With the Wraith ships heading for Earth destroyed, Michael was again turned into a human. But it didn’t take him long to once again figure out that there was something about himself that the team was hiding from him, and he escaped again — his Wraith physiology again reasserting itself (“Misbegotten”).
In Season Three the team discovered Asuras and the Replicators, and narrowly averted an attack on the city (“Progeny”). Dr. Weir was infected with Replicator nanites (“The Real World”), Sheppard was captured by Commander Kolya (“Common Ground”), and McKay was reunited with his estranged sister, Jeannie (“McKay and Mrs. Miller”).
A ship of Ancients returned to reclaim Atlantis — only to themselves be wiped out by the Replicators (“The Return”). The team found a laboratory where Michael was experimenting on human beings (“Vengeance”), and a freak accident cost the life of Carson Beckett (“Sunday”).
As the season ended, Earth fly-overs discovered that the Replicators were building a fleet of warships. Believing that Atlantis and even Earth was their target, they launched a preemptive strike that devastated the planet (“First Strike”). The Replicators retaliated, sending a satellite weapon to attack Atlantis with a sustained energy beam. The only way to save the city was to fire up the star drive and leave the planet. During the exodus, Elizabeth Weir was critically wounded.
NEXT: Season Four