While Atlantis and Earth successfully test a “multiple gate” bridge between their two galaxies, the Daedalus detects another ship. When they try to make contact with the ship, the ship drops out of its time dilated hyper-warp. They learn it is a Lantian war ship returning from a long journey, headed back to Atlantis.

When the Lantian crew learns that all their people had all left Atlantis ten thousand years ago, and that they are the only ones that remain, they politely ask the SGA crew evacuate back to Earth. Gen. O’Neill and Richard Woolsey arrive in Atlantis to try to negotiate with the Lantians, but they are reluctantly forced to agree to leave Atlantis, while Ronon and Teyla decide to stay behind in the Pegasus galaxy.

However, the newly found Latians turn out to be overly confident on their ability to control an impending attack by the Asuran Replicators. Gen. O’Neill and Woolsey then become trapped on Atlantis; as Sheppard, Weir and the rest of SGA break rank with the SGC to try to rescue them and defeat the Replicators’ attack on Atlantis.

Dr. McKay can get them back into the heart of Atlantis, but what sort of resistance will they encounter?