The Intruder

"The Intruder" is the second episode of the second season of Stargate: Atlantis.

Synopsis
After a return journey from Earth back to Lantea, an unexplained death happens on board the Daedalus. He was killed when he figured out that a Wraith computer virus has uploaded itself into the Daedalus' computers, and is taking over the ship.

Previously on Stargate: Atlantis
The Daedalus arrives at Atlantis with a Zero Point Module and Dr. Rodney McKay uses it to power Atlantis' shield. With the Wraith constantly bombarding the shield, the ZPM will soon be depleted. Major John Sheppard comes up with a plan to fake a Self-destruct and Cloak the city. During the fighting with the Wraith, Lt. Aiden Ford is fed on by a Wraith warrior and falls into Lantea's ocean. He survives but becomes addicted to the Wraith enzyme and escapes in a Puddle Jumper.

Plot
While the Daedalus flies through hyperspace en route to Atlantis, Dr. Elizabeth Weir talks with Lt. Colonel John Sheppard in the Mess hall about several things like his promotion; the return journey to Atlantis takes 18 days in hyperspace without the Zero Point Module. Their conversation is cut short when someone calls them; one of the engineers, Dr. Monroe, is dead. The crew are not sure what killed him; Dr. Rodney McKay begins reviewing the security-camera footage, but at the precise moment Monroe is killed, the camera cuts out. McKay concludes that the circuitry in the Engineering door was rewired to deliver a fatal electric shock, taking power from the security camera. McKay recommends dropping out of hyperspace so that they can check the electrical systems, but Colonel Steven Caldwell is unconvinced. He then talks with Weir, prompting a flashback of the Atlantis Command crew's return to Earth; the first is of a discussion at Stargate Command. During this meeting Major General Henry Landry and Weir discuss the military situation in Atlantis, and that Caldwell will be the new military commander, overlooking Sheppard because of his rank. However Weir wants Sheppard to stay military commander and threatens that she still has support from the president. Eventually The Pentagon backs down, promoting Sheppard to the rank of Lieutenant Colonel and placing him in charge of the military personnel.

Back on the Daedalus, McKay informs Caldwell that Monroe's death may not be an accident; Caldwell finally agrees and orders the crew to disengage the hyperdrive. In the Engine Room, McKay searches the computers for problems together with the ship's Asgard engineer Hermiod (with whom he quarrels) and Dr. Lindstrom. When Lindstrom stumbles upon something in the computers, another 'accident' occurs which turns out to be a coolant leak. While McKay is able to leave the room, Lindstrom has to hide in an airlock. Suddenly the outer doors open and Lindstrom is blown out into space.

Later the command crew discuss what or who could have caused the accident. Caldwell orders all civilians to be confined to their quarters since at this stage, no-one can be trusted. Another flashback occurs in which the civilian leadership at the SGC talks about whom should join the Atlantis expedition. During this discussion it turns out that Dr. Simon Wallis, Weir's fiancée, doesn't want to join the expedition. She later confronts him but he needs time.

On the Daedalus, Hermiod discovers a virus in the computer systems and, running a translation system, McKay concludes it is an Artificially-Intelligent virus written by the Wraith and most likely uploaded to the ship during one of the battles in the previous episode. The crew concludes that the virus was designed to surrender the ship to the Wraith; it began by terminating personnel as it learned to use the ship's systems. Without warning, the vessel's communications array begins broadcasting a wide-band long-range distress call which the Wraith cannot fail to miss. McKay suggests performing a full shutdown of the ship's computer system to clear the active memory and then reboot the whole system using backups of the network. Meanwhile, attempts to deactivate the communications array have failed and Sheppard decides to use an F-302 fighter-interceptor to physically destroy the communication system. A few minutes later, he takes out a fighter and successfully disables the ship's communications systems, but as he tries to return to the ship, the F-302 doesn't respond to his commands. The team conclude that the virus managed to upload itself to the fighter's guidance computer and has taken over control. Sheppard suggests using the Asgard transporter to transport him out of the fighter, but the targeting systems were part of the array he has just destroyed. While the crew works on how to rescue him, Sheppard has a flashback when he visits Lt. Aiden Ford's cousin Lara to tell her that Ford is missing. Afterwards McKay is able to beam out Sheppard with the Asgard beam using the signal from Sheppard's radio as a locator beacon, a technique last used on Prometheus before the Asgard installed their own sensors onto the ship.

Soon after, the ship's computer system is shut down. Weir has a flashback in which she talks with Simon, who decided not to join the expedition since he met someone. Back on the ship, the system is rebooted successfully and Caldwell orders the ship to leave the area with sub-light engines. However they suddenly veer off course; the virus was not fully removed, has taken control of the ship's engines and is now taking the vessel into a star. It turns out that the virus is adapting to its environment and is attempting to remove the source of resistance on board with the star's radiation. McKay concludes that the virus survived by uploading itself into an F-302 by referring to an incident at the SGC; McKay and Sheppard head to the hangar to resolve the situation but the virus has anticipated their course of action and sealed the doors. Because they can't enter the bay normally, Sheppard orders them to be beamed in, despite the risk. Transported successfully, McKay and Sheppard get to work disconnecting the navigational computers in the fighters. The virus opens the hangar doors but Hermiod is able to activate the hangar shield, preventing a decompression but not for long. The two quickly remove all memory units and then enter a F-302 just before the shield deactivates.

Afterwards the computers are again shut down, but on reboot the virus once again returns. It survived this time by copying itself into the F-302 Sheppard used to destroy the communications array and is now floating in space. Sheppard makes the decision to destroy it (much to McKay's disagreement) and a battle between the two fighters occurs (taking them very close to the star's surface leading to McKay complaining about radiation). They are finally able to destroy it and this time the reboot works.

Back in Atlantis Weir discusses the incident with Teyla Emmagan. Dr. Radek Zelenka informs the team that they made many interesting discoveries since they installed the Zero Point Module. Before he can launch into the details, Weir tells them all to get back to work.

Notable Quotes
Sheppard: Couldn't sleep. Must be the, uh, burden of command - you know, ever since I was promoted to Lieutenant Colonel.

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!

(Sheppard stares at Hermiod suspiciously)

McKay: Don't stare. He hates it when people stare.

Sheppard: (whispers) Am I the only one who thinks it's strange we're working with an alien?

McKay: Intergalactic hyper drive technology is kind of new to us, so we need his help.

Sheppard: Is he supposed to be naked like that?

Weir: You said you wanted the best.

Beckett: But all of these people are more qualified than I am, how am I supposed to choose between them?!

Weir: Carson, you're my chief surgeon. No-one is more qualified than you.

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?!

McKay: For what? What are you looking at?

Hermiod: The sabotage we've been searching for.

McKay: It's a virus.

Hermiod: How perceptive of you.

Hermiod: What are you doing?

McKay: I'm just checking something—I'm sure it is impossible.

(Types a command into a console. The numbers on the screen change to symbols)

McKay: Crap!

Hermiod: What did you do?

McKay: I just ran it through a translation program—it's Wraith.

(Hermiod looks at the screen, then at Dr. Mckay)

Hermiod: "Crap" indeed.

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 radio) Rodney seems to think you'll be OK.

(after Sheppard's transportation on Deadalus's board)

Weir: Are you alright?

Sheppard: Yeah. Two arms, ten fingers ... (he looks down) I'll check the rest later.

Sheppard: This is what I do when I'm having problems with my laptop. I turn it off, then I turn it on again.

Weir: I think it's a little more complicated than that.

Sheppard: I'm just saying, if we're taking a page from the John Sheppard Book of Computer Repair, we're really desperate.

McKay: We should really really be dead right now.

Sheppard: I don't feel dead.

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?

Sheppard: Lots.

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.

Sheppard: He's making a break for the coronasphere.

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 don't think so.

Sheppard: You did great back there, Rodney. Wanna take the stick?

McKay: (perking up) Really?!

Sheppard: No.

Goofs

 * Dr. Rodney McKay and Lt. Colonel John Sheppard were forced to retreat to a F-302 fighter-interceptor due to the virus opening the fighter bay doors. Then in the scene of them taking off to go after the F-302 controlled by the virus it shows the fighter bay doors being opened for them.
 * When a person is transported via Asgard beaming technology, whatever they're doing at the point of departure is continued when they reach their destination. One example being Lt. Colonel Samantha Carter being beamed from Thor's ship to Brigadier General Jack O'Neill's office while walking/moving toward Thor in "Reckoning, Part 1". Lt. Colonel John Sheppard was sitting in an F-302 when he was beamed out, and should have been in a sitting position when he arrived on the bridge of the Daedalus.
 * Lt. Mark Stuart, after the fighter bay decompresses, calls the bay a 'cargo bay' rather than a fighter bay.

Character

 * Airman Frank Levine