Several strange events in Atlantis - the crash and subsequent sabotage of a satellite that McKay believes was built by Replicators, and Sheppard's discovery that he can heal improbably quickly from injuries - put Sheppard, McKay, Teyla and Ronon on their guard.
After Dr. Keller dismisses Sheppard's self-healing with suspicious carelessness, he and Teyla run their own medical tests and learn that their bodies can heal quickly because they are swarming with Replicator nanites. Meanwhile, McKay discovers that Atlantis's scanners show only five human life-signs - Sheppard's team, plus one - even though the city appears to be full of people.
When McKay and Ronon investigate the fifth life sign on the city's outskirts, they're shocked to find Elizabeth Weir, disoriented but alive.
Just then, the team is confronted by Dr. Keller and Maj. Lorne, who reveal that this isn't the real Atlantis. Keller, Lorne and most of the Atlantis personnel are actually renegade Replicators who are pursuing the spiritual process of Ascension.
Because they believe that they must study humans as part of this process, they have populated a duplicate Atlantis with duplicate flesh-and-blood versions of Sheppard, Weir, McKay, Teyla and Ronon. They've been given the memories of their real counterparts (stolen during mind-probes when the real team was once captured) and infused with nanites to keep them healthy.
The Replicators tried to prevent the duplicate team from finding out that they weren't real, but events have exposed the truth. As if that isn't shocking enough, Keller adds that the real Weir died at the hands of her Replicator captors.
As the team, now locked in a cell by their creators, struggles to absorb all this, the planet comes under attack. The renegade Replicators have incurred the wrath of their mainstream brethren, who have come to wipe them out. Hurriedly, Weir talks Keller into demonstrating compassion - an essential trait for Ascension - by setting the humans free. Liberated, the team escapes as the Replicators battle each other.
The duplicates contact the real Atlantis and invite their counterparts to a meeting on a neutral planet so they can share the Replicator intel they've gained. The real Sheppard, McKay, Teyla and Ronon are grieved to learn of the original Weir's death ... and unnerved by their duplicates. For her part, Weir is pensive, convinced that she and the other duplicates face an uncertain future, because they can never fit in at Atlantis.
Then a fleet of Replicator warships arrive. They've tracked down the escapees and plan to kill all the humans, original and duplicates alike. Weir's musings must take second place to a life-or-death fight.