With the team still trapped in what remains of Michael's compound, and Teyla still in Michael's hands, Colonel Carter must hurry to rescue them before the game of 'Lantean in the middle' takes an even more deadly turn. So when someone asks, "How much worse can it get?" you just know that things are not going to go according to plan.
When the IOA replaces Carter as the head of the Atlantis Expedition, and the first thing that happens is the alienation of long standing allies, in spite of Sheppard's best efforts, trouble can't be far behind. Woolsey's command is given a baptism of fire when the Alpha team is ambushed off world, and hampered by a lack of intel they truly are on their own.
The team continues to battle the Wraith. Teyla wakes in the infirmary on Atlantis. She has no memory of what Michael has done to her; knows only one thing: he has her son. Upset by repeated attempts at debriefing, because she cannot - or will not, as certain expedition members insist - tell them what happened, what will she do when Woolsey pushes her too hard... too far?
The conflict escalates between the Wraith, Michael's army, and the Atlantis expedition. The stakes have never been higher for any of them, nor the price of failure more costly. Teyla must fight to find her way to the truth, while others find the truth concealed from them, and two powerful enemies come to blows when one is forced to assume the mantle of the other.
Atlantis' new member of staff proves an unwelcome interference in verifying disturbing Intel on the Wraith. Sheppard's regular contact, kept too busy by his Queen, is of no use and, already frayed, tempers reach boiling point. Teyla participates in a potentially deadly meditation to unlock her memory. Will she discover the truth is a key to freedom – and a desperate cry for help?
Ronon receives what he believes is a call for help from Teyla's people and, rushing to help, he finds the settlement destroyed, and Teyla herself in the hands of the enemy. It falls to him to save her from the darkest of fates, but in doing so, will Ronon be able to save himself from ghosts of past and present, and will what's left of the team, caught up in events, be able to avert disaster?
Cornered in a narrow gully on a planet with three Stargates, Ronon, Mckay and Sheppard find their only escape is through the third Gate. What they find as they step through the wormhole is not at all what they expected and with everything, stacked against them, how will they manage to find their way safely back to 'Kansas'?
Keller works with Todd to cure Sheppard, but the research reveals a course of action, wherein ethics and loyalties become strained. With teams caught in the escalating conflict between Michael's forces and the strengthening Wraith Alliance, some in the team begin wondering just how much of what they saw in the alternate universe could come to pass in their own.
When Teyla learns that Michael is in Wraith hands many old feelings surface, and hoping to bring herself peace, she returns to Atlantis to ask for help in ending her conflict once and for all. Sheppard and the team join her in the mission to recapture Michael from the Hive, but things go terribly wrong, and though Teyla's struggle is ended, it is not at all in the way that anyone intends.
Sheppard and co relentlessly pursue the Hive responsible for Teyla's death, believing Todd to be behind the attack. The Elder Queen and her Wraith struggle to rebuild after their defeat. Meanwhile, Michael begins to undo the harm he suffered in Wraith captivity, and formulate the next step for The Cause. Each must decide where lie their loyalties, and for some, that means irrevocable change
Sheppard and the others aboard the Daedalus relentlessly pursue those he feels responsible for the death of their lost companion. Meanwhile Michael, under threat from the Wraith has gone to ground in order to keep Teyla safe. Back on Atlantis, Beckett grows increasingly more worried for Keller, and prepares to take an utlimate, personal risk in order to save her.
On the brink of death, Todd risks an untested serum and is thrust into a spiral of madness and instinct. Meanwhile, Kenny must persuade the inhospitable Wraith Sentinels to transfer the Queen's young to the Nursery facility. On Atlantis, Haddad continues the desperate race to save Keller, that may lead her to follow Beckett into the deepest peril she has yet faced.
Wraith Hives gather under the protection of Atlantis. Ronon returns with refugees, and the team has to investigate. Beckett returns from Michael with a treatment that could save Keller and a disturbing truth behind her condition - a truth that Michael diagnosed, and Haddad, still facing issues of her own, guessed. When matters come to a head, who will be left standing?