The story opens one year ago at the ruins of the Xavier Institute, which is marked as a no trespassing zone by order of H.A.M.M.E.R. The scene moves forward to the present day as Cable and Hope arrive in the midst of the wreckage. Cable is understandably confused at the state of the Institute and realizes something has happened. Hope is visibly upset and fears the X-Men are dead. Before they can react further, Cable and Hope are attacked by members of the Right. Meanwhile on Utopia, the X-Men are assessing the death count of Selene's attack, declaring Onyxx, Meld and Diamond Lil among those slain. Cyclops says that every attack on Utopia could end in death and that they have to hold out. Doctor Nemesis says that it's too late for that and that the mutant populace is too low to perpetuate the species. He states that at the rate of deaths they are sustaining, mutantkind has seven years left at most. After the meeting, Cyclops lashes out in frustration and blasts a hole in the conference room roof with his optic blasts. After he does, the Stepford Cuckoos arrive and tell Cyclops that Cerebra has picked up Cable's return to the present. Although Cerebra did not detect Hope's presence as well, Cyclops knows that she is with him and dispatches Domino and Vanisher to San Francisco, assigns Rogue and Namor to protect Utopia, sends the New Mutants (Cannonball, Mirage, Karma, Magma, Sunspot, Cypher and Warlock) to the Midwest in the Blackbird and his Alpha roster (Angel, Colossus, Nightcrawler, Wolverine, Psylocke and X-23) along with Pixie and Magik to the Xavier Institute. Elsewhere, Cable and Hope defeat the Right assault troops, but are then confronted by members of the Sapien League and forced to flee in a stolen vehicle.
Cyclops and his team arrive at the Institute, via Magik's teleportational powers and find the dead Right troopers, but no sign of Cable and Hope. Wolverine picks up on their scents and Cyclops reemphasizes to them Hope's importance to mutantkind's future. Elsewhere the Sapien League have caught up to Cable and Hope. As they are about to open fire on their car, the X-Men arrive and attack the League, distracting them long enough for Cable and Hope to escape. Psylocke tries to psionically scan the minds of the League members the X-Men captured, but they are technologically shielded from her probes. Wolverine threatens one of them, demanding to know how they are tracking Cable and Hope, but he refuses to talk. X-23 then brutally executes another member by stabbing her claws through his head before the horrified eyes of the surviving League member and Nightcrawler. Wolverine's captive begs for mercy and tells him he has no idea how and that someone is sending them locations. Psylocke and Nightcrawler realize that Wolverine, Angel and X-23 are keeping something from them and demand answers.
Meanwhile in Washington, DC, Bastion receives status reports from Stephen Lang, Bolivar Trask, William Stryker, Graydon Creed and Cameron Hodge, stating that their forces are assembled and at his disposal. Bastion tells them that the Mutant Messiah has returned and gives them orders to kill her.