After their temporary alliance with the Wraith backfires, the Atlantis team must find a way to stop two Wraith hive ships that are headed for Earth. Weir (Torri Higginson) orders Colonel Caldwell (Mitch Pileggi) to attack the Hive ships using the Daedalus and the Orion before she is ordered to return to Earth to account for her team's failures. Sheppard (Joe Flanigan), who was able to survive by latching his F-302 to the hull of a Wraith ship, is forced to rely on a now ostracized Michael (Connor Trinneer) to help him save McKay (David Hewlett) and Ronon (Jason Momoa), who are being held prisoner by the Wraith. Ronon and McKay are able to free themselves from their cocoon prisons with a plan to sabotage the ship in a last act of heroism. All plans collide as the Daedalus and Orion engage the Hive ships while Sheppard, McKay and Ronon are still aboard.