The Intruder

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

Plot
While the Daedalus flies through hyperspace en route to Atlantis, Weir talks with Sheppard in the Mess Hall about several things like his promotion; the return journey to Atlantis takes 18 days in hyperspace without the ZPM. 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. 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 Col. 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 the IOA and Weir discuss the military situation in Atlantis, and that Col. 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 IOA back 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. Col. 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 Wallace, Weir's fiance, 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 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 beaming technology 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. Ford's cousin 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 onboard with the star's radiation. McKay concludes that the virus survived by uploading itself into an F-302; 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. Dr. Zelenka informs the team that they made many interesting discoveries since they installed the ZPM. Before he can launch into the details, Weir tells them all to get back to work.

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!

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.

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 the Wraith writing which is now on his screen, then turns back to Rodney.)

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.

McKAY: We should really really be dead right now.

SHEPPARD: I don't feel dead.

McKAY: Uh, I'm just saying, because if this doesn't work and we have to come up with another plan, 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: You did great back there, Rodney. Wanna take the stick?

McKAY (perking up): Really?!

SHEPPARD: No.

External sources

 * Official Stargate Atlantis site. MGM. Visited June 8, 2006.
 * Transcript from GateWorld. Transcribed by Callie Sullivan. Visited May 14, 2006.
 * Summary from GateWorld. Visited May 14, 2006.
 * Review from GateWorld. Reviewed by Taylor Brown. Visited May 14, 2006.
 * Gatenoise from Moon-catchin'. Visited June 23, 2006.
 * Gatenoise from Moon-catchin'. Visited June 23, 2006.