The Long Goodbye

"The Long Goodbye" is the sixteenth episode of the second season of Stargate Atlantis. In this episode, the team picks up some unexpected cargo and finds that human nature's flaws have followed them to the Pegasus Galaxy.

Plot
While scouting an isolated moon by Jumper, Sheppard and his team discover two battered escape pods in decaying orbit. They bring them to Atlantis, where Dr. McKay opens the first pod. An aged, unconscious woman lies within, near death. When Dr. 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, 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. The hunt goes on as Dr. 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, 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 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. But if Teyla fires the last shot in this war, she'll be killing Sheppard, as well. 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 while Sheppard seems to regain control and the imprinting seems to end in the way Phoebus described it would but it is unclear if Thalan is faking it as he heard Phoebus' description of what would happen as well. Pheobus arrives but before she can kill Thalan or Sheppard, Teyla gives him a stunner while he pretends to be knocked out and he stuns Phoebus before she can realize the truth. Reinforcements arrive moments later and Sheppard (or Thalan its still unclear) 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 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.