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.
Uncanny X-Men Vol 1 523 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. Cable and Hope arrive at a small motel where Hope is delighted to see a small refrigerator full of food and a real bed after so long. Cable then reads a newspaper where a headline reads that San Francisco has welcomed the X-Men back with open arms. He then decides it is there that they must go next. Later on as Hope finishes taking a shower, Cable apologizes to Hope for his outburst earlier and presents her with the hairbrush set she had been admiring earlier. She emerges from the bathroom a few minutes later in a new green and gold outfit, reminiscent of Jean Grey's original Phoenix costume. She finds Cable connected to the telephone and its local landlines through his cybernetic arm, gathering information. Suddenly the connection goes dead and all of the power and the lights in the area shut down as well. Outside, William Stryker orders the Purifiers to move in for the attack and to kill anyone (including civilians) who tries to flee. Cypher detects the dead zones area and reports to Cyclops, who then relays the information to the Alpha team. As a firefight between Cable and Hope and the Purifiers breaks out, Wolverine and the others arrive to help them. At the same time, the New Mutants arrive at Cameron Hodge's facility and move in for the attack.
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. In St. Louis, the New Mutants begin their attack on the Right's weapons base. As the team tears their way through the base, Cameron Hodge takes matters into his own hands to stop them and plugs himself into a replica of his old battle armor (from the X-Tinction Agenda) and confronts the New Mutants. On Utopia, as Danger is checking the status of some of the prisoners in detention, Rogue somehow manages to hear Hope's thoughts. Meanwhile in battle with Cameron Hodge, Karma is severely injured.
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". Wolverine's team find Cable and Hope and after a short confrontation with another group of Sapien League members, the X-Men and Cable decide for a diversionary tactic. Cable remains behind with some of the X-Men, after learning from the New Mutants that Cable was being tracked, while Rogue, Nightcrawler, and Hope leave in order to protect the girl. To that end, Rogue absorbs the power sets of Colossus, Wolverine, X-23, Angel and Psylocke. Logan subsequently announces that it's time for their next mission.
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. When the Alpha Team returns to Utopia, Colossus wants Pixie to rescue Magik from Limbo. When Psylocke notices the look on Cyclops and Emma's faces, she simply asks "Who?", though Wolverine already knows the answer: "Elf". In Nevada, Bastion repairs himself and tells his followers to prepare for Plan B.
Col. Moran of the Mutant Response Division is briefing on the futility of mounting a direct assault on X-Factor HQ due to the intervention of heroes responding to collateral damage, thus exposing Bastion's agenda. When Trask begins to act self-righteous in response, Moran points out that X-Factor is a business and has broken no laws, giving the MRD nothing to respond to. Bastion begins to speak through Trask, but Trask resists. Moran may disagree with Trask, but he respects the chain of command and will follow orders to take out X-Factor. Later, One of the MRD agents has an idea to lure X-Factor away from the city by hiring them for a job. Meanwhile, another MRD unit has been dispatched to South America to kill St. Croix and Strong Guy, only to find Strong Guy fighting Baron Mordo, who had apparently drained St. Croix's energy. The MRD attack Mordo unaware of his background and incite his Wrath. Back in the US, Madrox and his team are following Titania, whose husband, the Absorbing Man, suspects of adultery. Arriving at an isolated cabin, Madrox notices that Titania is waving good-bye to him, not noticing the multiple laser sights on his forehead. Suddenly their car is riddled with bullets, apparently killing everyone inside. MRD agents sweep the car, confirm their deaths, and Moran states that they just "need to nail the ones in South America and Ireland and we can call it a day."
In the aftermath of Nightcrawler's death on Utopia, Hope is introduced to Cyclops as Cable's father, much to her amazement. Back in the war room, the X-Club is preparing to retrieve Magik from Limbo while the rest of the mutants determine the purpose of Bastion's towers. Later, Hope and Cable are examined in the infirmary, where she meets Kitty Pryde and Magneto, who expresses his cynicism of Hope's destiny as the 'mutant messiah'. Meanwhile, Danger is checking on her prisoners, not noticing Donald Pierce is missing. Pierce apparently allowed himself to be captured so that he could sabotage Utopia's defenses including Cerebra, communications and general security. Bastion, now having the appearance of Archangel, gives him further instructions to destroy all vehicles to isolate the mutants on Utopia, giving him directions to the hangar. As evening falls, Nightcrawler's funeral is held, with Beast arriving to place blame on Cyclops' shoulders. After the eulogy, various X-men remember ways Nightcrawler touched their lives, most notably Wolverine, who said he was the only person who treated him like man, not an animal. He then points at Hope angrily, saying "You had better be worth this, I swear to God."
Domino and Cyclops discuss how Bastion is trying to eliminate the X-Men's teleporters. When The Vanisher overhears this, he flees to Portugal and is gunned downed by Steven Lang and his operatives. Donald Pierce, Bastion's mole inside Utopia, receives the green light from Bastion to proceed with their plan. Three and a half miles away from San Francisco, the X-Club investigate an oil rig and discover a ticking timer. At Utopia's mess hall, Cable tells Hope that she must eat something. Mirage, upset that her team has suffered in the war over Hope, confronts Cable. Hope takes offense and initiates a fistfight. Suddenly, an explosion is felt and Cyclops is certain that the X-Men's jets, the Blackbirds, have been decimated. Pierce, responsible, stands amid the debris, and rues that he will not live to witness the decimation of the mutant race. Cyclops eliminates him with an optic blast, and alerts the X-Men to expect an attack. Hope confesses to Cable that she was not truly ready to return to the present.
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. Back at the ruins of the oil rig, the X-Club attempts to analyze and dispose of the dome. After a detailed scientific explanation provided by Madison Jeffries, the X-Club find themselves face to face with the Avengers. According to Hawkeye, the Avengers have arrived to help the X-Men and punish those responsible for the dome. In San Francisco, Magma, Namor and Cyclops survey the damage caused by the dome via jetpacks, meeting at the Golden Gate Bridge. At the bridge they observe a smaller, silver dome and conclude that it is powering the dome. Back on Utopia, Cable tells Hope that she must decide whether or not to abandon the X-Men. Hope asks him if he would really be willing to leave all his friends and loved ones behind to help her; Cable tells her that his first responsibilities are to her. Touched by his words, Hope states that the X-Men got into this fight because of her, and that she will not leave them to fight alone. Back on the bridge, the X-Men arrive. Under Cyclops’s orders, Iceman attacks the silver dome only to be choked by a big metal arm. The other X-Men watch in horror as a legion of Nimrod type Sentinels begin to emerge.
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. With battle preparations in full swing, Hope is seen running after Cable. Hope finally catches up to him and asks him why he has to go. Cable explains that it’s a good plan and that it wouldn’t work with out the tech in his arm. Hope begs him to stay addressing him as “Nathan”, Cable cuts her off and enters a room containing the entire X-Force team. After Wolverine tells him to get it over with, Cable reaches out and hugs Hope, telling her that he loves her and goodbye. The Stepford Cuckoo’s inform Cyclops that another wave of Sentinels are arriving. Colossus, Namor, Rockslide and Dust get ready to fight. Cable initiates the jump and X-Force leaves this timeline. Standing behind Cyclops, Emma asks him if he truly believes that they will survive this. After a moments hesitation Cyclops and says yes. Emma then asks what it is Cyclops is keeping from her; with Hope and Emma looking at him Cyclops reveals that he has indeed given X-Force a suicide mission. As things start to heat up Cyclops tells Emma and Hope that he has sacrificed his son to save the world.
Picking up where the last issue left off, the MRD is inspecting the wreckage of X-Factor's car. It becomes apparent that the vehicle had been occupied by holograms, the only actual mutant present being Darwin, who evolved to be bulletproof and teleported away to escape some giant machine with a buzzsaw. Madrox reflects on seeing the trap because Longshot handled the Absorbing Man's money, which he got from an MRD agent, revealing the whole ambush. Meanwhile, Strong Guy escapes with Baron Mordo into a hidden chamber inside the nearby Temple in South America, who proposes a temporary alliance to deal with the MRD. Elsewhere, Siryn attempts to board a plane in Ireland and is stopped by MRD agents posing as airport security, stating, ironically, that she is on a no-fly list. When she resists, armed agents attempt to attack her and succeed in subduing her, but are prevented from finishing her off by Shatterstar and Layla Miller, who promptly slaughter them. When Trask considers giving up in the face of this, Bastion overrides him and compels him to 'take control', which Trask repeats in a mechanical fashion.
With Illyana being dragged to hell in Chapter III, Colossus is adamant that he is not losing his sister again and confronts Cyclops. Cyclops explains that he needs Piotr's strength in Utopia but that doesn't mean that he won't be sending someone else. Cyclops assigns Cannonball as team leader who assembles the team, not only of people Cyclops is willing to spare, but the right people for the job. They need speed and recon, so Cannonball gets Northstar and Trance. They need power in case of trouble so Dazzler is asked to join. They also need someone to keep their eye on the prize so Gambit agrees to join the team. They also need a way in to Limbo and Pixie is asked, at first she refuses after Illyana has torn out a piece of Pixie's soul, but for her moral Anole is invited, though he too is not happy due to him losing an arm on his last visit to Limbo.
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 Francisco 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. Back on Utopia, Cyclops asks Professor Xavier to work with Legion as part of a larger plan and then charges Rogue of finding and protecting Hope. Outside, the Thing's and Thor's efforts to destroy the dome have met with very limited success and pressed them both to the brink of exhaustion. Mister Fantastic tells them that their attacks on it have only weakened it by fifteen percent. Iron Man further states that between all of them, they are at least a day away from getting inside. Doctor Nemesis grimly declares that within a few hours, every man, woman and child inside will be dead and the mutant race will be extinct.
Professor Xavier enters David Haller/Legion's mind to enlist him and his multiple personalities to battle the Nimrod invasion of Utopia. As Cyclops realizes that the situation is dire he turns to all mutants on the island and issues a statement, "fight or die". Rogue has been left in charge of Hope. Rogue is supposed to keep Hope safe from the Nimrods and take her into hiding. Instead, Hope decides that if she is to be the mutant messiah then she will fight. All over the island Nimrods are arriving from the future in waves every five minutes. In the tunnels below Utopia, Husk, Avalanche, Sunspot and Boom Boom are attempting to keep the Nimrods at bay. As it takes all of their combined strength to stop one, more teleport in. On the bridge into San Francisco Colossus, Namor, Magma, Dust and Rockslide are trying to keep the Nimrods from advancing. Colossus is overwhelmed by the Nimrods and they manage to compensate for his strength and break his arm. Meanwhile, the X-force unit (Wolverine, Domino, X-23, Cypher, Angel and Cable) sent into the future begin their assault on the Master Mold facility that is sending the Nimrods into the past. Cypher is able to stop assault machines by speaking in their language and the team advances into the facility. Back on the bridge Colossus is about the be taken down by the Nimrods when they sense a much greater threat. An omega level mutant. Legion begins his assault on the Nimrods with personality 115 which seems to have a destructive sonic power. As the Nimrods begin to adapt to this power Legion switches to personality 762, a pirate with the ability to belch what seems to be an acidic compound. Just at that moment Cyclops arrives with Iceman, Psylocke, Surge, Gentle, Storm and Armor. Back to the future, the X-force team has successfully infiltrated the Sentinel facility and realizes there are two Master Molds. One creating the Nimrods that are attacking Utopia and one that is aggressive in nature. Back on Utopia a small contingent of mutants consisting of Litterbug, Scalphunter, Random and possibly the Morlock Sack have decided to fight the Nimrods. Toad is tagging along and attempting to convince them to stay on the island as Cyclops' team is luring them away. As he says this to Sack, Toad's finger is disintegrated by a beam of energy which also takes of Sack's head. The scene ends in the infirmary where Beast is treating Hellion and the Nimrods are beginning to get inside. Magneto rises from his bed and tells Beast to tend to the injured while he fights the Nimrods.
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. In the present, with the battle officially over, Cyclops attempts to talk to Hope and explain his command decisions to her. Hope once again threatens him and calls him a heartless monster that uses others like pawns to achieve his own goals. Hope then tells him that nothing he says has any worth to her, as she will always hate him for what he has done. Before an increasingly enraged Hope can act on her feelings, a figure emerges from the time portal, this figure is then revealed to be Cable. As Cable continues his walk through the portal it is revealed that he has given his body over to the techno organic virus that has long plagued him. Outside of the dome, Bastion appears with the reanimated Graydon Creed and Stephen Lang, commenting that while the Nimrods are gone, mutantkind is still trapped and that he will deal with the remaining mutants himself.
Thor tries to uneffectively break the dome from the outside, where thousands have gathered to pray for the X-Men to save their relatives trapped on the inside. Inside the dome, Cable, in full techno organic form, manages to keep the temporal door open long enough for the X-Force team to walk through it. He then looks at Hope and suddenly explodes, leaving only his metallic arm behind. Bastion, Lang and Creed watch from the top of a mountain as the time sphere collapses. Creed and Lang try to convince Bastion that the game is over. Bastion refuses to let the girl live, turns into battle mode, and flies towards the bridge. Hope remembers the moment she asked Cable how she would know when she's ready, and he told her she would know the same way she has ever known anything else. Cyclops tells Hope he's sorry and tries to put his hand over her shoulder, when she replies that if he ever put his hand on her again, he will lose it because it was all his fault. Suddenly Bastion destroys the Golden Gate Bridge passing through it. Most X-Men falls into the water. Hope emerges from it, only to be confronted by Bastion, Lang and Creed, all in Nimrods form. They attack her, when, suddenly, she forms an armor. Bastion realises that her mutant powers just appeared, but he can't classify them, nor calculate them. Hope then blasts him with an optic blast he can't adapt to. Her hand turn into metal, and she punches right through him. As she remembers Cable's words, Hope touches the ground and forms an energy shield. Bastion says she is not the messiah, but the adversary, and that if she survives, nothing will survive. Hope turns into the Phoenix and blasts Bastion. Wolverine, Colossus and Emma are shocked. Logan tells Emma there's nothing she can do now. Bastion manages to grasp Hope's neck, and states that despite his original programming, he will take great pleasure in killing hope. Cyclops blasts his arm, and Wolverine jumps on him, killing him "for Kurt". Hope touches the ground again, saying she's ready now, going full Phoenix Force, and blasting Bastion and the dome all at once. The Avengers rejoices that Summers managed to pull it, while, in Utopia, every mutant just stares at Hope, levitating, like a true Phoenix...
Cannonball's rescue team find themselves splintered and with different concepts of how long each has been in Limbo. Pixie and Trance attempt to make their way to Magik, but are confronted by the demons S'ym and N'astirh, the latter who offers Pixie a deal-- he will restore the missing fragment of her soul in exchange for killing Magik and turning over her Soulsword. Trance attempts to dissuade Pixie but her astral form dissipates and she jolts back to her physical form on Utopia in the midst of the Nimrod invasion. Gambit, transformed into Apocalypse's Horseman Death by Limbo's evil influence, is able to corrupt Dazzler and Northstar into their respective incarnations of Death. They confront Cannonball and Anole.
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. Cyclops begins writing a condolence letter to Nightcrawler's sister, as Beast asks Namor why he takes residence with the X-Men, Namor refuses to answer seeing Beast as a deserter of his people, telling Cyclops that his army has no need of a pacifist like Beast. Cyclops attempts to find comfort with Emma who has taken her diamond form to escape emotions, much to Cyclop's disdain. At a celebratory bonfire, Emma notices the flames around Hope take the shape of the Phoenix, and Hope speaking in the same tone as its dark counterpart, terrified Emma runs to Cyclops to warn him but before she can, Cyclops tells her that Cerebra has found five new mutants that have appeared around the globe.
- In an online interview with ComicBookResources.com, X-Writers Craig Kyle and Christopher Yost stated that after Necrosha, Elixir stayed on Genosha to heal and bury the corpses left by Selene and her Inner Circle. Thus is absence on Utopia during the Second Coming. This sabbatical is because Elixir is having trouble reverting back to his Golden state from his Black form.
- The 3rd Printing Variant covers for Chapters 1-5 say "SHE HAS RETURNED".
The Second Coming had various effects on the Marvel Universe:
- Various mutants were wounded or (seemingly or not) killed (See the list of casualties)
- The Human Council is decimated, Bastion killed, the M.R.D. is deployed and aborted. Globally, the anti-mutant coalition is severely weakened. (See the list of casualties)
- The X-Men are reinstalled as heroes.
- X-Factor is unified again.
- Hope reveals her powers and an obvious relation to the Phoenix.
- The first wave of new mutants start with the Five Lights.
- Human Council
- 1 appearance(s) in handbook(s) of Second Coming
- 1 minor appearance(s) of Second Coming
- 122 image(s) of Second Coming
- 22 article(s) related to Second Coming