Atlantis escaped the Replicator attack, only to find itself floating in deep space with its power running out (“Adrift”). The expedition’s only hope was to take a Puddle Jumper on a covert mission to the Replicator homeworld and steal a Z.P.M. Thanks to help from Dr. Weir, whose life was saved by reactivating and reprogramming the dormant Replicator nanites still in her system, the mission was a success. But Weir herself was lost, allowing herself to be captured by the Replicators so that the rest of the team could escape (“Lifeline”).
The team also managed another major victory — reactivating the base directive that causes the Replicators to attack the Wraith. A war broke out between Atlantis’s two greatest enemies.
It wasn’t long before an old “friend” of Colonel Sheppard’s — a Wraith scientist they would come to know as “Todd”, who shared a Genii prison block with Sheppard a year earlier — brought them devastating news. The Replicators had began destroying human populations, in order to eliminate the Wraith’s food supply (“The Seer”). Todd and Atlantis’s scientists worked together for weeks to find a way to disable the base directive.
They were finally unsuccessful, but an all-out assault by allied human, Wraith, and Traveler forces (with vital intel from the rebel Replicator faction) managed to destroy the Replicators and their entire home planet (“Be All My Sins Remember’d”). Only a single ship of rebels survives (unbeknownst to Atlantis) — led by a version of Dr. Weir herself.
With the Replicator threat neutralized, the Wraith returned to their in-fighting. Atlantis’s attention was soon occupied by a mysterious new virus affecting human population centers in the Pegasus Galaxy, with a mortality rate of some 30 percent. The conclusion was unmistakable: someone was randomly spreading the Hoffan drug (created three years earlier with help from Carson Beckett) to taint the Wraith’s food supply. Never knowing if their next meal would be their last, the Wraith turned to Atlantis for help. Todd made contact.
Soon they learned who was responsible: none other than Michael himself, who had also kidnapped the Athosians for his experiments (“The Kindred, Part 1”). With help from a cloned copy of Carson, Michael had made great strides forward in his hybrids, engineering a small army of followers. All this he revealed to Teyla, after kidnapping her.
Now Michael plans to deliver her baby, and use him for his own ends. Since both Teyla and Kanaan have “the gift” — Wraith DNA that allows them to telepathically link to and even influence other Wraith — their child is unique and absolutely indispensable for Michael’s hybrid plans. Meanwhile, the team rescued Carson’s clone, but was forced to put him into stasis when they learned that he cannot survive without the regular injections Michael was giving him (“The Kindred, Part 2”).
The future of the Pegasus Galaxy hinges on whether or not Michael gets his hands on that baby, as Sheppard learned when he was accidentally sent into the future (“The Last Man”). Though he returned home with a lead on Teyla’s whereabouts, a booby trap brought Michael’s laboratory down on the entire team.
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