Transcript by Callie Sullivan.

[Transcriber’s note: This isn’t the most accurate transcript I’ve ever done. The sound quality of the tape I was working from was extremely poor and sometimes I just couldn’t make out what was being said. I have either made my best guess or left out the bits I couldn’t hear properly.]

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 wanders 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 Elizabeth.)
WEIR: Alright, John – it’s been almost a month. When are you gonna stop trying to bringing 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. (She sits back in her chair and raises her eyebrows at him.)
SHEPPARD: What about you – what are you still doin’ up?
WEIR: I think I got used to falling asleep to the sound of the ocean.
SHEPPARD: Well, McKay says we’re only 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. It was extremely convenient to be able to step through the Gate and be at Stargate Command in an instant, and now this (she looks around the room) feels extremely inconvenient. It must be eighteen days cooped up in the ship to get back.
SHEPPARD: Well, until we find another ZeePM to power the Earth Gate, that’s just the way it’s gonna have to be.
(An Airman runs into the room.)
AIRMAN: Doctor Weir, Colonel Sheppard – there’s been an accident.
(Elizabeth and John get up and follow the Airman out of the room.)

ELSEWHERE ON THE SHIP. John and Elizabeth arrive to find Carson Beckett bending over a man lying on the floor.
WEIR: That’s Doctor Monroe. What happened?
BECKETT: I don’t know – but he’s dead.

LATER. Doctor Monroe’s body is being zipped into a body bag by Carson and another medic.
BECKETT (to the medic): Alright – one, two, three. (He and the medic lift the body and put in onto a gurney.) Carry on. (A couple of medics wheel the body away as Colonel Caldwell arrives.)
CALDWELL: How did he die?
BECKETT: I’m not a hundred percent certain, but there were burn marks on his fingertips.
SHEPPARD: Obviously there was a short. Door’s open, circuits are charred.
CALDWELL: There’s not enough juice in those circuits to kill anyone. Doctor?
BECKETT: I’ll know more once I’ve had a chance to examine the body more thoroughly.
(Elizabeth looks at Rodney, who is sitting at a nearby console.)
WEIR: Do you know what he was working on?
McKAY: It was computer diagnostics, strictly routine. I’ve got security camera footage. (He calls up the footage and everyone gathers around to watch. We see Monroe sitting at the console, then getting up to work on another part of the console. He reaches over to touch a panel, then the footage goes to static.)
WEIR: What happened there?
McKAY: I don’t know – it’s a camera malfunction.
SHEPPARD: Right before he was killed? Interesting coincidence.
McKAY: Actually, I think it makes sense. Colonel Caldwell was right – there’s not enough ‘juice’ in those circuits to kill someone – at least not normally.
WEIR: What are you thinking?
McKAY: It’s possible there was some sort of isolated power surge in this section – that would explain the lost camera, the malfunctioning door ...
CALDWELL: So, when the door didn’t respond, he took out the panel to bypass the circuits and received a fatal jolt?
McKAY: Like I said, it’s possible. Look, I recommend we drop out of hyperspace, run a full diagnostic on the power distribution systems ...
CALDWELL: No, if we drop out now, we risk being detected.
McKAY: That’s true. I just think if we ...
CALDWELL (interrupting): We’ll be back in Atlantis in less than two days. You can do your diagnostic then.
WEIR: Colonel, are you sure that’s right?
CALDWELL: With all due respect, Doctor, you got back to Earth through the Stargate. This is my third trip on the Daedalus between galaxies.
WEIR: I understand that, but this ship is relatively new. There might be some problems ...
CALDWELL (interrupting): Doctor. A word please? (He gestures to her to step outside the room. She follows him outside. Once they’re in the corridor, he turns to face her.) I know the chain of command can get a little fuzzy on Atlantis, but that’s not gonna happen here. You got a problem, whatever it is, take it to me in private, otherwise keep your opinions to yourself.
WEIR: Are you sure that’s what this is all about?
CALDWELL: I got a job to do, Doctor.
WEIR: But not the one you wanted.

FLASHBACK. EARTH. STARGATE COMMAND (SGC). BRIEFING ROOM. General Landry, the head of SGC, is sitting at the briefing table with Elizabeth, Caldwell and various other personnel, none of whom we recognise.
LANDRY: I understand the International Committee has approved a significant increase in personnel and resources for the Atlantis mission.
WEIR: Now that we have a ZeePM, the city can support a much larger contingent.
CALDWELL: Of course a corresponding increase in military presence would also be prudent.
WEIR: I agree. That’s why I wanted Major Sheppard to come back with me. In fact, I brought all my senior staff back. I think it’s only fair that they participate in the selection process of the new personnel in their respective departments.
LANDRY: That’s kind of what we wanted to talk to you about. In your report, you singled Major Sheppard out for a lot of credit.
WEIR: That’s right.
LANDRY: You were also candid enough to document several occasions on which you and the Major didn’t exactly see eye to eye. In particular, there was an incident involving an alien nanovirus in which Major Sheppard directly disobeyed one of your orders.
WEIR: He also saved a lot of lives that day.
LANDRY: The Major’s courage and ingenuity are not in question here. His ability to follow the proper chain of command is.
WEIR: I’m not military, General.
CALDWELL: But you are the leader of the expedition.
LANDRY: You see, Doctor, from our point of view, Major Sheppard’s independent nature poses a bit of a problem. If he could disobey you, he may see fit to do the same to the new commander of the military contingent on Atlantis.
WEIR: Excuse me? When did this happen?
LANDRY: Of course, the decision hasn’t been made yet – but we do have a candidate in mind. (He looks at Caldwell, who tilts his head at Elizabeth.)
WEIR: Atlantis has a military commander.
LANDRY: You had a military commander – Colonel Sumner. When he was killed, Major Sheppard correctly assumed the position until a proper replacement could be brought in.
CALDWELL: Doctor, you can’t be suggesting that a mission of this importance be trusted to a Major, and one with a questionable record at that.
WEIR: 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.
LANDRY: Doctor ...
WEIR (interrupting as she stands up): I shouldn’t have to remind you gentlemen that I continue to have the support of the President and our foreign allies. (She smiles sweetly at Landry.) You don’t wanna fight me on this one.
(She leaves the room. Landry smiles ruefully at Caldwell.)

THE PRESENT. DAEDALUS. Caldwell is looking at some papework being shown to him by one of his personnel. As the crewman walks away, Rodney comes out of an elevator to join Caldwell.
McKAY: Colonel Caldwell.
CALDWELL: What is it, Doctor?
McKAY: I realise you’re not big on the whole ‘dropping out of hyperspace’ thing, which I understand given that we’re in some uncharted section of the Pegasus galaxy with who-knows-what waiting for us around the corner ...
McKAY: Look, I think it’s possible that Doctor Monroe’s death might not have been an accident.
CALDWELL: What are you talking about?
McKAY: I checked the power distribution logs against the time code on the security camera. There was an unexplained spike, but it happened thirty seconds after the camera went off.
McKAY: So it means the malfunction in the door and the camera were not caused by the same problem. Major Sheppard was right – that’s too much of a coincidence.
CALDWELL: You mean Lieutenant Colonel Sheppard.
McKAY: Uh, right. Oh, that’s gonna take some getting used to.
CALDWELL: Is that the only evidence you have?
McKAY: No, there’s something else. It looks like Doctor Monroe was in the process of enabling certain computer security protocols – they’re designed to isolate and shut down corrupted programmes.
CALDWELL: What programmes?
McKAY: I don’t know. That’s just it – he was killed before he could finish.
CALDWELL: You’re telling me there’s a problem with the ship and someone killed Monroe to cover it up?
McKAY: I know this sounds crazy, but there is definitely more going on here than random malfunctions.
(Caldwell activates his radio.)
CALDWELL: Bridge, this is Caldwell. Drop us out of hyperspace immediately.
(Daedalus drops to normal speed.)

ENGINEERING. Rodney and Hermiod are in Engineering.
HERMIOD: If I may be so bold, what exactly are we looking for?
McKAY: Any indication that somebody’s been tampering with the ship’s computers.
HERMIOD: Perhaps you could be more specific.
McKAY: Not really, no.
(Hermiod sighs and mutters to himself in Asgard.)
McKAY: What was that?
HERMIOD: Nothing.
McKAY: Look, just check the major systems – propulsion, navigation, life support. Look for anything out of the ordinary. Once we’ve checked out the power distribution system, maybe we can figure out what caused the power spike.
(John walks in.)
SHEPPARD: How’s it going, Rodney?
HERMIOD: It’s going to take a while.
(John looks at him suspiciously. Rodney walks over.)
McKAY: Don’t stare – he hates it when people stare.
SHEPPARD: Am I the only one who thinks it’s strange we’re working with an alien?
McKAY: Intergalactic hyperdrive technology’s kind of new to us, so we need his help.
SHEPPARD (glancing at Hermiod again, and whispering to Rodney): Is he supposed to be naked like that?
McKAY (rolling his eyes, then looking across to a technician working nearby): Lindstrom! (He and Lindstrom leave the room. John looks round at Hermiod again, who scowls back at him. John turns and leaves the room. Hermiod mutters angrily to himself in Asgard.) Asgard translation: "These humans are infants"

(The doors open to a small room and Rodney and Lindstrom walk in.)
McKAY: OK, let’s speed this up – you take the logs and I’m gonna take a look at ... (he looks around the room and finds what he wants) junction box. (He walks over to the junction box and opens the door to it, while Lindstrom goes deeper into the room and starts working on a console. After checking the junction box, Rodney goes to another panel.) I got nothing – you?
LINDSTROM: Uh, give me a second. ... Wait a minute.
McKAY: What?
LINDSTROM: I think I got something here.
McKAY: Well, what?
(At that moment, alarms sound and coolant starts spraying from the ceiling.)
LINDSTROM: Coolant leak! We’ve gotta get out of here! (He tries to run through the spray but ducks back, crying out in pain as he is burnt.)
McKAY: Lindstrom!
(Realising that he can’t reach the door, Lindstrom runs towards a rear compartment.)
McKAY: Lindstrom! (Knowing that he has to seal off the room, Rodney runs outside and closes the door. Lindstrom, still clutching his burnt arm, seals off the door to the compartment. Outside the room, coughing, Rodney activates the comms to the compartment, which show a visual image of Lindstrom.) Lindstrom! Lindstrom! Are you alright?!
(Coughing, and nursing his damaged arm, Lindstrom activates the comms.)
LINDSTROM: Yeah, I’m OK. How am I gonna get out of here?
McKAY: I dunno – just sit tight. We’re gonna need to shut down the leak and vent the ...
(At that moment, the sound ceases and Lindstrom can’t hear Rodney any more. He hits the comms button.)
(Outside the room, Rodney can still see Lindstrom on the camera but can’t hear him any more.)
McKAY: Lindstrom! Lindstrom, are you reading me? (Lindstrom gestures into the camera to show that he can’t hear him. Rodney picks up a phone.) Lindstrom! Are you reading me?
(In the compartment, another alarm sounds. Lindstrom turns and stares to his right, where warning lights are flashing around an door which leads directly out to space. We realise that he is in an airlock.)
McKAY (hearing the same alarm): What the hell are you doing?! (Lindstrom pushes a button on the wall to stop the procedure, but nothing happens.) The airlock’s opening! Override the system!
LINDSTROM: Rodney, help me!
McKAY: Lindstrom! (He stares in horror as Lindstrom silently screams, “Rodney! Help me!” into the camera.) Lindstrom!
(The airlock doors open and Lindstrom is blown into space.)
McKAY: Oh my God!

LATER. People have arrived, and Carson is checking Rodney, who is holding an oxygen mask to his face. After a moment, he lowers the mask.
McKAY: I already told you – I’m fine.
BECKETT: He’s right – it appear he didn’t inhale enough toxins to cause any permanent damage, (he pushes the mask up to Rodney’s face again) although a few more seconds of exposure would have been quite a different story.
CALDWELL: Thank you, Doctor. (Carson pats Rodney’s shoulder and walks away as Caldwell addresses Rodney.) I assume this time we can definitely rule out random malfunctions?
McKAY (lowering the mask again): Lindstrom found something – he was trying to tell me what it was when the leak happened.
WEIR: What were you looking for?
McKAY: We were trying to trace the source of the power spike that killed Doctor Monroe.
CALDWELL: Who else knew what you were doing?
McKAY: A lot of people knew we were running diagnostics but no-one knew we were in that particular room at that exact moment.
SHEPPARD: Security cameras. If the person who killed Monroe was able to get into the system to erase evidence, there’s no reason he couldn’t do the same thing to keep tabs on our investigation.
McKAY (taking another drag on his oxygen before speaking): Assuming it’s a he.
CALDWELL: How many personnel on board have the technical skills to do something like this?
McKAY: Almost everybody! That’s what you get for assembling a team of brilliant scientists.
WEIR: I can’t believe it would be one of our own people. Isn’t it possible there’s an intruder on board?
CALDWELL: We used the lifesigns detector to do a head count. We didn’t get any extra signals.
WEIR: Well, hibernating Wraith – they can avoid detection.
SHEPPARD: We’ve seen that tactic before. Beam in, lay low, then look for the chance to conduct sabotage.
CALDWELL: That was on Atlantis. It’s been at least two months since this ship encountered the Wraith. There’s no way one of them could have stowed on board for that long.
McKAY: He’s right. They did a full decontamination sweep back on Earth. They would have found something.
CALDWELL: Alright then. (He turns to one of his officers.) As of this moment I want our civilian personnel confined to their quarters.
(The officer leaves to carry out his orders.)
WEIR: What?!
CALDWELL: Present company excepted, of course.
McKAY: Uh, Colonel, with due respect, some of those people could be extremely helpful in the investigation.
CALDWELL: I’m sorry, Doctor, but I can’t trust any of them for the simple reason that I didn’t have any say in their selection. Somebody else was in charge of the process. (He looks pointedly at Elizabeth.)

FLASHBACK. SGC. BRIEFING ROOM. Carson is sitting at the briefing table, going through a huge pile of personnel files.
BECKETT (indicating the file he’s looking at): Look at this! Four years’ relief work in the Sudan and Ethiopia; graduate studies at John Hopkins and Harvard; half a dozen research grants – oh, and she also enjoys judo, horseback riding, origami and something called base jumping.
WEIR: Parachuting from cliffs and tall buildings.
BECKETT: Oh! Of course(!)
WEIR: You said you wanted the best.
BECKETT: But all these people are more qualified than I am! How am I supposed to choose between them?
WEIR: Carson, you are my chief surgeon. No-one is more qualified than you. (She smiles at him. He smiles back.)
BECKETT: Well, I’ve managed to make a shortlist. (He hands her the list.) I was hoping you’d make the final selections.
WEIR (looking at the list): This is your shortlist?! (Carson smiles ruefully. She looks at the list.) Did you review the file of a Doctor Simon Wallace?
BECKETT: Why? He was also more qualified than I am.
WEIR: Why isn’t he on the list?
BECKETT: Well, the candidates were required to sign off on a blind commitment to a one-year term.
WEIR: Doctor Wallace has been given security clearance. He knows what this is all about.
BECKETT: Maybe that’s the problem.
WEIR: What do you mean?
BECKETT: He hasn’t signed.

SIMON’S HOUSE. In his kitchen, Simon Wallace – Elizabeth’s boyfriend – is preparing a meal as Elizabeth stands nearby.
WEIR: When were you gonna tell me?
SIMON: There’s nothing to tell. I mean, I haven’t said yes, but I haven’t said no either.
WEIR: You do realise you are not gonna make the final list of candidates unless you commit?
SIMON: Elizabeth, you know you can’t just come back after a year and expect me to drop everything on two weeks’ notice. I have responsibilities here – I have patients, I have research.
WEIR: I know, I know, and I would never diminish the importance of your work. But you have to understand that every single person on this entire expedition is in the exact same situation. In fact it’s why they were chosen in the first place.
SIMON: I understand. Look, I just need a little more time.

HERMIOD: Doctor McKay. You are just in time.
McKAY: For what? What are you looking at? (He looks at the screen behind Hermiod’s station. A series of ones and zeros are scrolling up it.)
HERMIOD: The sabotage we’ve been searching for.
McKAY: It’s a virus.
HERMIOD: How perceptive of you.
McKAY: Where did you find it?
HERMIOD: One of the navigational computers. There is evidence of it in communications and some of the propulsion systems as well.
McKAY: So it’s spreading.
HERMIOD: Yes – and changing.
McKAY: What do you mean?
HERMIOD: It appears to be rewriting itself as it grows. It is unlike any human-engineered programme I have ever encountered.
McKAY: Really? (He goes to another console where a woman is working.) Airperson – I gotta be there. (The woman moves away from the console.)
HERMIOD: What are you doing?
McKAY: I’m just checking something – I’m sure it is impossible. (He activates some controls and the ones and zeros turn into a type of writing.) Crap!
HERMIOD: What did you do?
McKAY: I just ran it through a translation programme – it’s Wraith.
(Hermiod turns and looks at his screen, then turns back to Rodney.)
HERMIOD: ‘Crap’ indeed.

BRIDGE. Rodney has explained the situation to the others.
WEIR: A Wraith computer virus.
McKAY: It was probably downloaded during our last little encounter.
CALDWELL: Well, if it’s been there all this time, why are we just noticing it now?
McKAY: Well, in all likelihood it was transmitted in a compressed format – it took a while to unfold, to spread to the point where it could affect our systems. I think it probably happened during the return flight to Earth. Since then, it’s been dormant, waiting for some kind of a trigger.
SHEPPARD: Like what?
McKAY: Possibly the fact that we’re once again in close proximity to Wraith territory? I think it was ultimately designed to take control of the navigational system – fly the ship right to them.
WEIR: If they get their hands on the Daedalus, they’ll not only have access to the intergalactic hyperdrive technology but they’ll have all the navigation data that’ll lead them straight to Earth.
McKAY: That’s what they wanted all along. A new feeding ground.
CALDWELL: That still doesn’t explain who killed Doctor Monroe and Doctor Lindstrom.
McKAY: That’s what I’m trying to tell you. It was the virus. Look, it’s an A.I. – an artificial intelligence – it can think for itself, adapt itself to new situations ...
SHEPPARD: Protect itself.
McKAY: Exactly. It knew that Lindstrom and Monroe were gonna expose it, so it got rid of them.
WEIR: Can it take over the whole ship?
McKAY: Not entirely. You have to remember that there are hundreds of individual computers on board. A lot of them are interconnected so we tend to think of them as one big machine but that’s not really the case. There are dozens of back-ups and redundancies, and some systems – like life support – are deliberately isolated.
SHEPPARD: So they can’t kill us all by venting the atmosphere?
McKAY: That was the good news. The bad news is that some of the more complex systems like navigation and propulsion require a certain amount of interconnectivity to function properly. In all likelihood, the virus has spread so far through those systems that to isolate it will make the ship impossible to fly. Until we figure out how to get rid of it, we’re stuck here.
(An alarm starts to beep.)
BRIDGE LIEUTENANT: Colonel Caldwell. Sir, we just began broadcasting a distress call.
CALDWELL: What are you talking about?
BRIDGE LIEUTENANT: It just came on by itself, sir.
CALDWELL: Shut it down.
BRIDGE LIEUTENANT: I’m locked out, sir.
McKAY: It’s the virus. That’s what I mean about adapting itself to new situations. It doesn’t have enough control yet to fly us to the Wraith so instead it’s calling the Wraith to us – and right now, we are sitting ducks.

A LITTLE LATER. Rodney is working on a console on the Bridge. John goes over to him.
SHEPPARD: What are you doing?
McKAY: Theoretically we should be able to cut power to the long-range transmitter. You won’t be able to send messages, but, uh, neither will the virus.
SHEPPARD: Theoretically.
McKAY: Well, it’s pretty smart. So far, whatever we’ve tried, it’s been one step ahead of us. (To the Bridge Lieutenant) Try it now.
BRIDGE LIEUTENANT (trying to cut the transmission, then shaking his head): It’s no good, sir. We’re still broadcasting.
McKAY: Alright, that leaves us one choice. We need to do a full systems shutdown. We’ll wipe everything, reboot, load from back-ups.
WEIR: Will that really work?
McKAY: Absolutely ... I think.
CALDWELL: How long will it take?
McKAY: Well it’s not like the ship’s got an on/off button. We need some time to prepare – say, an hour, maybe two?
SHEPPARD: And while we wait, we increase our chances of being detected. We need to shut off the transmitter array now.
CALDWELL: Do you have an idea?
SHEPPARD: As a matter of fact, I do ... but you’re not gonna like it.

FIGHTER BAY. John flies out of the ship in an F-302.
CALDWELL (over comms): Alright, Colonel, we’ve evacuated all sections in the vicinity of the array and sealed the bulkheads.
SHEPPARD: Understood.
CALDWELL (over ship’s comms): All personnel – prepare for impact.
(John loops the glider around and fires several missiles at the array, blowing it up. Daedalus jolts under the impact.)
CALDWELL: What’s our status?
BRIDGE LIEUTENANT: Transmitter is offline. Distress signal has been disabled.
CALDWELL: Well done, Colonel – return to the ship.
SHEPPARD: With pleasure. (He flicks a switch, then frowns and flicks it a few more times.) Uh, there’s a problem. My controls aren’t responding.
CALDWELL: Say again?
SHEPPARD: Well, the Daedalus is behind me. I can’t seem to turn around and ... a lot more, we’ve picking up speed.
McKAY: I should have seen this coming. The navigational software on the F-302 is compatible with our sublight system which has already been infected. The virus must have uploaded itself onto his ship.
WEIR: What about the transport beam?
McKAY: That would work. Those systems are still clean.
(Rodney turns to his console and Elizabeth activates her radio.)
WEIR: John, this is Elizabeth. Rodney seems to think the virus has taken over your ship, so we’re gonna try to beam you out.
SHEPPARD: Acknowledged.
WEIR: Stand by.
(Rodney turns around from the console.)
McKAY: Uh, small problem.
WEIR: What?
McKAY: The transport beam is tied to an Asgard sensor – it’s what we use to lock on to targets.
McKAY: So, so, that particular piece of equipment was located in the array that we just destroyed. (He has a thought and clicks his fingers several times.) The key is to lock onto his radio signal. That’s what they used to do on the Prometheus before they had Asgard sensors.
CALDWELL: You’d better do it quick, ‘cos in about three minutes he’s gonna be out of range.
(Rodney turns back to the console and starts working.)
WEIR (over comms): John, we’ve run into a slight snag. Rodney just has to make a few adjustments before we can get you out of there.
SHEPPARD (nervously): OK.
WEIR: Don’t worry – we’re not about to give up on you just yet.
(John has nothing to do but wait.)

FLASHBACK. EARTH. John, wearing a suit, is sitting on a sofa. He picks up a framed photograph of Aiden Ford in military dress uniform. A young woman brings in a tray holding cups and a pot of tea and puts it down on the coffee table before sitting down on another sofa.
LARA: Here we go.
LARA (pouring the tea): I appreciate you coming here in person, Colonel. Aiden and I were only cousins but since he didn’t have any brothers or sisters, we became very close.
SHEPPARD: I want you to understand – as far as I’m concerned, he’s still alive. Until I see evidence to the contrary, I intend to keep looking for him.
LARA: But you can’t give me any details. You can’t tell me where he was stationed, or how he went missing, or what the chances are that I’ll ever see him again.
SHEPPARD: I’m sorry.
LARA: This is exactly why I didn’t want you to speak with Aiden’s grandparents. They can’t take this kind of thing right now. I’m starting to think that maybe I should just tell them that he’s not coming home. At least then they would have some closure.
SHEPPARD: We’re not there yet.
LARA: You know, Aiden mentioned you in that tape message he sent. He said you were a good man; that he trusted you with his life. You tell me, Colonel – was that trust misplaced? (John doesn’t answer, wrapped up in his own thoughts.) Colonel?

WEIR (over comms): Colonel? John, are you still there?
SHEPPARD (pulling himself together): Uh ...
WEIR: We’re gonna use your radio to target the transport beam. We’ll have you out of there in just a minute.
SHEPPARD: Sounds good. So I’m still in range, right?
(On Daedalus, Rodney turns round to Elizabeth, deactivating his radio so John can’t hear him.)
McKAY: Truth is, this has never been tested from this distance.
WEIR (into comms): Rodney seems to think you’ll be OK.
SHEPPARD: Well, that’s good.
McKAY: We’re ready. We’re beaming him directly to the Bridge.
(Everyone turns to face the front of the Bridge. On the F-302, the transporter beam envelops John and whisks him away. A few moments later, the beam appears on the Bridge, and when the light fades, John is standing there.)
WEIR: Are you alright?
SHEPPARD: Yeah. Two arms, ten fingers ... (he looks down) I’ll check the rest later.
(Caldwell turns to Rodney.)
CALDWELL: Alright, Doctor, I’ve had enough of this. I’d like to have my ship back, please.
McKAY: Right! (He turns back to his console. Elizabeth puts a congratulatory hand on his shoulder.)

ENGINEERING. In the corner of the room, a camera is watching Rodney as he moves from console to console, preparing for the shutdown.
McKAY (to a technician): Move! (He checks that console.) Yes. (He moves to another one, almost bumping into John.) Do you mind?
SHEPPARD (to Elizabeth): This is what I do when I have problems with my laptop. I turn it off, and then I turn it on again.
WEIR: I think this is a little bit more complicated than that.
SHEPPARD: I’m just saying that if we’re taking a page from the John Sheppard Book of Computer Repair, we’re really desperate.
McKAY: Alright, Colonel, we’re ready.
CALDWELL (over comms): Thank you. All personnel, this is Colonel Caldwell. Prepare for a full system shutdown.
(As the cameras around the ship continue to watch the crew, everybody stops what they’re doing.)
CALDWELL (into comms): Alright, Doctor, go ahead.
McKAY: And ... (He gestures to Hermiod, who activates controls on his console. Everything shuts down and the ship is plunged into darkness.)

A match strikes, and is lowered towards a candle to light it. The person holding the match raises it again to blow it out and we see that it’s Elizabeth, wearing a pretty dress. Simon walks into the room behind her. We realise that we’re in a flashback.
SIMON: What’s all this?
(Elizabeth turns around from the table, holding a bottle of wine.)
WEIR: Well, I figured we won’t have many more chances for a really good dinner. I mean, the food on Atlantis, it’s alright, and some of the Athosian dishes are fantastic, but ...
SIMON (interrupting): Elizabeth ... I’m not going.
WEIR: I don’t understand.
SIMON: You’re the adventurer, not me.
WEIR: But I’m not – I mean at least I wasn’t, not before. Look, the first time I stepped through that Gate, I was terrified. I knew I wasn’t prepared for what I was getting into, but I took a chance.
SIMON: I know, and I’m proud of you for that.
WEIR: Simon ...
SIMON: There’s something else. (He hesitates for a long time before speaking again.) I met someone. (Elizabeth gasps, then turns away to face the table again. Simon looks at her back.) You were gone for a long time, Elizabeth.
(He opens his mouth to say more but knows that nothing else he can say will make the situation better. Eventually he walks away. Elizabeth, her eyes full of tears, stares at the candle for a while, then licks her thumb, reaches out and extinguishes the flame.)

THE PRESENT. DAEDALUS. The lights come back on.
CALDWELL: Engine Room, what’s our status?
McKAY: All systems are functioning normally. No sign of the virus. Looks like it worked, Colonel.
HERMIOD: May I suggest we vacate this system? Our current position may well have been compromised.
CALDWELL: Can you give me hyperdrive?
HERMIOD: That will take longer to get back online.
McKAY: I can get you sublight.
CALDWELL (to his pilot): Get us out of here, Major.
(The sublight engines fire up, and Daedalus starts to move. Moments later, an alarm sounds on the Bridge.)
CALDWELL: What is it?
BRIDGE PILOT: We’re veering off course. Navigational controls are not responding.
(In Engineering, Rodney checks a console.)
McKAY: Dammit!
CALDWELL (over comms): Engine Room, what’s happening?
McKAY: The virus – it’s back. It must have full control of sublight navigation.
SHEPPARD: I thought all systems were clean.
McKAY: They were. When we did the reboot there was no sign of the virus. This shouldn’t be happening.
BRIDGE PILOT: Sir, we’ve got another problem. It’s our new heading – we’re on a collision course with the nearest star.

HERMIOD: The virus returned almost immediately after we restarted the system.
SHEPPARD: At the risk of repeating myself, I thought you said we wiped it out.
McKAY: We did. We must have missed something.
WEIR: And it’s gonna crash us into a sun.
HERMIOD: Not exactly. A more precise calculation of our heading shows that we will not collide with the star, but rather make a close approach, near its chromosphere. The ship will survive, but the radiation will kill everyone on board.
WEIR: Why kill everyone if they already have full navigational control?
McKAY: The virus has access to our database. It knows our tactics, our tendencies ...
SHEPPARD: They know we’d destroy the ship before we’d allow it to fall into Wraith hands.
McKAY: Wait a minute. There was a situation similar to this back at Stargate Command. I remember reading the report. An alien entity took control of the base computer, so they did a systems shutdown to destroy it. It survived by uploading itself into a MALP.
WEIR: OK, we don’t have any MALPs.
McKAY: No – we’ve got a bay full of F-302s. We already know the virus can upload itself into the ship’s navigational computer, but it could have used any one of those ships as a hiding place while we wiped the Daedalus systems clear. It’s the only possible explanation.
WEIR: So ...?
McKAY: So, we physically pull the memory storage modules from the 302s – we do another shutdown – that should do the trick.
SHEPPARD (to Elizabeth): Contact the Bridge, tell Caldwell we’re on our way to the bay now. (He and Rodney hurry out.)

CORRIDORS. As John and Rodney make their way to the fighter bay, the cameras watch them. As they reach an access door, it closes in front of them. Rodney pushes a button to open it but nothing happens.
McKAY: It’s not working.
SHEPPARD: Let’s try another way.
(They head off in another direction, but another door closes to block their route.)
McKAY: It’s the virus – it must know what we’re trying to do.
SHEPPARD: How’s that possible?
McKAY: It’s thinking ahead; anticipating our moves, like in a chess match.
SHEPPARD: Well, I hope you’re good at chess.
McKAY: I don’t get to play much – it’s tough finding challenging opponents.
SHEPPARD (into comms): Bridge, this is Sheppard. Are there any open paths to the 302 bay?
(Caldwell looks at his pilot, who shakes her head.)
CALDWELL: That’s a negative, Colonel. Looks like the entire section’s been sealed off. We’ve tried to override it but we’re not having any luck.
SHEPPARD: You’re gonna have to beam us in.
McKAY: Whoa-whoa-whoa-whoa-whoa. Wait a minute. The Asgard beam wasn’t designed to beam from one point to another point inside a ship. We could end up rematerialised half inside a wall.
SHEPPARD: Well, we’re just gonna have to take that chance.
McKAY: Right(!) Of course(!) Why not?(!)
(As John steps next to him, Rodney scrunches himself down to make himself as small as possible, pulling his arms and shoulders as tight into his body as he can and bending at the knees. John looks at him in disbelief.)
SHEPPARD: Colonel – we’re ready.
CALDWELL: Stand by. Hermiod says we need to make a few adjustments first. (John looks across at Rodney, who is still in his ridiculous crouching position.) Activating transport beam now.
(The beam activates and whisks them away. They reappear in the fighter bay. Rodney looks around and straightens up.)
McKAY: It worked!
(As they walk forward, alarms sound and lights by the bay doors which exit into space start to flash.)
McKAY: Oh boy!
(He turns to look at John, who stares back at him as the doors begin to open. On the Bridge, the Lieutenant sees what is happening.)
BRIDGE LIEUTENANT: Sir, the bay doors are opening!
CALDWELL (over comms): Bridge to Engine Room, beam them out now!
(In the fighter bay, John and Rodney are still staring at each other as the doors finish opening.)
McKAY: We should really really be dead right now.
SHEPPARD: I don’t feel dead.
HERMIOD (in Engineering): Colonel Sheppard, Doctor McKay, can you hear me?
SHEPPARD: Yeah, we’re reading you.
HERMIOD: I have raised the fighter bay shield in order to prevent the atmosphere from escaping. However, the virus has invaded the system and it is only a matter of time before it gains control. (John and Rodney run to the two nearest F-302s.) Therefore, I suggest you complete your task as quickly as possible. (The boys are already busy pulling out the memory modules, and race on to the next ships. Rodney finishes the second glider and runs to a third, jumping up to see into the cockpit. When he sees that John is already in that ship, he runs to the next one.)
CALDWELL: Colonel Sheppard, how’s it coming?
SHEPPARD: We’re gettin’ there.
(In Engineering)
HERMIOD: I can no longer prevent the virus from gaining complete control of the shield.
WEIR: Well, beam them out.
HERMIOD: Unfortunately, it appears I have lost control of that system as well.
(On the Bridge)
BRIDGE LIEUTENANT: Sir, the shield is down. The cargo bay is decompressing. [Transcriber’s note: “cargo bay”?!]
CALDWELL: Colonel Sheppard, come in. ... Colonel Sheppard, do you read me? ... Colonel Sheppard, do you read?
(In the fighter bay, John and Rodney have got into an F-302 and have the canopy sealed.)
SHEPPARD: This is Sheppard. We’re OK. We managed to get into the last F-302 before we lost atmosphere. Any chance you can beam us out?
WEIR: Sorry, John, we lost the transport beam. You’re gonna have to sit still for a while.
McKAY: We pulled all the memory units. Another shutdown should work.
WEIR: Understood.
(On the Bridge, the pilot sees something on her screen.)
CALDWELL: I see it. (Into comms) Engine Room, this is Bridge. We’ve not got a lot of time before we approach lethal radiation levels.
HERMIOD: Most of the shutdown protocols are still in place from our first attempt. This will only take a few minutes.
CALDWELL: Let’s hope we have a few minutes.

F-302. Rodney is breathing very fast.
McKAY: You know, I’ve never actually been inside one of these before today. It’s a little, uh, cramped, huh?
SHEPPARD: Just relax, Rodney. We’re safe ... for the moment.
McKAY: Great. Quick question, though, just out of curiosity: how much, uh, air do these things carry?
McKAY: Uh, I’m just saying, because if this doesn’t work, we’ll have to go over the whole plan and who knows how long we could get stuck in here, and, and, so it-it-it would ...
SHEPPARD: You know what, Rodney? You’re exactly right – it’s a limited supply, so why don’t we conserve it by you not talking? (Rodney opens his mouth. John raises a finger.) At all.

CALDWELL: All hands, this is Colonel Caldwell. We’re gonna give this another shot. We’re initiating total systems shutdown now.
(The ship is plunged into darkness again. After a few moments ...)
HERMIOD: Reinitialising. (The lights come back on.)
WEIR: Did it work?
HERMIOD: We will know momentarily.
SHEPPARD: This is Sheppard. What just happened?
CALDWELL: Stand by – we’re trying to figure that out.
BRIDGE PILOT: I’m sorry, sir. We had navigational controls for a second but we just lost them again.
(Outside the Bridge windscreen, the star comes back into view as Daedalus veers back onto its course towards it.)
CALDWELL: It didn’t work. We’re still on course for the chromosphere.
(In Engineering, Hermiod engages in another burst of colourful Asgard swearing.) Asgard translation: "The incompetence of these humans is beginning to make me angry!"

SHEPPARD: This thing is like a damned cockroach – you just can’t kill it!
McKAY: This should have worked. We’ve disabled every navigational computer in this bay. There’s nowhere else on the ship the virus could hide.
SHEPPARD: You’re right – there’s nowhere on the ship for it to hide – but we didn’t get every computer.
McKAY: What are you talking about?
SHEPPARD: We missed one.
(Rodney looks blank for a moment, then stares in shock as he realises what John is talking about.)
(Outside Daedalus we see that the F-302 which John was beamed out of is following behind the ship.)

FIGHTER BAY. John is prepping the F-302 for flight.
McKAY: What-what are you doing?
SHEPPARD: It’s the last F-302, Rodney – the one we left behind, and it’s driving us.
McKAY: Yeah, but we can’t go after it. We have no computer system navigation.
SHEPPARD: We don’t need a navigational computer to fly this thing. Besides, we’re not going far.
(Rodney stares at him for a moment, then starts to strap himself in. John does the same.)
SHEPPARD: Engine Room, this Sheppard. Prepare to initiate another shutdown on my command.
WEIR: John, what are you doing?
SHEPPARD: Getting rid of the last place the virus can hide.
McKAY: Wait-wait-wait-wait-wait. I’m nearly done.
(Without waiting for Rodney to finish strapping in, John starts to taxi the F-302 to the bay doors.)
CALDWELL: You’d better make this quick, Sheppard – radiation levels are beginning to rise in the outer hull.
SHEPPARD: Understood.
(The F-302 launches, and loops over the top of the ship to head towards the F-302 behind. However, the virus-infested F-302 has already anticipated John’s arrival and has flown to the side of the ship. As John’s glider passes, the virus ship swings over the top of Daedalus and falls in behind John. Inside John’s cockpit, alarms beep.)
McKAY: What was that beeping?
SHEPPARD: Somebody just locked onto us. Hold on.
(He throws his ship into a roll. The virus ship rolls in an attempt to stay with it. Some very fancy flying ensues, with both ships hurtling around the sky and rolling in all directions. John is unable to shake off the virus ship. Inside John’s ship, Rodney groans.)
McKAY: Uh! What happened to the inertial dampeners?
SHEPPARD: At these speeds, you’re gonna feel the tight turns even with the dampeners.
McKAY: Uh! Now he tells me!
(The fancy flying continues. In Engineering, Hermiod is working his console.)
HERMIOD: I have them on my screens. (A computer image of the two gliders comes up on the screen.) The computer-controlled ship is preparing to fire.
SHEPPARD: Hold on – we’re just gonna tap on the brakes here. (He pulls a lever back and he and Rodney shoot forward in their seats as the F-302 decelerates rapidly. The virus ship flashes past underneath them. Rodney gulps, trying not to be sick. In Engineering, Elizabeth and Hermiod watch the ships change position.)
WEIR: Nice move!
HERMIOD: Indeed.
SHEPPARD: He’s making a break for the chromosphere.
McKAY: Would it be good to mention that we have less protection in this ship than we did on the Daedalus?
SHEPPARD: Not really.
McKAY: I didn’t think so.
(John’s ship chases the virus ship towards the sun.)
HERMIOD: Radiation levels in the Colonel’s ship are beginning to rise.
(In John’s ship, the sun is shining directly into the cockpit.)
McKAY: Is it just me, or is it getting a little hot in here?
(In Engineering, the ships disappear from the screen.)
WEIR: What happened?
HERMIOD: They are approaching the chromosphere. There is too much interference.
(In John’s ship, Rodney is shielding his eyes from the sun.)
McKAY: The thing is, I have very fair skin. I tend to burn easily.
SHEPPARD: Just a few more seconds. (He looks at his control screen. The screen fritzes for a moment, but then comes back, and then the virus ship is in the centre of the screen and a target lock is shown. John fires a missile, which flies towards the virus ship and blows it to bits.)
(In Engineering)
WEIR: How long can they survive those radiation levels?
HERMIOD: I believe it has already been too long.
WEIR (into comms): John, can you read me? ... Rodney, come in?
SHEPPARD: Daedalus, this is Sheppard. Target is destroyed. I repeat, target is destroyed. If you try one more shutdown, I think it might just work.
(In John’s ship, Rodney is anxiously examining the skin on his arms.)
WEIR: Well done, both of you. You had us a little worried there for a minute.
SHEPPARD: Sorry about that.
CALDWELL: This is Caldwell. We’ll rendezvous as soon as we’ve eradicated the virus once and for all.
SHEPPARD: Roger that. Sheppard out. (He cuts comms.) You did great back there, Rodney. Wanna take the stick?
McKAY (perking up): Really?!
(Rodney’s face falls.)

ATLANTIS. The new crew are milling around in the Gateroom as the regular command crew head up the stairs to the Control Room where Teyla is waiting for them.
TEYLA: Doctor Weir, Doctor McKay, Doctor Beckett, welcome back – and Lieutenant Colonel Sheppard! Congratulations.
SHEPPARD: Thank you. Anything happen while we were gone?
TEYLA: There has been no sign of the Wraith. It would appear that they continue to believe that Atlantis has been destroyed, but I understand that your trip was not so happily uneventful.
WEIR: No, not exactly.
(Rodney scratches his nose, then stares at his hand in horror.)
McKAY: My nose is peeling! (To Carson) Do you have a moisturiser?
BECKETT (sighing): Yes, Rodney.
McKAY: Well, maybe we should get that.
BECKETT: Yes, Rodney! (He throws an amused glance at the others as he follows Rodney away.)
SHEPPARD: Any word from your offworld contacts?
TEYLA: We have received several intelligence reports. However, as of yet there is no news of Lieutenant Ford.
SHEPPARD: I’d like to read those reports when you’ve got a moment.
TEYLA: I thought you might – I prepared you this copy. (She hands him a file.)
SHEPPARD: Thank you! Ladies. (He heads off.)
TEYLA (to Elizabeth): I am sorry your journey was so difficult.
WEIR: Well, we got here – that’s what counts.
TEYLA: Still, it must have been pleasant to return to Earth – a chance to reunite with your friends and loved ones.
(Elizabeth smiles at Teyla but doesn’t reply. Radek hurries over.)
ZELENKA: Doctor Weir. Doctor Weir – I’m glad you’re back. We have several reports from around the city. Ever since we installed ZeePM, we’ve made many interesting discoveries. (He goes to hand her his report but Teyla stops him.)
TEYLA: Could this not wait? Doctor Weir has only just arrived.
ZELENKA: I’m sorry, I ...
WEIR: No, that’s fine, really. (She takes the report.) Let’s get back to work.