Ronon Dex is captured by Tyre, who wants to hand him to the Wraith in order to maintain his role in their circle. However, when the deal turns sour, and Tyre is left for dead, the Atlantis expedition persuade him to take back their friend. Meanwhile, The Wraith turn Ronon into a Wraith worshipper.
The Atlantis expedition mysteriously finds the Daedalus, abandoned and drifting in space. When Lt. ColonelJohn Sheppard's team come to investigate, the ship mysteriously disappears. They soon discover that the ship is actually an alternate Daedalus from a Alternate reality, and the team must find a way back to their Universe or risk being stranded forever in an unfamiliar reality.
While on a mission, Lt. ColonelJohn Sheppard's team inadvertently brings a mysterious entity to Atlantis. They soon learn that the entity is nothing more than Dr.Elizabeth Weir, who was thought to have been killed after her capture by the Asurans.
Dr.Carson Beckett is called in to help a team investigating a lab that once belonged to Michael Kenmore. But soon, they realize that a group of experiments that even Michael couldn't control are hellbent on killing the team.
Dr.Jennifer Keller is kidnapped by a runner named Kiryk. While Dr.Rodney McKay and Ronon Dex tracks them, Kiryk takes Keller to a seriously injured young girl. She must do it fast, since the Wraith have found him, and are hunting them down.
Dr.Daniel Jackson arrives in Atlantis to investigate a hidden lab left behind by the rogue Ancient scientist Janus. Their discovery has attracted the attention of a mysterious group of aliens, who infiltrate the city. Meanwhile, "Todd" and a delegation arrive on the Daedalus to bring forward Dr.Jennifer Keller's gene therapy.
As Dr.Rodney McKay and Dr.Daniel Jackson is held prisoner by the Vanir, they make a startling discovery about who they really are. Meanwhile, "Todd" and his Wraith hijack the Daedalus to find and destroy those who activated the Attero device. The Travelers arrive and Lt. ColonelJohn Sheppard must help them get to the planet before "Todd uncovers a way to discover the device for good, even if it means sacrificing McKay and Jackson's lives to do so.
Dr.Carson Beckett, now a traveling doctor in Pegasus comes across a planet, where some of the villagers are refugees from Balar, a planet infected with the Hoffan drug, and destroyed by the Wraith. However, the Wraith arrive on the planet and gives the village an ultimatum, hand over the Balarians, or face destruction of the entire civilization.
Dr.Rodney McKay reluctantly returns to Earth to witness the triumph of his rival Dr.Malcolm Tunney, but must help shut down a deadly weather device when the new technology goes horribly awry.
Dr.Jennifer Keller's body is inadvertently taken over by a cunning thief, Neeva Casol. While Neeva tries to escape Atlantis, Keller finds herself imprisoned with a death sentence on another planet, forcing the team into a race against time to return Keller to her original body before she is put to death.
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