All hope seems lost, until Colonel Everett arrives suddenly from Earth. He is determined to defend the city until the arrival of a ZPM, brought by a new ship.

Sheppard is infected with the Wraith retrovirus and slowly turns into an Iratus bug. To provide a treatment, stem cells must be retrieved from one of their eggs.

While on a regular mission, Ronan runs into some Satedan friends from his past. As old emotions start to return, new thoughts come with them, one of which involves leaving Atlantis. But could danger be lurking just around the corner?

When what appears to be a satellite crashes into Atlantis, the team becomes aware of strange behaviour on the base.

Slowly, everyone on Atlantis comes to terms with the sudden re-appearance of Dr. Carson Beckett who, he claims, has been Michael's prisoner for some two years. He tells them what he was doing in Michael's laboratory and they set off to find the kidnapped Teyla. Dr. Keller figures out just how he's come to there at all. Sheppard meanwhile has been using all of his contacts to try and locate Teyla but they come across someone from the past. Teyla in turn has found some of the Athosians alive but they are few in number as a result of Michael's experiments. Michael explains to her just what it is he wants from her as well as his own plans for the future.

Dr. Carson Beckett is removed from stasis because he's the only one who can find the antidote to a mysterious virus that has incapacitated base personnel, beginning with Dr. Jennifer Keller.

A group of beings stranded in sub-space seek help from Atlantis to return to normal space. But their outrageous claims and erratic behavior strains the trust of their benefactors and forces a painful solution.