Seven years after Atlantis returned to Earth, they send the city back to Pegasus. Upon returning, a new system of sensor buoys detects a derelict Ancient warship. With the crew reveled to still be alive, in stasis. The Atlantis team proceeds to enact a contingency plan and prepares to return the Ancients to their former glory and liberate the Galaxy from the Wraith.

The fate of two civilizations was decided a millennia ago. The plans of a now extinct race come to fruition as two societies separated for thousands of year meet. The Colonials erupt onto the galactic stage with a tenacious fury. The Galaxy prepares for war on all fronts and unseen forces watch from afar.