The Long Goodbye

"The Long Goodbye" is the sixteenth episode of the second season of Stargate: Atlantis.

Synopsis
Lt. Colonel John Sheppard's team finds two pods adrift in space. When they recover them, they find an aged person in each one. The two consciousnesses make it into Sheppard and Dr. Elizabeth Weir, and convince the team that they are old lovers. However, the two are actually enemies trying to kill each other over a war that ended a long time ago.

Previously on Stargate: Atlantis
The Trust implants a Goa'uld in Colonel Steven Caldwell and has him attempt to blow up Atlantis. The Atlantis expedition discovers this and is able to save Atlantis and remove the Goa'uld.

Plot
While scouting an isolated moon by Puddle Jumper, Lt. Colonel John Sheppard and his team discover two battered escape pods in decaying orbit. They bring them to Atlantis, where Dr. Rodney McKay opens the first pod. An aged, unconscious woman lies within, near death. When Dr. Elizabeth Weir approaches for a closer look, an energy beam lances out of a black box-like device in the pod and strikes her, which causes her to collapse.

She awakens moments later, claiming to be a woman named Phoebus. Because her body is dying, the pod has automatically stored her personality and imprinted it on the first living person to approach. Before Sheppard, Colonel Steven Caldwell and the other observers can grow too alarmed by this strange story, Weir seems to resurface. She confirms what Phoebus said and adds that the imprinting will last only a few hours. Before Phoebus's personality vanishes forever, however, she has a request. Her husband, Thalan, is in the second pod. If Sheppard will volunteer to host him, the two can briefly be reunited before they die.

Sheppard reluctantly agrees and receives the imprinting. Phoebus greets Thalan with a kiss — but then the two grab whatever weapons are handy and start firing at each other. In fact, they're actually the last surviving opponents in an ancient, devastating war, and each is fanatically determined to defeat the other.

As the team scrambles to capture them, Phoebus and Thalan carry their vendetta into the corridors of Atlantis. They have total control over Weir and Sheppard's bodies, can impersonate them perfectly, and also have access to their knowledge of the city. Thalan soon sabotages the power systems, plunging Atlantis into darkness. During the struggle, Phoebus shoots Ronon Dex. The hunt goes on as Dr. Carson Beckett struggles to remove the bullet by flashlight.

The moment McKay gets the power back on, Phoebus completely locks down the city, trapping everyone in rooms and corridors and blocking all computer usage. Teyla Emmagan, locked into the same section as Thalan, manages to stun him. Then Phoebus contacts Caldwell — who has assumed command — and threatens to turn the city's fire-suppression halon gas against its population unless Caldwell helps her defeat Thalan.

Knowing that the hazardous gas could kill up to three quarters of Atlantis's residents, Caldwell reluctantly orders Teyla to drag Thalan to a security camera so Phoebus can see her ancient enemy. Pleased, Phoebus then orders Teyla to execute Thalan - and Sheppard. Caldwell orders her to decide for herself and while Teyla waits as long as possible, McKay takes over control from Phoebus. To finish the job herself Phoebus moves to Teyla's position. Sheppard seems to regain control of his mind and body, and the imprinting seems to end in the way Phoebus described it would, but it is unclear; Thalan might be faking it as he heard Phoebus' description of what would happen as well. Pheobus arrives but before she can kill Thalan/Sheppard, Teyla gives him a Wraith handblaster while he pretends to be knocked out and he stuns Phoebus before she can realize the truth. Reinforcements arrive moments later and Sheppard/Thalan asks Teyla why she gave him the stunner as she could not be sure who was in control of Sheppard. She replied either way he would have shot Phoebus, because it was just a stunner and if it was Sheppard, he knew it wouldn't have killed her so he wouldn't have hesitated if he was in control and not Thalan. On the other hand, if Thalan had still been in control, he still would have shot Phoebus to end the feud.

Later Caldwell (who is the only one to believe that Phoebus and Thalen are gone besides Beckett) meets Weir and Sheppard, who have been freed of the other consciousnesses, in the infirmary and taunts them about what has happened, especially the kiss, which causes Weir to look embarrassed.

Notable Quotes
Ronon: So people just sit and watch this box for hours at a time?

Sheppard: Yeah, people do.

Teyla: Is it that engaging?

Sheppard: Depends what's on it. There are lots of programs on dozens of channels, every day, all day.

McKay: Most of which are fictional representations of ridiculously attractive people in absurd situations.

Sheppard: There are educational programs, all sorts of documentaries. Not many people watch 'em but, uh, well, they're on.

Ronon: And that's what everybody on your planet does for entertainment? Watch a box?

McKay: Not everyone, although I will confess to the occasional half hour of Jeopardy.

Ronon: Jeopardy?

McKay: It's the name of the show: Jeopardy.

Ronon: Sounds dangerous.

Sheppard: Double jeopardy, that's twice as dangerous.

Phoebus/Weir: Now radio security and tell them everything's fine.

Beckett: Everything's not fine!

Phoebus/Weir: (shoots Beckett) Rodney?

McKay: (triggers radio) Security, this is Dr. Rodney McKay. Everything is fine, never been better. Uh, Col. Caldwell was kidding when he said what he said.

Phoebus/Weir: Oh, forget it. (shoots McKay)

Ronon: All right, we need to split up. I'll take Sheppard, you go after Weir.

Teyla: Why?

Ronon: Cause I know how he thinks. I don't have the slightest clue how she thinks.

Beckett: (after hearing Phoebus and Thalen threaten to kill each other despite supposedly being married) Well they're headed straight for divorce!

Beckett: (when the power comes on after he just finished surgery on Ronon) Lovely! Now it comes on!

McKay: I would just like to state, for the record, that it is astounding to me that I find myself once again in the position of having to save this city when you and your…space marines can't figure out how to track down two people!

Caldwell: They're two people with the skills and resources of Dr. Weir and Col. Sheppard who probably know this city better than anyone else. And, also for the record, I was against this from the very beginning.

McKay: Yes!....(much quieter) Yes, you were.

(Weir wakes up, back in control)

Sheppard: Good morning.

Weir: Good morning.

Sheppard: What's her name sure hung in there for a while.

Weir: When did she?

Sheppard: Some time in the middle of the night, kicking and screaming.

Weir: That was the...strangest feeling you know? The entire time I was shouting to everyone but nothing I wanted to would come out of my mouth.

Sheppard: I know. It was a real nightmare. Especially when you shot Ronon.

Weir: Oh God, but I wasn't...

Sheppard: I know, I know, it was her.

Weir: How is he?

Sheppard: He's fine. Teyla and Rodney just went to see him in post-op.

Weir: Did they believe you were...you?

Sheppard: To be honest, I think the only people who believe one hundred percent are Beckett and you.

Caldwell: And me.

(Caldwell enters)

Caldwell: In fact I can safely say that I know how you feel.

Sheppard: Yes sir.

Weir: Thank you Colonel, for keepign a potentially explosive situation under control.

Caldwell: Yeah, well it was a lot closer than I would like to admit.

Sheppard: For what it's worth, McKay says you did a good job.

Caldwell: Did he? Well, maybe there's still hope for me yet.

Weir: Oh God no, don't believe anything she might have said...

Caldwell: I'm kidding. Don't give it another thought. Well if you'll excuse me, I'm sure you'll both agree that the paperwork on this is going to be a nightmare. Especially that kiss.

(Awkward moment)

Sheppard: Yes sir.

Caldwell: Well, try not to kill each other while I'm gone.

Goofs

 * Phoebus/Dr. Elizabeth Weir is incorrect. Halon gas does not "extinguish life as well as fires." It is biologically inert and not lethal except at concentrations high enough to displace large amounts of oxygen. 1301 systems were used in computer rooms, airliners, ship engine rooms and other inhabited spaces. Although it does extinguish fires the same way as lives, by displacing oxygen needed for the fire to burn.
 * While operating on Ronon Dex, Dr. Carson Beckett wears a surgical mask, but no surgical cap. No experienced surgeon would do this except in dire situations, e.g. being under fire.