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 and Richard Woolsey. They thank the Stargate team for taking care of the city in their absence, but ask them to vacate Atlantis immediately.

Teyla begins to see apparitions of ancients in distress and believes they are the ghosts of the Ancients recently massacred by the Replicators. Meanwhile Rodney McKay believes he's found the whale that saved him a year ago while trapped in a submerged puddle jumper. But while taking a jumper out with Col. John Sheppard to investigate his old friend they discover the whale is not alone but is one of dozens of its kind, all headed directly to Atlantis.