Stargate: Atlantis s02e02 Episode Script

Previously on Stargate Atlantis We saw the hive ship blow up.
I assure you Dr McKay that Major Sheppard is alive and well.
Who is this? Steven Caldwell.
Commander of the Daedalus.
We are ready to assist you.
Rodney we need the shield up in 40 seconds or we're dead! With only one functioning ZPM, we can't expect to hold on that long.
Are we talking months, weeks? Days.
- What if they thought we were gone? - Destroy the city you mean? No, we just make it look like we did.
We fake a self destruct.
Is it working or not? I think they bought it.
He should be dead.
- I'd like to report for duty ma'am.
- Dr.
Beckett released you? Where's Ford.
I assume that's him in the Jumper? - Shut it down! - I can't the Jumper's in control! We'll find him.
Maybe.
Hey, what are you doing up so late? Couldn't sleep.
Must be the burden of command.
You know, ever since I was promoted to Lt Colonel.
Alright John, it's been almost a month.
When are you going to stop trying to find a way to bring that up in every single conversation.
You gotta understand.
There's a lot of people in the Air Force who never thought I'd make it past Captain.
Well obviously, the people who's opinions matter the most thought otherwise.
What about you? What are you still doing up? I think I got used to fall asleep to the sound of the ocean.
Well McKay say's we're already at the edge of the Pegasus Galaxy.
You'll be fine once we get back to Atlantis.
You know it's funny.
I spent the past year wondering if I'd ever see Earth again and as soon as I got there I know how you feel.
God, it was extremely convenient to be able to step through the gate and be at Stargate Command in an instant and now this feels extremely inconvenient.
Having to spend 18 day's cooped up in this ship to get back.
Until we find another ZPM to power the Earth gate, that's just the way it's gonna have to be.
Dr Weir.
Colonel Sheppard.
There's been an accident.
That's Doctor Monroe.
What happened? I don't know.
But he's dead.
Right, one, two, three.
Carry on.
How did he die? I'm not 100% certain, but there are burn marks on his fingertips.
Obviously there was a short.
Panels open, circuits are charred.
There's not enough juice in those circuits to kill anyone.
Doctor? I'll know more once I've had a chance to examine the body more thoroughly.
Do you know what he was working on? Computer diagnostics.
Strictly routine.
I've got security camera footage.
What happened there? I don't know.
It's a camera malfunction.
Right before he was killed? Interesting coincidence.
Actually, I think it makes sense.
Look, Colonel Caldwell is right.
There's not enough juice in those circuits to kill someone.
At least not normally.
What are you thinking? It's possible there was some sort of isolated power surge in this section.
That would explain the lost camera, the malfunctioning door.
So, when the door control didn't respond he took off the panel to bypass the circuits and received a fatal jolt? Like I said, it's possible.
Look, I recommend we drop out of hyperspace, run a full diagnostic on the power distribution system.
No.
We drop out now, we risk being detected.
That's true.
I just think that if we were We're back in Atlantis in less than two days.
You can do your diagnostic then.
Colonel, are you sure that's wise? With all due respect Doctor, you got back to Earth through the Stargate.
This is my third trip on the Daedalus, between galaxies.
I understand that, but this ship is relatively new and there might be some problems Doctor! A word please.
I know the chain of command can get a little fuzzy on Atlantis, but that's not gonna happen here.
You got a problem with my orders, you take it to me in private.
Otherwise keep your opinions to yourself.
Are you sure that's what this is all about? I got a job to do, Doctor.
But not the one you wanted.
We understand the international community has approved a significant increase in personnel and resources for the Atlantis mission.
Now that we have a ZPM, the city can support a much larger contingent.
Of course, if there's a filling in a corresponding increase in military presence would also be prudent.
I agree.
That's why I want the 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.
That's kind of what we wanted to talk to you about.
In your report, you single Major Sheppard out for a lot of credit.
That's right.
You were also candid enough to document several occasions in which you and the Major didn't exactly see eye to eye.
In particular, there was an incident involving an alien nano-virus, in which Major Sheppard directly disobeyed one of your orders.
He also saved a lot of lives that day.
Well, the Major's courage and ingenuity are not in question here.
His ability to follow the proper chain of command, is! I'm not military General.
But you are the leader of the expedition.
You see Doctor, from our point of view, Major Sheppard's independant nature causes a bit of a problem.
If he can disobey you he may see fit to do the same to the new Commander of the military contingent on Atlantis.
Excuse me? And when did this happen? Of course the decision hasn't been made yet.
But we do have a candidate in mind.
Atlantis HAS a military Commander.
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.
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.
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.
Well, if that's not good enough for you? You're just gonna have to promote him.
Doctor I shouldn't have to remind you gentlemen, that I continue to have the support of the President and our foreign allies.
You don't wanna fight me on this one.
Colonel Caldwell! What is it doctor? Look.
I realise that you've already made it clearly that you're not big on the whole dropping out of hyperspace.
Which I understand, given that we're in the middle of some uncharted section of the Pegasus Galaxy with who knows what waiting for us around the corner.
Doctor? Look, I think it's possible that Dr Monroe's death might not have been an accident.
What are you talking about? 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 out.
So? So that means the malfunction in the door and the camera were not caused by the same problem.
Major Sheppard was right.
There's too much of a coincidence.
You mean, Lt.
-Col.
Sheppard.
Right.
That's gonna take some getting used to.
Is that the only evidence you have? No, something else.
It looks like Dr Monroe was in the process of enabling certain computer security protocols.
Designed to isolate and shut down corrupted programs.
What programs? I don't know, that's just it.
He was killed before he could finish.
You're telling me there's a problem with the ship and someone killed Monroe to cover it up? I know this sounds crazy, but there is definitely more going on here than random malfunctions.
Bridge this is Caldwell.
Drop us out of hyperspace immediately.
If I may be so bold.
What exactly are we looking for? Any indication that someone's been tampering with the ships computers.
Perhaps you could be more specific.
Not really, no.
What was that? Nothing.
Look, just check the major systems.
Propulsion, navigation, life support.
Look for anything out of the ordinary.
Lindstrom and I will check power distribution, see if we can figure out what caused the power spike.
- How's it going Rodney? - It's going to take a while.
Don't stare.
He hates it when people stare.
Am I the only one who thinks it's strange we're working with an alien? Intergalactic hyperdrive technology is kind of new to us, so we need his help.
Is he supposed to be naked like that? Lindstrom! OK, let's speed this up.
You take the logs and I'm gonna take a look at junction box! I got nothing.
You? Give me a second.
Wait a minute.
What? I think I got something here.
Well what? Coolant leak, we gotta get the hell out of here! Lindstrom! Lindstrom! Lindstrom! Lindstrom! You alright.
Yeah, I'm OK.
How am I gonna get out of here? I don't know.
Just sit tight.
We're gonna need to shut down the leak and vent the room Rodney! Lindstrom! Lindstrom you reading me? Lindstrom, are you reading me? What the hell are you doing? The airlock is opening! Override the system! Rodney help me!! Lindstrom! Rodney! Lindstrom! Oh my God.
I already told you I'm fine.
He's right.
It appears he didn't inhale enough toxins to cause any permanent damage.
Although, a few more seconds of exposure, it would have been quite a different story.
Thank you Doctor.
I assume this time we can definitely rule out random malfunctions? Lindstrom found something new.
He was trying to tell me what it was when the leak happened.
What were you looking for? We were trying to trace the source of the power spike that killed Dr Monroe.
Who else knew what you were doing? A lot of people knew that we were running diagnostics, but no-one knew that we were in that particular room at that exact moment.
Security camera's.
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 the investigation.
Assuming it's a he.
How many personnel onboard have the technical skills to do something like this? Everybody.
That's what you get for assembling a team of brilliant scientists.
I can't believe it would be one of our own people.
Isn't it possible there's an intruder onboard? We used the lifesigns detector to do a head count.
We didn't get any extra signals.
Well a hibernating Wraith? They can avoid detection.
We've seen that tactic before.
Beam in, lay low, then look for the chance to conduct sabotage.
That was on Atlantis.
It's been at least two months since this ship encountered a Wraith.
There's no way one of them could have stowed onboard for that long.
He's right.
They did a full decontamination sweep back on Earth.
They would have found something.
Alright then.
As of this moment I want all civilian personnel confined to their quarters.
What? Present company excepted of course.
Colonel, with all due respect, some of those people could be extremely helpful in the investigation.
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 selections.
Somebody else was in charge of that process.
Look at this.
Four years relief work in the Sudan and Ethiopia.
Graduate studies at John Hopkins and Harvard.
Half a dozen research grants.
And she also enjoys judo, horseback riding, origami and something called base jumping.
Parachuting from cliffs and tall buildings.
Oh! Of course.
You said you wanted the best.
All of these people are more qualified than I am.
How am I supposed to choose between them? Carson, you're my Chief Surgeon.
No-one is more qualified than you.
Well, I've managed to make a short list.
I was hoping you'd make the final selections.
This is your short list? Did you review the file of a Dr Simon Wallis? Aye.
He was also more qualified than I am.
Why isn't he on the list? Well, the candidates were required to sign on for a blank commitment to a one-year term.
Doctor Wallis has been given security clearance.
He knows what this is all about.
Maybe that's the problem.
What do you mean? He hasn't signed.
When were you gonna tell me? There's nothing to tell.
I mean, I haven't said yes, but I haven't said no either.
You do realise you are not gonna make the final list of candidates unless you commit! Elizabeth, you know you can't just come back after a year and expect me to drop everything on two weeks notice.
I have responsabilities here, I have patients, I have a surge.
I know, I know, and I would never diminish the importance of you work.
But you have to understand that every single person on this entire expedition is in the exact same situation.
I mean, In fact it's why they were chosen in the first place.
I understand.
Look, I just need a little more time.
Doctor McKay.
You are just in time.
For what? What are you looking at? The sabotage we've been searching for.
It's a virus.
How perceptive of you.
Where did you find it? One of the navigational computers.
There is evidence of it in communications and some of the propulsion systems as well.
So it's spreading.
- Yes, and changing.
- What do you mean? It appears to be rewriting itself as it grows.
It is unlike any human-engineered programme I have ever encountered.
Air person, move to there.
What are you doing? I'm just checking something, I'm sure it is impossible.
Crap.
What did you do? I just ran it through a translation programme.
It's Wraith.
'Crap' indeed.
A Wraith computer virus.
It was probably downloaded during our last little encounter.
Well, if it's been there all this time, why are we just noticing it now? 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.
Like what? Possibly the fact that we're once again in proximity to Wraith territory? I think it was ultimately designed to take control of the navigational system, fly the ship right to them.
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.
That's what they wanted all along.
A new feeding ground.
That still doesn't explain who killed Dr.
Monroe and Dr.
Lindstrom.
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 - Protect itself.
Exactly.
It knew that Lindstrom and Monroe were gonna expose it, so it got rid of them.
Can it take over the whole ship? 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.
So they can't kill us all by venting the atmosphere? That was the good news.
The bad news is 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.
Colonel Caldwell.
Sir, we just began broadcasting a distress call.
What are you talking about? It just came on by itself, sir.
Shut it down! I'm locked out, sir.
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.
What are you doing? Theoretically we should be able to cut power to the long-range transmitter.
You won't be able to send messages, but neither will the virus.
Theoretically.
Well, it's pretty smart.
So far, whatever we've tried, it's been one step ahead of us.
Try it now.
It's no good, sir.
We're still broadcasting.
Alright, that leaves us one choice.
We need to do a full system shutdown.
We'll wipe everything, reboot, load clean back-ups.
Will that really work? Absolutely I think.
How long will it take? Well it's not like the ship's got an on/off button.
We need some time to prepare say, an hour, maybe two? Every minute we wait, we increase our chances of being detected.
We need to shut off the transmitter array now.
Do you have an idea? As a matter of fact, I do.
But you're not gonna like it.
Alright, Colonel, we've evacuated all sections in the vicinity of the array and sealed the bulkheads.
Understood.
All personnel, prepare for impact What's our status? Transmitter is offline.
Distress signal has been disabled.
Well done, Colonel, return to the ship.
With pleasure.
Uh, here's a problem.
My controls aren't responding.
Say again? The Daedalus is behind me.
I can't seem to turn around and I am however picking up speed.
I should have seen this coming! The navigational software in the F-302 is compatible with our sublight system which would be infected.
The virus must have uploaded itself onto the ship.
What about the transport beam? That'll work.
Those systems are still clean.
Do it.
John? This is Elizabeth.
Rodney seems to think the virus has taken over your ship, so we're gonna try and beam you out.
Acknowledged.
Standby.
Ah, slight problem.
What? The transport beam is tied to an Asgard sensor.
It's what we use to lock onto targets.
So? So that particular piece of equipment was located in the array that we just destroyed.
I could key the system to lock onto his radio signal.
It's what they used to do on the Prometheus before they had Asgard sensors.
You'd better do it quick, because in about three minutes he's gonna be out of range.
John, we've run into a slight snag.
Rodney just has to make a few adjustments before we can get you out of there.
OK.
Don't worry.
I'm not about to give up on you just yet.
Here you go.
Thanks.
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.
I want you to understand.
As far as I'm concerned he's still alive.
Till I see evidence to the contrary, I intend to keep looking for him.
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.
I'm sorry.
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.
- You know, we're not there yet.
You know, Aiden mentioned you in that taped 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? - Colonel? - Colonel? Colonel! John, are you still there? Go ahead.
We're gonna use your radio to target the transport beam.
We'll have you out of there in just a minute.
Sounds good.
So I'm still in range, right? The truth is, it's never been tested from this distance.
Rodney seems to think you'll be okay.
Well that's good.
I don't wanna leave any parts behind.
We're ready.
I'm beaming him directly to the bridge.
Are you alright? Two arms, ten fingers.
I'll check the rest later.
Alright Doctor, I've had enough of this.
I'd like to have my ship back please.
Right.
Do you mind? This is what I do when I have problems with my laptop.
I turn it off and then I turn it on again.
I think this is a little bit more complicated than that.
I'm just saying, that if we're taking a page from the John Sheppard book of computer repair, we're really desperate.
Alright, Colonel! We're ready.
Thank you.
All personnel, this is Colonel Caldwell.
Prepare for a full system shutdown.
Alright Doctor.
Go ahead.
And What's all this? 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 Elizabeth.
I'm not going.
I don't understand.
- You're the adventurer, not me.
- 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.
- I know.
And I'm proud of you for that.
- Simon, we - There's something else.
I met someone.
You were gone for a long time, Elizabeth.
Engine room, what's our status? All systems are functioning normally.
No sign of the virus.
Look's like it worked, Colonel.
May I suggest we vacate this system? Our current position may well have been compromised.
Can you give me hyperdrive? That will take longer to get back online.
I can get you sublight! - Get us out of here, Major.
- Yes, sir.
What is it? We're veering offcourse.
Navigational controls are not responding.
Damn it! Engine room, what's happening? The virus, it's back! Now it's got full control of sublight navigation.
You said all systems were clean.
They were.
When we did the reboot there was no sign of the virus.
This shouldn't be happening.
Sir, we've got another problem.
It's our new heading.
We're on a collision course with the nearest star.
The virus returned almost immediately after we restarted the system.
At the risk of repeating myself, I thought we said we wiped it out.
We did.
I must have missed something.
And it's gonna crash us into a sun? Not exactly.
A more precise calculation of our heading show's that we will not collide with the star, but rather, make a close approach near it's coronasphere.
The ship will survive, but the radiation will kill everyone onboard.
Why kill everyone if they already have full navigational control? The virus has access to our database.
It knows our tactics, our tendencies They know we'll destroy the ship before we'll let it fall into Wraith hands.
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 onto a MALP.
OK, we don't have any MALP's.
No, we've got a bay full of F-302's.
We already know that the virus can upload itself onto the ships navigational computers.
But it could use any one of those ships as a hiding place while we wiped the Daedalus systems clean.
It's the only possible explanation.
So? So, we physically pull the memory storage modules from the 302's, we do another shutdown.
That should do the trick.
Contact the bridge.
Tell Caldwell we're on the way to the bay now.
It's not working.
Let's try another way.
It's the virus.
It must know what we're trying to do.
How's that possible? It's thinking ahead, anticipating our move, like in a chess match.
I hope you're good at chess.
I don't get to play much.
It's tough finding challenging opponents.
Bridge, this is Sheppard! Are there any open paths to the 302 bay? That's a negative Colonel.
Look's like the entire section's been sealed off.
We're trying to override it but we're not having any luck.
You're gonna have to beam us in.
Wait a minute! The transport beam wasn't designed to beam from one point to another point inside the ship.
We could end up rematerializing half inside a wall.
We're just gonna have to take that chance.
Right.
Of course.
Why not.
Colonel, we're ready.
Standby.
Hermiod says we need to make a few adjustments first.
Activating transport beam now! It worked! Oh boy! Sir, the bay doors are opening! Bridge to engine room! Beam them out now! We should really, really be dead right now.
I don't feel dead.
Colonel Sheppard.
Doctor McKay.
Can you hear me? Yeah we're reading you.
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.
Therefore, I suggest you complete your task as quickly as possible.
Colonel Sheppard, how's it coming? We're getting there! I can no longer prevent the virus from gaining complete control of the shield.
Beam them out.
Unfortunately, it appears that I have lost control of that system as well.
Sir, the shield is down.
The cargo bay is decompressing.
Colonel Sheppard, come in! Colonel Sheppard, do you read me? Colonel Sheppard, do you read? This is Sheppard.
We're OK.
We managed to get in the last F-302 before we lost atmosphere.
Any chance you could beam us out? Sorry John, we lost the transport beam.
You're gonna have to sit still for a while.
We pulled all the memory units.
Another shutdown should work.
Understood.
Sir! Understood.
Engine room, this is bridge.
We don't have a lot of time before we approach lethal radiation levels.
Most of the shutdown protocol's are still in place from our first attempt.
This will only take a few minutes.
Let's hope we have a few minutes.
You know, I've never actually been inside one of these before today.
It's a little, cramped, huh? Just relax Rodney.
We're safe for the moment.
Right.
Quick question though, just out of curiosity.
How much air, do these things carry? Lots.
I'm just saying, because if this doesn't work and we have to go off to another planet, who knows how long we could get stuck in here and so it would You know what Rodney? You're exactly right.
It's a limited supply, so why don't we conserve it, by you not talking? At all! All hands, this is Colonel Caldwell.
We're gonna give this another shot! We're initiating total systems shutdown now.
Reinitialising.
Did it work? We will know momentarily.
This is Sheppard.
What just happened? Standby.
We're trying to figure that out.
I'm sorry sir.
We had navigation controls for a second, but we just lost them again.
It didn't work.
We're still on course for the coronasphere.
This thing is like a damn cockroach.
You just can't kill it! This should have worked! We've disabled every navigational computer in this bay.
There's nowhere else on this ship, the virus can hide.
You're right.
There's nowhere on the ship for it to hide, but we didn't get every computer.
What are you talking about? We missed one.
What are you doing? It's the last F-302 Rodney.
The one we left behind? It's tracking us.
That makes sense, but we can't go after it.
We need help from computers or navigation.
I don't need the navigational computer to fly this thing, besides we're not going far.
Engine room, this is Sheppard.
Prepare to initiate another shutdown on my command! John? What are you doing? Getting to the last place the virus can hide.
Wait, wait, wait, wait, wait! I'm nearly done! You'd better make this quick, Sheppard.
Radiation levels are beginning to rise in the outer hull.
Understood.
What is that beeping? Something just locked onto us.
Hold on! What happened to intertial dampers? At these speeds you're gonna feel the tight turns even with the dampers.
Now he tells me.
I have them on my screens.
The computer controlled ship is preparing to fire.
We're just gonna tap on the brakes here.
Nice move.
Indeed.
He's making a break for the coronasphere.
Did I mention that we have even less protection in this ship than we did in the Daedalus? Not really.
I didn't think so.
Radiation levels in the Colonel's ship are beginning to rise.
Is it just me? Or is it getting a little hotter in here? Hold on.
I almost got him.
What happened? They're approaching the coronasphere.
There is too much interference.
You see the thing is, I have very fair skin.
I tend to burn very easy.
Just a few more seconds.
How long can they survive those radiation levels? I believe it has already been too long.
John can you read me? Rodney, come in.
Daedalus this is Sheppard.
Target is destroyed.
I repeat.
Target is destroyed.
If you try one more shutdown, I think it might just work.
Well done both of you.
You had us a little worried there for a minute.
Sorry about that.
This is Caldwell.
We'll rendez-vous as soon as we've eradicated the virus once and for all.
Roger that, Sheppard out.
You did great back there, Rodney.
Wanna take the stick? Really? No.
Dr Weir, Dr McKay, Dr Beckett, welcome back.
And Lt Colonel Sheppard.
Congratulations.
Thank you.
Anything happened while we were gone? 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.
No, not exactly.
My nose is peeling.
Do you have moisturiser? Yes Rodney.
Well we should get that.
Yes Rodney.
Any word from your offworld contacts? Well we have received several intelligence reports.
However, as of yet, there is no news of Lt Ford.
I'd like to read those reports if you don't mind.
I thought you might.
I prepared you this copy.
Thank you Ladies.
I'm sorry your journey was so difficult.
Oh, well we got here.
That's what counts.
Still, it must have been pleasant to return to Earth.
A chance to reunite with your friends and loved ones.
Dr Weir.
Dr Weir, I'm glad you're back.
We have several reports with new information on the city.
Ever since we installed ZPM, we've made many interesting discoveries.
Can this not wait? Dr Weir has only just arrived.
- I'm sorry - No, it's fine.
Really.
Let's get back to work.