Lt. Col. Sheppard (Joe Flanigan) leads his team on a daring raid on the Replicator home world in a bid to secure a ZPM that will save Atlantis. The key to their operation is none other than Dr. Elizabeth Weir (Torri Higginson). Directed by Weir and McKay (David Hewlett) from the jumper, Sheppard and Ronon (Jason Momoa) head deep into the Replicator city to acquire the sought after prize. But a surprising revelation concerning a long-dormant Replicator sub-routine changes the plan, forcing Sheppard and company to forego their quick escape. When the Replicators become aware of the incursion, Sheppard's team must keep them at bay or else abandon the mission and their hope of saving Atlantis. Meanwhile Colonel Carter (Amanda Tapping), aboard the Apollo, searches in vain for the missing city.