The Return, Part 2 is the eleventh episode of the third season of Stargate Atlantis.

Woolsey and O’Neill are hiding out in a section of the city where the sensors are not working when Sheppard’s team comes through the gate, taking fire from the Asurans. Sheppard contacts the two and tells them to stay put, dropping an explosive device into Stargate Operations before piloting the Jumper through the window directly behind the gate. The device detonates, damaging critical systems and all but destroying the upper section of the central spire. With the critical systems, including sensors, destroyed, the Asurans attempt to repair the damage. They are also aware of Sheppard’s message, and because they had killed all of the Lanteans, suspect that there are humans hiding within Atlantis.

The team then take the Jumper to retrieve Niam, who is still floating in space where they left him (”Progeny”). McKay plans to use Niam to transmit a program that will make all the Asurans freeze, allowing them to finish them off with the ARGs. Niam has been damaged by his long exposure to vacuum and solar radiation, and is unconscious. McKay begins uploading the program but notes that they need to be very close to the city in order to make it work. Any attempts to extend the program’s range would mean increasing Niam’s power levels, which risks reactivating him.

When the Jumper returns to Atlantis, it is attacked by drone weapons. Sheppard maneuvers the Jumper between the city buildings but cannot shake them. He takes the Jumper into the ocean, heading for an underwater docking bay. However, the bay will not repressurize, and due to the damage taken earlier, the Jumper is taking on water. They radio O’Neill for help, and he swims down to the docking bay control room, holding down a dead man’s switch to drain the docking bay while Woolsey keeps a lookout. O’Neill succeeds, but an Asuran search party finds and captures both him and Woolsey.

McKay continues to work on Niam, as the others discover that O’Neill and Woolsey have been taken, possibly to be mind-probed. This is indeed the case, and having discovered Sheppard’s plan, the Asurans reactivate Niam, forcing McKay to destroy him with an ARG. With “Plan A” gone, Ronon suggests they simply go on a killing spree with the ARGs but McKay warns them that eventually the Asurans will determine the frequency the disruptors use and develop an immunity. McKay comes up with another plan and asks Sheppard how much C-4 they have.

The team splits into three groups, each going to different shield control units around the city. Sheppard and McKay go to the cell where O’Neill and Woolsey are being kept. McKay tells the two captives that the plan is to disable the city’s shield emitters with C-4, allowing the Daedelus to beam nuclear bombs directly into the city and vaporize it after they get away. However, McKay is apparently unable to override the coded lock to free them, and he and Sheppard are forced to leave.

The Asurans finish repairs to Stargate Operations and, with the city now being powered by ZPMs, activate the city’s Stardrive. Beckett and Teyla head to the chair room where Beckett launches drones to damage the stardrive. The Asurans, however, have extracted information about the plan from Woolsey’s mind, and capture Sheppard’s team just as the last of the C-4 is planted. The Asurans remove the C-4 and gloat to Sheppard that the humans’ plan has failed. Detecting the Daedelus entering orbit, the Asurans raise the shield…

…and, in flashback, McKay describes his plan to Sheppard: to insert the disruptor crystals from the ARGs into the shield control units, turning the Atlantis shield into a giant disruptor weapon. A fake plan is told to Woolsey and O’Neill to feed disinformation to the Asurans and the C-4 left as misdirection. When the Asurans activate the shield they are destroyed in one fell swoop. At the last second the team contacts the Daedalus and convinces Col. Steven Caldwell not to destroy the city.

The city recaptured, the Atlantis expedition moves back in, and with O’Neill and Woolsey’s approval Weir will once again be in command.

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