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.

Cable and Hope stop at a nearby grocery store to procure food and supplies. After tying up some of the customers and the employees, Hope becomes distracted with a hair brush set. This angers Cable, which in turn upsets Hope. They quickly steal a car from the parking lot and they leave. Meanwhile, Wolverine (after killing the last surviving member of the Sapien League who were pursuing Cable and Hope), X-23 and Angel reveal to Nightcrawler, Colossus and Psylocke the existence of X-Force and Cyclops' involvement. Nightcrawler is furious and attempts to quit then and there, but he is convinced to stay by Colossus. On Utopia, Cyclops makes psionic contact via Emma Frost's telepathy and is appraised of the current situation by Wolverine. Nightcrawler demands to know from Cyclops if what he has learned from Wolverine about X-Force is the truth. After a second of hesitation and some urging from Emma, Cyclops tells him yes, but also to tells him that if he has issues over his decisions, to take it up with him after Cable and Hope are found and not while they are in the field. Nightcrawler reluctantly complies. Cyclops then makes contact with the New Mutants and sends them to a facility in St. Louis where Cameron Hodge has been manufacturing anti-mutant weaponry and orders them to destroy it. He then gives Cypher the task of locating Cable and Hope. Meanwhile, Bastion dispatches Stryker and the Purifiers to find and kill Cable. He then requests a status report on a mysterious series of towers he is building.

As the Alpha Team (Wolverine, X-23, Angel, Colossus, Nightcrawler, Psylocke and Magik) battles Stryker and his Purifiers, Magik makes her way toward Hope, under orders from Wolverine to teleport her to Utopia. But before she can do so, one of the Purifies fires on her with some sort of supernatural weapon that opens a portal to Limbo she cannot control and she is drawn into it by a cluster of demonic tentacles. Subsequently, they incapacitate Nightcrawler with disorienting weaponry to prevent him from teleporting. Cable, realizing something is seriously wrong, abruptly leaves with Hope. The remaining Purifiers attempt to pursue, but are all killed by Archangel, who transforms into his Horseman persona. On the road, Hope asks why Cable pulled them away from the Alpha Team and he tells her that says that Bastion must be tracing them somehow and believes there is a spy within the X-Men.

Cyclops assigns Ariel as teleporter for the X-Men's Alpha team, following the disappearance of Magik during battle. While traveling with Wolverine and X-23 in search for Hope, their vehicle is destroyed by a missile fired from a fighter plane that had been tracking them. As Archangel destroys the plane, Wolverine and X-23 survive the explosion due to their enhanced healing factors, but Ariel dies in the attack. Rogue is able to sense Hope's presence, like Destiny prophesied, although neither she nor Emma Frost can explain it. Meanwhile, the New Mutants download data from Bastion's base. Cameron Hodge and his whole army of "Smileys" are killed by Warlock of the New Mutants at the behest of Doug Ramsey when his lifeforce and the lifeforces of the Smileys are forcibly absorbed by Warlock via their shared connection of the techno-organic Transmode virus. As a result, Karma, who had one of her legs severed by Hodge, is saved. However, before meeting his demise, Hodge manages to trick Cannonball by using Karma as a human shield and knocks him unconscious. Hodge dumps Sam into a hole, announcing that "This is what's in store for all of your tainted bloodline. This is how it ends".

The New Mutants warn Cyclops of Bastion's towers, and he orders them to come home. Shortly after, Cyclops loses contact with the Alpha and Beta teams. The Alpha Team has been attacked by armored soldiers and a jet; in response, Psylocke telekinetically sends X-23 to the jet to commandeer it. Meanwhile, Nightcrawler, Rogue, and Hope arrive in Nevada. Despite being exhausted, Nightcrawler refuses to let Rogue borrow his powers so she can save her strength and protect Hope if something goes wrong. Bastion himself suddenly appears before them and Rogue engages Bastion in a deadly battle. However, Rogue is brutally beaten and Bastion turns his sights on Hope, whom he intends to kill because he is aware of the world that will come to be as long as she exists. Just as Bastion extends his arm to kill Hope, Nightcrawler teleports between them and is impaled in the chest as Rogue witnesses the event in despair. Nightcrawler asks God to strengthen him for one last jump; he lands on the rocks in Utopia and tells Hope that he believes in her before he dies.

With Pierce dead, Cyclops and the other X-Men have begun to uncover Bastion’s ultimate plan. With no teleporters, no planes, and no Cerebra, Cyclops announces that they are trapped on Utopia. Meanwhile, the X-Club Science team are caught in a trap of their own as they recover from the oil rig explosion. Through a conversation between Dr. Nemesis and the others, it is revealed that they are stranded just outside of San Francisco and Utopia. Back on Utopia, Hope is shown attempting to shake off her encounter with Mirage, while Cable attempts to counsel her. After repeating that she was never ready to return, Hope tells Cable that all of the pain and suffering inflicted upon the X-Men by Bastion is her fault. Hope also warns him that it is only going to get worse. Cable tells her that monsters like Bastion are not going to stop killing mutants just because she leaves. Cable then tells Hope that fanatics do not quit until the job is done, and the question is…does Hope? Suddenly, an offshore explosion rocks Utopia sending X-Men reeling. When the X-Men gather near the Bay, they find a massive dome of energy enveloping both San Francisco and Utopia. The X-Men quickly attempt to destroy the dome, but to no avail. Namor appears and informs Cyclops that the energy dome also descends into the ocean floor. Meanwhile, at Bastion’s base he is treated to a hero’s welcome and congratulated on the success of his plans and the death of mutantkind by his human council. Bastion calmly orders them to stand down and dismantle their forces as he will no longer need them.

With an army of Nimrod model sentinels’ continuing to emerge from Bastion’s time portal, a massive battle between the X-Men, their allies and Bastion’s forces ensues. The X-Men emerge from this battle victorious, but with several X-Men severely injured. As Cyclops surveys the damage, he orders the strongest members of the X-Men to guard the portal and prepare for another attack (among them are Namor, Colossus and Rockslide). Meanwhile those injured during the attack are quickly ferried back to Utopia. Then scene then shifts to Bastion and Stephan Lang, who discuss Bastion’s master plan. Bastion tells his minion that the host of Nimrod sentinels faced by the X-Men was only a scouting party. On Utopia, Cyclops gathers the core X-Men and briefs everyone on the state of things following the battle. Through their discussion it is revealed that Vanisher is reported missing in action, Iceman was severely burned and that Hellion has lost both of his hands. During the briefing it is also revealed that while San Francisco has descended into a state of panic, the residents have all chosen to fight with the X-Men. Next Beast explains that Bastion’s portal is powered by an unknown energy source and made from an unknown origin. Beast also notes that the portal is temporal in nature connecting them to another period in history (which is strongly implied to be the Days of Future Past reality). It also blocks telepathy, most of the technology available to the X-Men. Beast also reveals that he had Namor attempt to put his hand through the portal resulting in him being blown across the bridge. Prodigy of the New X-Men team scans the portal again and discovers that there are at least 170,000 Sentinels waiting on the other side. Horrified and overwhelmed by what he has found, Prodigy then begins to break down. Wolverine responds by yelling at him and telling Prodigy to get a hold of himself or he will kill him. Before Prodigy can respond enraged, Rogue steps between them and angrily tells Wolverine to back off. With the tension in the room reaching critical mass, Domino appears and lightens the mood with a clever one liner directed at everyone present. With the X-Men still recovering from everything that has happened, Cyclops begins to formulate a new strategy which hinges on Cable. Cyclops explains that because Cable has one last time jump left he will send a team of X-Men to the future to deactivate the sentinels. Beast angrily objects to the plan stating that due to the number of Nimrod Sentinels on the other side of the portal, there would be no way for a team of X-Men to survive, much less complete their mission. Cyclops counters Beast’s argument by reminding him that they have a resurrected Cypher on their side, who can speak the sentinels’ computer language and shut them down. Wolverine reminds Cyclops that while Cypher is powerful, he is not immune from things like bullets. Moonstar interrupts Wolverine calling Cyclops’s plan a glorified suicide mission and demands to know who else will be going to their deaths. Rogue volunteer’s stating that her ability to absorb several mutant powers at once would make her an invaluable part of the team. Cyclops refuses to let her go and explains that he has chosen to send X-Force. For a few moments everyone is silent, contemplating what Cyclops has said, finally Storm confronts Cyclops and asks him what he meant by X-Force. Beast takes the opportunity to inform everyone present that since he took over leadership of the X-Men in the wake of Messiah Complex, Cyclops has been using a covert black ops team of mutants to hunt down and kill enemies of the X-Men. A stunned and disgusted Storm then asks him if what Beast has said is true. Calmly, Cyclops admits to everything. Storm then demands to speak with him privately, Cyclops refuses but promises her that if they survive he will answer for everything he has done. With everything out in the open Cyclops orders the X-Men to carry out his various plans. To that end, Psylocke begins leading the people of San Francisco as far away from the bridge as possible. Meanwhile Rogue starts transporting all of the wounded down to the Alantean column. Cyclops then sends all battle worthy mutants to the portal and tells them to prepare for another attack. As Cyclops gives his orders scenes showing Beast overlooking Iceman, Mercury comforting a crying Surge and X-23 attempting trying to hold Hellion are shown.

An enraged Hope confronts Cyclops over his decision to send X-Force on a suicide mission into the future to stop the Sentinel invasion of Utopia at its source. Cyclops tries to calm her down, but Hope will have none of it, and furiously states that she hates him and runs off. Emma remarks sarcastically how well dealing with the situation went, but Cyclops ignores it and asks Emma if she had taken note of Hope's eyes, which had been glowing red with energy during the argument. Meanwhile, the Fantastic Four arrive outside of Bastion's dome and confer with the X-Club and the Avengers to formulate a strategy to disable it and to aid the X-Men. On Utopia, Cyclops conveys a status report to the other X-Men via Emma's telepathy and instructs them to use their familiarity with the neighborhoods and surrounding areas of San Fransisco to their advantage and to fight the Nimrod Sentinels more effectively. As he breaks contact, another Nimrod approaches Utopia and breaches its outer wall. Cyclops quickly shuts down several levels of the complex except for those most crucial and the resulting explosion from doing so destroys the Nimrod. Within the city, Storm, Surge, Iceman, Psylocke and Fantomex manage to destroy several Nimrods between them through coordinated efforts, while at the Port of Oakland, Namor fights several more by himself, but calls in for assistance as five more suddenly appear. Elsewhere, in the future, Cable, Cypher and the rest of X-Force find themselves in the middle of the Sentinel Processing Center. Cypher then notices a wall with a large poster spread across it, tallying the status of dozens of mutants as “Slain”, including all of them. Horrified and furious, Archangel tears the poster down. As Wolverine and Cable try to calm him, X-23 declares that the only way to prevent this future from coming to past is to kill everyone responsible, then return to the past and prevent it from happening again. Wolverine states that if they are supposed to be dead in this future, then the Sentinels will have no idea how to fight them effectively. Before they can react further, an anti-mutant assault team arrives and attacks, but they are quickly dispatched before they can report back to the Sentinels. After analyzing one of the assault unit's vehicles, Cypher determines that the Sentinels are sending the Nimrods back through the portal five at a time. Cable then says that they will fight their way into the processing center and will not come out until the future is razed and the past is saved.

A heavily injured Magneto uses his powers to battle a horde of Nimrods in an effort to buy Beast time to treat the wounded. Meanwhile, an overwhelmed X-Force is engaged in an epic battle of their own as they attempt to protect Cypher and Cable while they both attempt to deactivate Mastermold. In the present a battle weary Storm takes command of Legion and the remaining X-Men, taunting the Nimrods emerging from the portal and drawing their fire. Unfortunately, her ploy works and the Nimrods adapt to her powers and quickly subdue her. Before they can finish her off, Hope and Rogue appear and drive them back. Hope is able to destroy most of the Nimrods present with a weapon from the far future given to her by Cable. Meanwhile, Emma Frost informs Cyclops that Hope has joined the battle prompting him to head for the frontlines in an effort to retrieve her. On Utopia, Magneto manages to bait a trio of Nimrods trying to finish him off into landing, once the Nimrods land, Magneto uses his powers to create iron spikes and impales all of them. As the Nimrods smolder, Magneto informs them that all of Utopia is made of metal and as such they will never defeat him. Back in the future, Cypher and Cable continue to battle Mastermold. Just as things seem hopeless, Cypher finally manages to break through Mastermold’s programming and assimilate its mind. In the process of assimilating Mastermold, Cypher comes to a better understanding of his existence and takes complete control of every sentinel in the future and the Nimrods in the present. As all of the Nimrods suddenly shut down, the X-Men are seen staring in shock and attempting to understand what has happened. Their mission completed, X-Force retrieves Cable and Cypher and make their way to the time portal to escape back to the present. Unfortunately, in the ensuing chaos X-23 is brutally burned when she attempts to cross through the time portal. The members of X-Force come to the conclusion that only inorganic matter is able to pass through the portal. With no other alternative, Cable informs the other members of X-Force that he has an idea and that it will cost them dearly.

After destroying Bastion, Hope falls to the ground passing out as she cradles Cable's severed arm. She later awakens at the medical bay as Beast is mending Colossus's broken arm, after a brief check on Hope, Beast checks on the progress of Archangel's damaged wings as Dr. Nemesis examines them, meanwhile Dr. Rao tends Iceman's injuries, while Madison Jefferies fashions a cybernetic prosthetic leg for Karma. Magneto converses with Hope about her battle with Bastion, which is interrupted by Hellion who is angered over the loss of his hands, but quickly ends his tirade after an intimidating glare from Magneto. The X-Men hold a funeral for Cable, Cyclops attempts to present a eulogy to his son but is unable, Hope steps in stating that Cable as a soldier lived and died as he would have wanted, on his feet. After the funeral Cyclops reprimands Rogue for bringing Hope into battle and jeopardizing the mission, he removes her from the combat roster but assigns her to help Hope cope with the recent events. Storm finds Wolverine drinking in Kurt's old room, Storm discussing her displeasure with Wolverine and Cyclops actions with X-Force, involving the likes of Wolfsbane, Warpath, and X-23. Wolverine tells Storm that if he could do it all over again, he would kill even more people if it meant Kurt would still be alive, much to Storm's discontent. Wolverine later tells X-23 that she's out of X-force and that she needs to find her own path in life rather than continue to take orders. Cyclops and Wolverine discuss the other X-Men's feelings about X-Force, which he decides to disband believing that it has no place in the X-Men's future. Wolverine attends a secret gathering of a new X-Force team, consisting of Psylocke, Phantomex, Archangel, and Deadpool, stating that no one can know of their existence as a team.