M3, T10: While testing the new McKay-Carter intergalactic gate bridge, the Daedalus detects an Ancient Atlantian warship, traveling at just below light speed and heading towards Earth. Damaged in battle during the war with the Wraith, the Ancients aboard this ship fled the Pegasus galaxy and have spent thousands of years in stasis. Back on Atlantis, the now awoken Ancients meet with General O'Neill (Richard Dean Anderson) and Richard Woolsey (Robert Picardo). They thank the Stargate team for taking care of the city in their absence, but ask them to vacate Atlantis immediately. While Ronon and Teyla stay in the Pegasus galaxy, the remaining team members struggle to resume their lives on Earth. Sheppard (Joe Flannigan) doesn't gel with his new SG team, McKay (David Hewlett) is bored in his Area 51 lab, and Weir (Torri Higginson) has trouble finding meaning in a life after Atlantis. However, the SGC soon learns that the Replicators have overtaken Atlantis, as McKay had previously enabled the Replicators to re-write their own base code to override a safeguard preventing them from killing the Ancients that made them. Now, with O'Neill and Woosley trapped in Atlantis and General Landry (Beau Bridges) intent on protecting Earth by sending nuclear weapons through the gate to destroy Atlantis, the team must figure out a way to save O'Neill, Woolsey and Atlantis itself.