Remnants

"Remnants" is the fifteenth episode of the fifth season of Stargate Atlantis.

Synopsis
While being evaluated by the I.O.A. Richard Woolsey meets a beautiful scientist new to Atlantis, who is not what she appears. Meanwhile, Sheppard is captured and tortured by an enemy he thought was dead.

Plot
John Sheppard has been abducted. He regains consciousness, finding himself in a forest on the mainland of Atlantis's new home planet, to which the city was relocated a year and a half earlier. His hands and feet are bound, and Sheppard shuffles himself toward a sharp rock to try and free himself from his bonds.

Back in the city, Richard Woolsey encounters a new member of the expedition in a transporter chamber. She introduces herself as Dr. Vanessa Conrad, a scientist who has recently arrived on the Apollo. Woolsey is immediately smitten, and breaks the ice by telling her about Atlantis's regular social activities -- Yahtzee tournaments, movie screenings, organized sports, and more.

Soon, the two are on a first name basis. But there is certainly more to this woman than meets the eye.

Colonel Sheppard manages to free himself, and returns cautiously to his Puddle Jumper. He soon discovers who it is who tied him up: Acastus Kolya, the former Genii commander and torture master whom he shot dead two years ago.

In Atlantis, Woolsey, McKay, and the rest of the team are about to make a shocking discovery -- a discovery about an ancient race, Atlantis's fellow residents on this new planet, and what they need to survive. Ultimately it’s revealed that Vannesa Conrad is just a manifestation of the AI of a pod they discovered that holds the last hope for an extinct alien race, named the Sakari, to survive. She reveals that when McKay flew the Jumper out of the Underwater Bay during the plan to defeat Michael, it woke the dormant pod up. The pod had been searching for a suitable planet for its race to populate but a malfunction caused it to end up on M35-117 which was not suitable for it. The AI had been observing the Expedition for weeks to see if they were trustworthy and took on Conrad's form to communicate with Woolsey and ask for his help. At the same time Sheppard falls off a cliff after escaping torture by Kolya and having one hand cut off. Kolya tells him to use his other hand and pull himself up and a confused Sheppard does so and confronts Kolya who reveals he is not really Kolya: it’s another manifestation of the pod's AI set up to distract Sheppard as he would have the best chance of stopping them if it came down to it. The AI never intended him to die, it just wanted him distracted. It explains the same thing it explained to Woolsey. The AI also helps Woolsey who's under a performance evaluation from someone who covets his position to keep his job as a gift to him for his help. Woolsey has the Apollo transport the pod to a suitable world for the alien race to start over and before it leaves, the AI, still appearing as Dr. Vanessa Conrad, shows them the true form: an alien, however still very much humanoid.

Notable Quotes
Ronon: Sometimes when I walk past his quarters at night, I can hear him crying. Rodney: What...Really? Ronon: No.

Parrish: Look at this, huh? It's a plant not unlike the begonia eiromischa! Sheppard: (despairingly) Oh, God. Lorne warned me about this. (A reference to the episode Runner)

Zelenka: Come to think of it, I think it might have been those little green berries with the purple specks on them, because my tongue did seem a little bit numb afterwards ... McKay: Yeah, FYI, this conversation ended six seconds ago. Zelenka: Yeah, um, anyway, on the way back I had an idea. McKay: Well, have a little lie down. It'll pass.

Woolsey introduces Shen Xiaoyi to the technician team Woolsey: Hello there, Chet. Chuck: It's Chuck. Woolsey: Excuse me? Chuck: It's Chuck, sir. My name is Chuck. Woolsey: Oh, of course! Chuck. Chet's on the late shift. Chuck: (after Woolsey leaves, irritated) There is no Chet!

McKay: You realize it's highly unlikely you're actually gonna find anything? Radek: Well, then I will have wasted an hour of my time and you'll be able to tell me "I told you so." If, on the other hand, I do find something, perhaps they'll name something after me for a change. Rodney pauses for a few seconds McKay: Wait!

Rodney: Neat. Sheppard: "Neat"?! Rodney: Yeah well, she caught me off guard, what did you want me to say? What would you have said? Sheppard: Uh, "Weird."

Background notes

 * It's revealed in this episode that Kolya did in fact die when Sheppard shot him: Beckett confirmed his death afterwards and the Kolya that appeared here wasn't the real one.
 * It is revealed that several weeks have passed since Michael Kenmore infiltrated Atlantis. (the events of "The Prodigal")
 * It has also been revealed that it has been nine months since the events of "The Seed", when Woolsey takes command of Atlantis.
 * This episode marks the first time the view is inside an Atlantis transporter when it is activated.
 * Atlantis Expedition members shown by flag patches; Australia, Canada, Czech Republic, Russia, Spain, Sweden and United States of America
 * The capsule and the premise of the Humanoid median are very similar to the SG-1 episode of Scorched Earth, where a large ship had been sent across the Milky Way to search and terraform a planet for a Sulfur based life form, the Gadmeer, as well as all of the organisms of their homeworld and the knowledge of their race.