Above an isolated moon, Sheppard's team discovers two battered life pods in decaying orbits. 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 the pod and strikes her. Weir collapses.
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 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.