
BECKETT: There's one good thing: I doubt they can multiply. I
don't 
know how many nanites it takes to kill a human but eventually I 
imagine they'll spread themselves too thin.
WEIR: Could it be Wraith?
BECKETT: That would definitely be my first guess.
McKAY: I'm not so sure about that.
BECKETT: But the visions; the shrill sound you told me they make when 
they ...
McKAY: I'll give you that they're equally terrifying, but why
would 
the Wraith even create the equivalent of a WMD? They're killing
us, 
not because they sadistically want us dead, but because they need to 
consume us for food. Look – it would be like the equivalent of 
cattle farmers creating mad cow disease. I don't buy it.
WEIR: You *did* come across it in an *Ancient* lab.
McKAY: What, so wiping out the Wraith's food supply was a
last-ditch 
consideration?
BECKETT: I don't believe that for a moment. The Ancients would
never 
create something like this.
McKAY: It doesn't explain the visions either.
WEIR: OK, for the moment, who built the virus is really the least of 
our concerns.
McKAY: Good point.

MESS HALL. John and Teyla have arrived. John is looking at 
Peterson's body, which is lying on a table with blood coming from
his 
nose. Teyla is trying to explain the situation to the others.
TEYLA: We have yet to determine how one contracts the virus. It is 
*very* possible that none of you have been infected.
LIEUTENANT CROWN: Then why are you in hazmat suits?
TEYLA: Just as a precaution.
(Rodney contacts John by radio.)
McKAY: Major Sheppard, this is McKay.
SHEPPARD: What is it?
McKAY: I could use your help at my lab.
(John looks round at Teyla, who is being bombarded with nervous 
questions.)
TEYLA: Go. I will be fine.
(John leaves. The others cluster round Teyla, still firing questions 
at her.)

LATER. Rodney and Carson are explaining things to Elizabeth.
McKAY: Hays and I were infected at the same time. There's only
one 
thing that explains why I survived.
BECKETT: Rodney has the Ancient gene; Hays did not.
WEIR: But Rodney is not an Ancient.
BECKETT: Aye, but he's been inoculated with the ATA gene.
WEIR: You're saying the virus is designed to only kill humans?!
McKAY: Well, I'm *human*!
BECKETT: Yes, yes, we're making a point, Rodney.
WEIR: So we give everyone the gene therapy.
McKAY: No – it's not gonna do it.
ZELENKA: I've already been given the gene weeks ago – it
didn't take.
McKAY: I know. I'm already on it.
ZELENKA: The gene therapy is only effective in forty-eight percent of 
recipients.
FORD (to Beckett): If I was given the gene shot right now, how long 
would it take to kick in?
BECKETT: A minimum of four hours.
FORD: I don't *have* four hours! I met up with McKay and Hays
ninety 
minutes after they met up with Dumais. I have (he checks his watch) 
a little under an hour before my brain explodes.
BECKETT: Aidan, listen to me. You've been up for almost twenty
hours 
now – you're not thinking straight. Just try to stay calm.
FORD: Calm?! You told me I have a million tiny robots running 
through my veins whose only purpose is to terrorise and kill me. 
*You* stay calm!
ZELENKA: We are about to have hallucinations. We are infected, 
Carson – how do you *expect* us to act?!
FORD: There's gotta be another way.
McKAY: I have already told you – I am working on it.

LATER. John has reached Rodney's lab.
SHEPPARD: Alright, McKay, I'm here.
McKAY: D'you see it?
SHEPPARD: Is it the big thing in the middle of the room?
McKAY: Yeah, that's the one.
(We see part of the piece of equipment that John is looking at –
it 
is covered with yellow and black hazard strips, together 
with "Warning" and "Caution" stickers.)
SHEPPARD: Should I pay attention to all these warnings?
McKAY: Not today, no.
(The camera pulls back and we see that the device is an EM pulse 
generator [though it's smaller than the one we last saw Rodney 
playing with in the SG-1 episode "Redemption part 2"].)
FORD: What are you gonna do?
McKAY: Well, small as they are, the nanovirus is still effectively 
just a machine run by a computer. The best way to knock out a 
computer is with an electromagnetic pulse. Thankfully, that's 
something we can do.
(In the Control Room, the technicians are shutting down all the 
laptops and disconnecting them from the mainframe.)
WEIR: We're about through shutting down all the electronic gear
we 
brought from Earth. We're still locked out of the Ancient
controls, 
though. There's no way to power them down.
McKAY: Well, it's not gonna be necessary. Ancient technology
works 
differently than ours. An EM pulse shouldn't have any
long-lasting 
effect on `em.
GRODIN: We're ready.
WEIR: We're all set, Rodney.
McKAY: OK. Here we go.
WEIR: Wait! How're we gonna know if it works?
SHEPPARD: Well, Sheppard's dialling up the most powerful pulse
the 
generator can manage. It probably won't make it all the way down 
here but it should affect most of the central tower. I imagine once 
it wipes out the virus, the city should return control of it to you 
and end the lockdown.
FORD: It won't make it here?
McKAY: If the pulse works, it will simply be a matter of walking you 
down to my lab, sitting you down in front of the EMP and repeating 
the process. (Into radio) Major?
SHEPPARD: It's working. (We see that the generator is spinning
up to 
speed.) When should I hit the discharge button?
McKAY: OK – there should be a red overload light.
SHEPPARD: Yeah, I see it.
McKAY: Wait til it comes on, give it a good ten count, and then 
discharge.
SHEPPARD: A ten count?!
McKAY: Don't worry – I've probably been around more EMPs
than anyone.
SHEPPARD: This is gonna be, uh – I'm gonna be fine, right?
McKAY (rather sarcastically): Yes. That's a yes – you'll
be fine.
(In Rodney's lab, the overload light comes on. John flips open
the 
cover to the discharge button, moving his lips as he silently counts 
off the seconds. Then he pushes the button. The generator whooshes 
as it discharges.)
(In the Ancient lab, Rodney is waiting impatiently.)
(In Rodney's lab, the generator is powering down, then stops. 
John 
looks around expectantly.)
(In the Control Room, everyone is waiting.)
McKAY (over comms): Anything?
WEIR: Is it possible it might take some time?
McKAY (sighing): Doubtful.
(Peter turns to his console and starts trying to active it.)
McKAY: Are you still locked out of the Ancient mainframe?
(Peter turns to the screen that shows the mainframe, but there's
no 
response from it. He turns to Elizabeth and shakes his head.)
WEIR (to Rodney): Got any other ideas?
(Rodney has no reply. Aidan checks his watch anxiously.)
FORD: Twenty-nine minutes.

MESS HALL. The people locked in there are either milling around 
talking with each other or sitting at the tables. Suddenly one of 
the marines sitting down looks up in terror, jumps to his feet and 
starts backing away, whimpering and terrified. Almost immediately, 
everyone else in the room starts reacting to his or her own visions. 
Chaos reigns as they all run around the roam, flailing at the ghosts 
they think are attacking them. Lieutenant Crown runs over to Teyla.
CROWN: It didn't work! It didn't work!
TEYLA: It is still unclear.
CROWN: What's unclear? Either it worked or it didn't!
TEYLA: They are trying to determine ... (She trails off as Crown 
stares at her in terror.)
CROWN: They're everywhere!
TEYLA: You are experiencing a hallucination.
(Crown starts flailing at Teyla, trying to get the ghosts away from 
herself. She pushes Teyla over the top of a table. Glass smashes as 
the table falls over, then Crown and Teyla crash down on top of the 
broken glass. Teyla tosses Crown away from herself, then looks down 
and realises that the arm of her hazmat suit is gashed and her arm is 
exposed to the air.)
CROWN (seeing what she's done): Oh, my God!

RODNEY'S LAB. John has apparently been following some
instructions 
from Rodney.
SHEPPARD: I've already tried that – it's blown.
McKAY: That is before we re-set the sub-switch.
SHEPPARD: Well, maybe we shouldn't have overloaded it so much.
McKAY: Look, it's fixable, it's fixable – we just need to
use a 
little trial and error.
SHEPPARD: Look, even if we get this thing working, who's to say
the 
pulse is gonna get any bigger? Ford and Zelenka have twenty minutes 
before their arteries rupture. Are you *sure* an EMP will kill this 
thing?
McKAY: Yes.
SHEPPARD: Alright. I have an idea. (He hurries out of the lab.)

GENERATOR ROOM. John has gone to where one of the naqahdah 
generators is running.
SHEPPARD (into radio): What do you mean, no?
WEIR: It's too dangerous.
SHEPPARD: You'd rather lose a third of our population?
WEIR: We're not there yet, Major.
SHEPPARD: We *are* there! Ford and Zelenka are next. The people in 
the Mess Hall have a little over three hours. This is a full-blown 
outbreak. People are gonna keep dying unless we do this.
McKAY: Even if we were able to get the EMP generator back online, the 
chances are slim that we would ever be able to get it powerful enough.
WEIR: Can we bring the infected to the generator?
GRODIN: We can't. The city won't let infected personnel
through any 
of the doors.
McKAY: The major is right – the only way to create an EMP strong 
enough to wipe these little guys out is to ...
WEIR: ... to detonate a nuclear explosion in the atmosphere! Yes, I 
heard the first time!
McKAY: I know it sounds severe but if the major was able to overload 
a naqahdah generator twenty miles above the city, it would be 
perfectly safe from a radiological standpoint and the ensuing blast 
would be capable of creating a devastating electromagnetic shockwave
–
definitely enough to knock this virus out.
GRODIN: Hopefully without destroying all our own computer equipment!
SHEPPARD: It's worth the risk.
(Elizabeth thinks about it for a moment.)
WEIR (somewhat reluctantly): OK. You have a go.
(John lifts the control mechanism on the top of the naqahdah 
generator, twists it through ninety degrees and lowers it back down 
into place. The generator shuts down. John detaches its connecting 
cables, closes the generator down to make it more compact, lifts it 
up and carries it away.)

JUMPER BAY. John takes off in one of the Puddlejumpers.

LATER. PUDDLEJUMPER.
SHEPPARD: I'm almost in position.
WEIR: Understood. Would the EM pulse have any effect on the 
Puddlejumper?
SHEPPARD: I'm hoping not. Either way, I'm more worried about
the 
shockwave.
WEIR: Good luck.
SHEPPARD: You too.
McKAY: You're only gonna have thirty seconds once you release it 
before it explodes. You need to get as far away as you can.
SHEPPARD: Get as far away from the nuclear explosion as possible
– 
that's good advice, Rodney, thanks!
McKAY: You're welcome.
SHEPPARD: I'm releasing the generator ... now!
(Twenty miles above the planet's surface, the naqahdah generator
is 
jettisoned out of the top of the Puddlejumper. The Jumper 
immediately goes into a steep dive and heads away from the generator.)

CONTROL ROOM. Peter starts the countdown.
GRODIN: Detonation in twenty-five seconds.

MESS HALL. The crew's hallucinations have ceased temporarily. 
They're all listening to Peter's announcements.
GRODIN: Twenty seconds.

ANCIENT LAB. Rodney, Carson and the others are waiting nervously.
GRODIN: Fifteen seconds ... Detonation in ten, nine, eight, seven, 
six ...

PUDDLEJUMPER. John is racing to get away from the impending 
explosion. He looks very scared.
GRODIN: ... five, four, three, two, one.

ABOVE THE PLANET. The naqahdah generator explodes. The Puddlejumper 
is buffeted violently by the enormous shockwave.

ATLANTIS. Above the city, the night sky turns a brilliant white. 
All around the base, anybody near a window flinches away from the 
light.

CONTROL ROOM. The light fades.
WEIR: Major Sheppard, come in. (No response.) This is Weir –
please 
respond.
GRODIN: Communications may have been disrupted by the blast.
WEIR: Major, do you read me? (There is no response.)
(All around the base, people look concerned. Finally, after several 
seconds ...)
SHEPPARD: This is Sheppard. I've cleared the blast – I'm
returning 
home.
WEIR: I'm glad to hear it, Major.
SHEPPARD: Did it work?
WEIR: We're about to find out. (She walks over to Peter, who 
activates controls on his console, then turns anxiously towards the 
mainframe screen. After a moment, the screen flashes.)
McKAY: You should know almost right away. 
(In the Control Room, doors start to open. The technicians run to 
their laptops and start opening them.) 
McKAY: The pulse only lasts a couple of microseconds and then ...
WEIR: The city's already ahead of us, Rodney. You have a green
light 
to return.
(In the Ancient lab, Rodney claps his hands together in relief. 
Various team members hug each other. Rodney shakes hands with 
Zelenka. Aidan and Carson hug, then Aidan goes over to Rodney and 
hugs him too.)

LATER. WEIR'S OFFICE. Elizabeth and John are in there.
WEIR: Are you OK?
SHEPPARD: Yeah, just a little nuke – nothin', really.
WEIR: The naqahdah generator plan was very clever. Good work.
SHEPPARD: Thank you. Now, I'm going to bed. (He stands up to
leave.)
WEIR: We need to discuss what happened earlier.
SHEPPARD (turning round wearily): Now?
WEIR: That can never happen again.
(John looks at her for a moment, then comes back to the desk and sits 
down.)
SHEPPARD: Look, I'm sorry about ...
WEIR (interrupting): 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. Now, both General O'Neill and Colonel Sumner 
warned me that you don't respect the proper chain of command.
SHEPPARD: Well, sometimes I see a situation a little different 
than ...
WEIR: No. Listen to me, John. Now, 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?
(Rodney and Carson come in.)
McKAY: You guys have a minute? We've been able to spend some,
uh, 
quality time with the, uh, nanovirus samples.
BECKETT: From what we can tell, they've all been incapacitated.
WEIR: Well, that's good news.
McKAY: Yes. Also, upon further investigation, I think we can rule 
out that they were created by the Wraith. They're different than
any 
Wraith technology we've come across thus far.
SHEPPARD: If not the Wraith, then who made `em?
McKAY: I honestly don't know – but whoever they were,
let's just hope 
that they're not still around.
WEIR: Let's hope.