In the present, the X-Men face off against the newly reconstituted Brotherhood of Evil Mutants to save the life of Senator Robert Kelly. Thirty years in the future, the remnants of that team face the unstoppable Sentinels to save the world from nuclear Armageddon. Linking both battles is Katherine Pryde, who exchanged her consciousness with that of her past self to change the outcome of the crucial fight with the Brotherhood.
Apparently unaware of the danger he is in, Kelly blusters. How dare those freaks turn the Senate into a battlefield? He orders the marshals to arrest them, causing the Blob to chuckle that Kelly’s either the bravest man he’s ever seen or the dumbest. Either way, he’s gonna die today. He swats aside the marshals coming at him, while Avalanche unexpectedly launches a tidal wave beneath the feet of the X-Men, sweeping them off their feet.
The acrobatic Nightcrawler jumps off and attacks Avalanche. He uses his teleportation power to strike from all sides and thus keep his foe of-balance. However, the precog, Destiny, warns Avalanche of the next blow and so the villain is ready and hits Nightcrawler straight into the stomach.
Pyro sends a huge fireclaw against Colossus. Wolverine realizes that Pyro’s flames come from the flamethrower on his back. He threatens what he’ll do to it and to Pyro with his claws. Hearing that, Storm keeps him away from the villain with a whirlwind, while a torrential blast of rain extinguishes Pyro’s flames.
Angel, who has caught Sprite, gets why Storm acted that way – unlike Wolverine. With the growing anti-mutant sentiment, the last thing they need is Wolverine carving someone up. Kate reminds Angel that they have to find Kelly. He must be protected at any cost.
Moira MacTaggert asks Charles Xavier what’s going on. Quickly, he fills her in. He’s scanned Kitty’s mind. Her body is currently being possessed by the consciousness of the woman she’ll be in 30 years.
A female security agent addresses Xavier and Moira, asking them to follow her. They need to get out. As they do, Moira still theorizes about what timetravel could mean about the nature of reality. Suddenly, Xavier senses some sort of energy field around the woman. But the next moment, she uses some knockout gas on them. Turning into her true form, Mystique announces that he sensed the electronic damper field that kept him from reading her mind, but it was too late too do him any good. With Xavier out of the game and only the inexperienced Storm to guide them, the X-Men will be fatally crippled, she announces. She ponders whether to kill him but then decides to keep him as a hostage for the moment.
As her companion, Destiny, joins them, Mystique inquires after the future. Beyond a certain point, the images become too jumbled to read, Destiny admits. There is a random factor, an anomaly. So long as it exists, nothing is certain.
Speaking of the anomaly, Kate realizes that, so far, her presence doesn’t seem to have changed a thing. And the future X-Man have gambled so much. Was it all for nothing?
In the future, Storm, Wolverine, Rachel and Kate’s husband, Colossus, who carries Kate’s unconscious body, make their way through the ruins of Manhattan, trying to avoid Sentinel patrols on their way to the Baxter Building. Logan points out tat the Sentinels will expect them to try and hook up with the Canadian Resistance Army, not attack their main headquarters, the Baxter Building.
Storm takes the lead. She flies up and destroys one Sentinel standing guard at the entrance of the Baxter Building. She thinks to herself that she who was sworn never to kill has taken lives and of how tired her soul is.
Rachel stays behind in a doorway with the unconscious Kitty to protect her. Rachel wonders if Kate’s actions in the past will actually change anything for them. Perhaps instead an alternate timeline will be created. So it could be wasted effort? Wolverine announces. Great. The doors are locked and he asks Storm to help pick them. She does and the X-Men enter. Wolverine announces that this building is a high-tech paradise, which is why the Sentinels chose it but it has an Achilles heel – the Fantastic Four’s private elevator. The electric eye beam in his belt buckle activates it and the three X-Men ride up.
Watching the battle, Kate comes to the conclusion that, slowly but inexorably, the X-Men are losing. The reports never revealed which member of the Brotherhood killed Kelly, so Kate decides that she has to go to the Senator’s side.
Up in the air, Storm berates herself. Her debut as a leader is quickly turning into a debacle. She did not want this position but now she has it and does not intend to fail. They need more fighting room, she decides and blows all the combatants outside the Senate building.
The Blob jumps at Colossus, intending to use his increased mass to squash the young Russian. Fortunately, Colossus quickly moves aside but Blob tears away the ground beneath him.
Nearby, an army special weapons team has gathered but the soldiers are unsure whom to open fire against. Trash them all, the major decides and the first one to be hit by a repulsor ray is Colossus. Flame throwers are next - a fatal move, as Pyro shapes the flames into a fire monster, attacking the soldiers while he mocks that he hopes they have pensions – their families will need them.
Angel bravely tries to catch Pyro’s attention, hoping he’ll send the fire creature after him instead. It works in a way. However, when Pyro sees Blob in trouble, the fire monster splits into two and one grabs Wolverine in its claws. In the blink of an eye, Storm rises up to gather speed and then flies down straight through Pyro’s fire creation, her winds blasting it apart.
Nightcrawler comes to Wolverine’s side, asking how he is. Visibly shaken, Wolverine admits that another few seconds and he’d have been a goner. As it is, his unstable molecules outfit absorbed a lot and his healing factor is taking care of the rest.
Suddenly, another Nightcrawler attacks the one by his side, shouting that he’s an impostor. The two Nightcrawlers start beating each other up. Wolverine is still too woozy for his senses to sort them out. Easy solution – he’ll use his claws. The real deal can teleport away.
Storm orders him to sheathe his claw. He doesn’t have time for this in the middle of a fight, he curtly retorts. She repeats her order and Wolverine threatens her. She tells him that she is team leader and he will use his claws when she tells him to and at no other time. He wouldn’t take that from Cyclops, he snarls. He’ll take it from her, she insists. She numbers his strengths and abilities and tells him that he shouldn’t need his claws aside from the deadliest situations. He relents but warns her that this conversation isn’t finished.
Avalanche attacks the two X-Men with another tidal wave and Storm grabs Wolverine, who complains that they are in this mess, thanks to her squeamishness. Who’s going to help Nightcrawler now? He doesn’t want any help, both Nightcrawlers, who are still fighting each other, shout.
The X-Men have arrived on the Baxter Building’s top floor. Upstairs, the first thing they intend to do is take care of an Omega Sentinel via another fastball special, but this time the Sentinel is a fraction faster and disintegrates Wolverine in mid-flight. They were aware of their presence, the machine states and orders the other two X-Men to yield. Never, Storm shouts, as she flies up and fries the Sentinel’s brain. More Sentinels join them and Colossus topples one of them, while Storm creates a blizzard to fry it, but the other Sentinel skewers her. Holding the woman who was like a sister to him in his arms, Colossus is consumed by a berserker rage and attacks the robots.
Far below, Rachel cradles Kate’s body and feels Colossus’ age and, finally, his death. She wonders what will happen to Kate’s mind, should her body be killed here. She wishes her a happier life. They did all they could. Now everything is up to Kate.
Kate hides in the same room, where Destiny is threatening the Senator. She is aware of the fact that her colleagues have been arrested, but they will still triumph with Kelly’s death. Kelly tells her that murdering him will accomplish nothing. People will band together and destroy them as a result. Destiny announces that he is a greater threat alive. Kate wonders why Destiny’s powers don’t warn her of Kate’s presence – possibly due to the timeswitch. As Destiny fires her crossbow, Kate phases through her, solidifies her shoulders to throw the other woman’s aim off. The bolt misses Kelly. In that split-second, Kate and Kitty’s minds are exchanged once more.
Storm flies into the room, taking in the scene. The unconscious Destiny, the woozy Kitty and the still alive Kelly. Senator Kelly demands an explanation. Carrying the still groggy Kitty, Storm tells him that they are the X-Men and this child just saved his life. Mutants, like people, are both good and bad. He’d do well to remember that before he condemns them all. Xavier and Moira join them as well and Storm leaves with Kitty.
In her Raven Darkholme persona, Mystique watches from the shadows and vows that the authorities won’t hold Destiny for long.
Later, en route to the mansion, Xavier explains everything that happened to a dumbfounded Kitty and the X-Men speculate on whether their actions this day have changed the future.
One month later, the committee of the mutant hearings, led by Senator Kelly, has sent its report to the president. Kelly and his friend Sebastian Shaw are asked into the Oval Office. The president tells Kelly that some of his suggestions are draconian, possibly even unconstitutional. And didn’t some of the mutants save his life? Only after other mutants threatened it, Kelly replies.
Shaw chimes in, reminding the president of the national security aspect. An anti-government group of superbeings or a group employed by a foreign power could constitute quite a risk. The president agrees and states that, for the moment, their actions will remain covert. The new operation is codenamed “Project Wideawake” and is to be headed by the man behind him. He introduces the men to Henry Peter Gyrich and adds that Gyrich will only answer to him. His first priority will be to work with Shaw Industries and construct a new series of robot Sentinels. Gyrich promises that the mutant controversy will be resolved. If they find them to be a threat to humanity, they will be dealt with – permanently.