Remnants

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

Synopsis
While being evaluated by the International Oversight Advisory, Richard Woolsey meets a beautiful scientist new to Atlantis, who is not what she appears. Meanwhile, Lt. Colonel John Sheppard is captured and tortured by an enemy he thought he'd killed several years ago: his sworn enemy, Genii Commander Acastus Kolya.

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

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, Dr. Rodney 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 Sekkari, to survive. She reveals that when McKay flew the Jumper out of the Underwater Jumper bay during the plan to defeat Michael Kenmore, 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.

Teyla again asks Woosley to join them and this time he agrees. Rodney states that the only reason the AI didn't reveal itself to him was because he would have figured it out. Sheppard wonders why the device was recovered after Woosley and himself started hallucinating, and McKay says he found it with Zelenka's help. It is then revealed that Dr. Radek Zelenka has been off world the entire time. The episode ends with Rodney saying "Son of a. . ."

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.

McKay: Hey. What happened to your offworld foofoora? Thought you were the guest of honor at some big diplomatic dinner on M2J.

Zelenka: Yeah, I was, but the festivities ended early when three members of Lieutenant Donovan's team suffered a severe allergic reaction to something that we were served at the grand banquet.

McKay: Yeesh.

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!

Woolsey: You poached my private spot.

Conrad: What?

Woolsey: Uh, what I meant to say is you discovered my personal little area.

Conrad: I'm sorry I made you doubt your sanity.

Woolsey: Who are you? What are you?

Conrad: I'm a physical manifestation of your subconscious romantic and sexual ideals.

Woolsey: Oh, God...

McKay: Neat.

Sheppard: "Neat"?!

McKay: Yeah well, she caught me off guard, what did you want me to say? What would you have said?

Sheppard: Uh, "Weird."

Nominations

 * Nominated Leo for "Best Screenwriting in a Dramatic Series" (Joseph Mallozzi and Paul Mullie)