The third and final installment of the Messiah Trilogy, Second Coming was the culmination of a half-decade worth of stories, every one of them since House of M leading to this. Hope Summers, the mutant messiah, has grown to a young woman, and is ready to come to the present to being the fulfillment of her destiny. Following her however is the most powerful and dangerous Sentinel in history, Bastion, intent on finishing the X-Men off once and for all.
The moment Cable and Hope return to the present, Bastion gathers together a cadre of anti-mutant villains from the X-Men’s past, including William Stryker, Graydon Creed, Cameron Hodge, Stephen Lang, and Bolivar Trask, and orders them to kill Hope. They first strike at Cable and Hope at a motel, the two holding them off until the X-Men Alpha team, lead by Wolverine, arrive to help. As the battle rages, Magick takes Hope back to Utopia under Wolverine’s orders. The New Mutants arrive next, and tell Cable someone is tracking him. The group splits up, Cable staying with a few others to fight the Purifiers and their allies, while Rogue and Nightcrawler got to protect Hope.
The New Mutants meanwhile launch an attack on Cameron Hodge’s base. Though Karma is wounded, they managed to destroy the base and Hodge’s cyborg armies. After informing Cyclops the locations of Bastion’s towers, the X-Men are hit again, Bastion targeting the mutants’ teleporters in an effort to keep them in one place. Bastion manages to find Hope, and brutally beats Rogue into submission. He extends his bladed arm to kill Hope, but Nightcrawler jumps in the way, impaling himself as he teleports her to safety. As he dies, he looks up at a tearful Hope and tells her, “I... believe... in you.” As Bastion regroups, Colossus and Pixie go to retrieve Magick from Limbo, while the X-Men grieve over Nightcrawler’s death. Beast puts the blame solely on Cyclops’s shoulders, a weight that Scott already bears for himself.
Not long after, the X-Club finds a bomb on an oil rig just off the coast of San Francisco. When it goes off, Cyclops realizes that the X-Men’s Blackbirds were destroyed. He leads Alpha team to investigate, and they find Donald Pierce. Cylcops blasts him, but the damage was done. With no teleporters, no jets, and no Cerebra, the X-Men are now trapped on Utopia. To make matters worse, another explosion goes off, surrounding San Francisco in a giant sphere. The various X-Teams converge on the sphere, but when they try to attack it, Nimrod strikes with a legion of Sentinels from a portal at the centre of the sphere. Bastion’s group joins them, and a massive battle ensues. The X-Men manage to win out, but not without cost, many too wounded to be able to fight.
As the wounded are taken back to Utopia, Cyclops gathers the X-Men’s core members. It is deduced that the portal is a time portal to a specific future, and when Prodigy looks into it, he tells them that 170 000 Sentinels were waiting on the other side. Against his better judgement, Cyclops reveals the existence of X-Force, much to the dismay of the others. He sends Cable and X-Force, the former using his last time-slide, into the future to deactivate the Sentinels, while Cyclops prepares every mutant left standing for a final stand.
Utopia soon comes under siege, the X-Men fighting desperately to hold the Nimrod Sentinels at bay. In the future, X-Force succeeds in their mission, but when they try to return to the present, X-23 is badly burned. They deduce that the portal will only work for non-organic matter. Seeing no other way, Cable sacrifices himself to keep the portal open, allowing the others to escape.
Despite their victory, Bastion, along with Creed and Lang, still have the mutants trapped in San Francisco, and declares that they will destroy them all, with or without the Sentinels. Hope, tired of seeing the mutants die for her, comes forward, using her powers to mimic those of the other mutants, and enters the fight. She kills Creed and Lang, and with the help of the other X-Men, she destroys Bastion and his sphere, freeing the city. However, as the battle concludes, Emma Frost sees the Phoenix flames rise around Hope, forcing her to remember Jean Grey’s warning to her years before, “prepare”, and in that moment realizes what Hope is destined for. Emma tries to warn Scott, but before she can, he tells her that Cerebra has detected new mutants, and that Hope’s arrival has heralded a new age for the mutant race, and Emma elects to stay quiet.
Second Coming was the end of an era for the X-Men, the mutant teams going through hell and back after the events of M-Day. Hope Summers was indeed the messiah for their race, and many of the mutants most dangerous enemies had been eliminated. However, the cost was great, Nightcrawler’s death hitting the X-Men hard. Not only that, Hope’s destiny was apparently not over, the shadows of the Phoenix being cast as the X-Men begin a new journey towards the single biggest event in Marvel Comics to date.