Misbegotten

Misbegotten, originally named The Begotten then The Misbegotten before receiving its final name, is the second episode of season three of Stargate Atlantis and the third in a three-part arc.

Plot
In this episode the IOA agent Richard Woolsey is assigned to review whether or not Dr. Weir should maintain her command of Atlantis.

Having successfully used the Wraith retrovirus to turn an entire hive ship of Wraith into humans, the team returns to Atlantis with their prisoners in stasis. Meanwhile, Weir continues to defend her leadership in the face of an independent review being conducted by I.O.A. member Richard Woolsey.

Examining the hive ship that the team hijacked in an attempt to restore it to full working condition, Dr. McKay determines that the Wraith prisoners cannot continue to be held in stasis indefinitely. The team decides the best thing to do is to set them free on the planet M8G-352 under the guise that they were exposed to a viral outbreak.

Col. Sheppard and Dr. Beckett remain on the planet to manage the human-form Wraith, including a re-humanized Michael. But when Sheppard returns to Atlantis they discover a Wraith ship approaching the planet and the team must act fast to keep the existence of Atlantis a secret.

Lathan, one of the Wraith prisoners, begins to suspect something is wrong but is subsequently killed by Michael Kenmore and a group of humanized Wraith. They cover up this murder by setting up an accident site, where Lathan supposedly fell from a cliff. When Dr. Beckett discovers that something is amiss with the presumed accident, he finds that the Wraith are already reverting and that Michael didn't take kindly to this second betrayal.

As Beckett is returned to the camp, he learns that the soldiers have been killed and that the reverted Wraith intend to offer the remaining humanized Wraith as an offering to the coming Wraith hive ship. Michael proceeds to strap Dr. Beckett to the operating room table, preparing him for something. Meanwhile Atlantis cannot send Daedalus to the far off planet as their hyperdrive is still in repair.

Sheppard returns at the head of the stolen Wraith ship to save the prisoners and engage the fail-safe nuclear device, hoping to kill all Wraith on the planet before they can relate what they know to the coming Wraith ship. As Dr. Beckett is rescued they find that they cannot set off the nuke, correctly assuming that the Wraith have found and disabled the device.

Just as they begin firing on the campsite from orbit, the Wraith hive ship drops out of hyperspace and immediately begins attacking Sheppard's hive ship. When the Daedalus arrives at the planet, nothing but debris remains of Sheppard's hive ship, but the five Atlantis members are still alive inside a cloaked Puddle jumper. As they return to Atlantis, Woolsey briefs Weir about his report, telling her that she deserves to remain in command.