The Wraith invasion of Earth has been defeated, and the city of Atlantis has settled to the surface of the Pacific just off San Francisco. The team assumes that this is a temporary respite before the city returns to Pegasus, but it becomes clear that the IOA and its member governments would like to keep the city on Earth. Woolsey recruits Teyla to be “the face” for the people of Pegasus, and she and the rest of the team throw themselves into the unfamiliar political arena. Despite their best efforts, the IOA’s decision goes against them: Atlantis is to remain on Earth, to be slowly dismantled for its technology.
This hits the team hard, but there seems to be nothing left that they can do about it. Rodney McKay resigns in a temper, and takes a job at Area 51; Jennifer Keller goes with him, and they begin to build their new life together. Colonel Carter, now in command of the George Hammond, begins siphoning off the cream of Atlantis’s military personnel for her new ship; she also invites both Ronan and Teyla to join her team, as advisors. John Sheppard is left in limbo. There’s no place for him on the Hammond, and neither Woolsey nor Jack O’Neill will accept his resignation. The only good thing about still being on the city is that he is able to thwart the IOA’s attempt to take Guide, the captive Wraith known as Todd, for medical experimentation. Instead, John and Carson Beckett succeed in putting him into stasis, but that is only a temporary solution.
O’Neill, however, has one last card to play. As Atlantis has landed in US territorial waters, he claims the city for the United States, and in the ensuing uproar, the IOA agrees to send Atlantis back rather than see it fall into the sole possession of any one country. Woolsey resumes command, and the team reassembles to prepare the city for departure before the IOA can change its mind.
Atlantis lifts from Earth, and begins the long trip to Pegasus. Despite the shortened preparations, everything seems to be going well — until a hyperdrive emitter fails, throwing them out of hyperspace and using up nearly all of the power in their ZPM. There is a single planet close enough to reach at slower-than-light speeds. It’s a cold world without a Stargate, but it’s their only choice. After a difficult flight, John successfully lands the city, but there’s not enough power left in the ZPM to move the city or gate back to Earth.
The crew reestablishes contact with their old allies in Pegasus, only to discover that things have not been going well in their absence. The Wraith have united under a new queen who calls herself Death, and they have destroyed a number of human worlds. As the team investigates the devastation on one such planet, Todd manages to escape, only to discover that he has lost control of his alliance and has only a single hive under his command. In a bid to weaken Queen Death and regain his former power, Todd informs Atlantis of the location of the queen’s next great attack.
Trusting Todd is always a gamble, but John sees this as a chance to stop Queen Death in her tracks. The team travels to the planet Levanna, where they join with the local ruler and a detachment of Genii to wait for Queen Death’s attack. The Wraith arrive in force, Darts and drone infantry backed by a hiveship in orbit. The battle is close and hard fought, but at last the Wraith retreat. For the first time, Queen Death has been defeated, and even it if it’s only temporary, it’s a boost for humans throughout Pegasus.
However, Queen Death’s response is rapid and devastating. Atlantis receives a distress call from New Athos, warning of a Culling. John leads the team through, only to find — nothing. There has been no attack; everything is perfectly normal in the settlement. As they try to figure out what happened, the Wraith attack in truth — and the Darts target Rodney. Before the others realize what’s going on, the attackers have snatched up Rodney and have vanished back through the gate.
Their first desperate searches turn up nothing, and the team splits up to pursue two sets of leads with two sets of reluctant allies.
John, Teyla and Carson Beckett meet with the Genii leader Ladon Radim, who promises them the aid of his spies all over the galaxy if they will help him with a project of his own. The Genii have found an Ancient warship that had crashed on a remote planet. Genii salvage teams have been repairing it but they need someone with the ATA gene to fly it back to the Genii homeworld. John agrees that they will accompany Radim’s sister Dahlia and bring the warship back to the Genii in exchange for their help. Unfortunately, the Wraith ambush them, forcing them to make a long hike across a hostile desert to reach the warship. An attack by carnivorous lizards leaves Teyla and Carson injured, and John questioning his own judgment about his rash decision to do this without consulting Atlantis or getting additional personnel — this is too much like the mission in Afghanistan that cost the life of his friend Holland many years ago.
Meanwhile, Ronon and Jennifer have been sent to meet with Todd on a world controlled by Wraith Worshippers. Despite Todd’s assurances that the Wraith consider this world neutral ground, all bets are off when Queen Death’s people arrive and Ronon and Jennifer are forced to hide in a tomb. One of the Wraith Worshippers double crosses Todd and tries to kill them, thwarted only by Jennifer’s quick thinking. Ronon blames Todd, but he assures them he is no fonder of Queen Death than they are, and says that he will let them know if he finds out anything about Rodney’s fate. They must be satisfied with that, desperate as they are to save Rodney.
At the same time, Rodney is in a situation that’s far more horrific than his friends have imagined. Queen Death’s men have reverse engineered the retrovirus created by Dr. Beckett that turned a Wraith into the human the Atlantis expedition called Michael, and Rodney is now a Wraith! Known as Quicksilver, and believing himself to be fully part of Queen Death’s court, he is now bending all his attention to helping the Wraith conquer Atlantis.
After a dangerous flight home, John returns to Atlantis with his team and the badly damaged Ancient warship. Shortly thereafter Sam Carter arrives in Atlantis with the George Hammond. When Todd contacts Atlantis and tells them where Queen Death’s ship will be powered down briefly for repairs, it seems like a good time to attack and retrieve Rodney. However, the mission goes wrong when Rodney, believing he’s a Wraith, resists the attempts of the team to rescue him. He stuns John and as the hive ship powers up, Sam beams off John and the rest of the team before they can be captured. But Rodney is still in the hands of the Wraith, and now Atlantis faces a more dangerous foe than ever before — their own man, turned against them.