Misbegotten

"Misbegotten" is the second episode of season three of Stargate: Atlantis.

Synopsis
The Atlantis expedition stopped the Wraith from reaching Earth, and now that they turned Human, they send them to an isolated world to teach them to administer the Iratus bug retrovirus themselves. However, some of them, including Michael Kenmore, are starting to remember their past.

Previously on Stargate: Atlantis
With two Wraith Hive ships on their way to Earth, Dr. Elizabeth Weir sends the Daedalus and the Orion to intercept them. The Queen and the Wraith view Michael Kenmore as unclean. The International Oversight Advisory questions Weir's decisions. Michael helps Lt. Colonel John Sheppard, Dr. Rodney McKay and Ronon Dex escape the Hive and beam to the Daedalus. During the battle, the Daedalus is badly damaged and loses life support. The crew beam the Iratus bug retrovirus to the Hive and board the ship to find the Wraith transformed into humans.

Plot
International Oversight Advisory agent Richard Woolsey is assigned to review whether or not Dr. Elizabeth Weir should maintain her command of Atlantis.

Having successfully used the Iratus bug 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 Woolsey.

Examining the Hive ship that the team hijacked in an attempt to restore it to full working condition, Dr. Rodney 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.

Lt. Colonel John Sheppard and Dr. Carson Beckett remain on the planet to manage the Human-form Wraith, including a re-humanized Michael Kenmore. 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 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 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 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 warhead, hoping to kill all Wraith on the planet before they can relate what they know to the coming Wraith ship. As 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 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.

Notable Quotes
Woolsey: Nothing renews your appreciation for the military like the threat of invasion from life-sucking aliens.

Woolsey: I've never met an Asgard.

Weir: You, I think, will love them. They have a great sense of humor.

Woolsey: Really?

Weir: No.

Sheppard: Just out of political curiosity, how much trouble is it going to cause you if I knock this Woolsey guy in the head?

Weir: May I ask why you'd like to do that?

Sheppard: It's just an impulse I had, really, one I suspect I'm going to have again next time I see him. He may not even have to say anything.

(Weir looks amused)

Weir: I've never seen you like this. What did Woolsey say to you?

Sheppard: Besides judging every damn decision you've ever made?

Weir: John Sheppard, are you defending my honor?!

(Sheppard hesitates a moment)

Sheppard: And judging me for agreeing with you.

Weir: Well, don't be too hard on him. I think of all the circling wolves, he's the least likely to actually bite. In fact, he might even convince the others to leave us alone.

Sheppard: Alright, so... no head knocking.

Weir: It's the thought that counts.

Sheppard: You're a genius Rodney.

McKay: Yes, I know... but I didn't do anything.

Sheppard: How're you doing with the weapons?

McKay: We couldn't hit the side of a barn.

Sheppard: Hive ships are a hundred times bigger—

McKay: A giant flying barn, we couldn't hit that.

Goofs

 * Shortly after the fail-safe bomb fails to detonate and Michael Kenmore is talking to the other Wraith, Lathan can clearly be seen near the back of the crowd, despite his death earlier in the episode.
 * Michael somehow probed Dr. Carson Beckett's mind although it has been said that no Wraith can do this unless the Human has Wraith DNA and initiates contact first. Only a Hive queen has been shown to have enough telepathic capabilities to read a Human's thoughts when they do not have Wraith DNA.

Planet

 * M8G-352

Deaths

 * Morrison
 * Lathan