Legion tries to go back in time to kill Magneto, to make up with his father, Professor X. The X-Men follow him into the past and try to stop him, but they fail. When Legion is just about to kill the Magnus of the past, the Charles Xavier of the past jumps in front of the blast, ending his life. This causes the Earth-295 alternate reality to begin.
In Israel, Mystique prepares to assassinate Legion, but is stopped as Legion wakes from his coma. Mystique does a runner, escaping from X-Factor. Wolfsbane begins to track Mystique, while Polaris prevents Mystique from causing harm to civilians. Gabrielle and her son share some touching moments, while in his mind, Legion is confronted by Destiny, ordering him to pass on a message to Mystique. But Mystique has reached the marina, where she meets up with Avalanche, requesting his help. Valerie and X-Factor show up, and harsh words are exchanged between Mystique and Val, before Avalanche creates a tidal wave. X-Factor are left to deal with the repercussions of the wave, while Mystique flees, knocking Val unconscious into the water, though Strong Guy rescues her. Wolfsbane tracks Mystique back towards the hospital, and the two battle, before Forge steps in, and he and Mystique fight. However Legion arrives on scene and pulls Mystique inside his mind, where he passes on Destiny’s message. X-Factor arrive on scene and attempt to stop Legion - only he makes X-Factor disappear, and announces that he is going to make everything better, before flying away.
Legion builds a black dome in the Negev Desert, and the X-Men are called in to investigate. The X-Men enter the Dome and battle Legion but they are unable to stop him from opening a portal in time. Storm, Iceman, Bishop and Psylocke are sucked through it with him, whilst Jean Grey, who is left behind sends a distress call to Professor Xavier. In the Shi'Ar palace Lilandra is informed by Jahf, the M'kraan Crystal's guardian, that the end of all is coming soon.
Legion has transported himself and four of the X-Men (Storm, Bishop, Psylocke and Iceman) 20 years to the past, where they all emerged with amnesia. The rest of the X-Men find Jean Grey in the desert and, after receiving medical treatment, she tells them what happened previously. Cable arrives to help out just as Lilandra appears to give them a warning directly from the Watchers. In the past the amnesiac Legion has been transported to the hospital in Israel where both Xavier and Eric "Magnus" Lehnsherr work. A touch from Lehnsherr causes a psychic backlash, resulting in illusions of Eric’s past. Magnus calls Xavier for help and when they both get back to their patient they witness more illusions, this time of the present day X-Men.
In the present, Cable and Jean Grey are strapped into an amplifying machine, with the purpose to pass on a message to the time-displaced X-Men. In the past in Israel, Charles and Magnus chat and drink before get into a bar brawl whilst defending an disabled war veteran. Meanwhile, posing as Xavier, Legion seduces his own mother. Xavier mentally hears her cries of agony and he and Magnus rush to the hospital to find Legion waiting for them. Cable reaches his teammates in the past just long enough to pass on a message to Bishop before being pulled back to the present.
Legion is fighting with Eric in the Past. Whilst they are fighting the time-displaced x-men are trying to reduce the damage being caused to the surrounding area. Psylocke contacts Charles and tell him that they need to stop Legion. In the future Xavier realises that the he and the x-men failed, the M'kraan crystal is destroying the universe and there is nothing they can do. The X-men spend their final moments with loved ones. In the Past Apocalypse decides it is the time for ascension. Legion is winning the fight when Iceman freezes him solid. The x-men believe that they have saved the day however Legion hasn't finished and he knocks them all out. He is about to kill Eric when Charles leaps in the way, and is killed instead. Legion and the X-men, apart from Bishop, disappear and the crystalline wave hits Earth in the present.
Cable returns from his trip to the past, where he tried to remind the lost X-Men of their mission. He was able to pass on a message, however he and the X-Men are still unsure if it was enough and tempers flare. Through a holographic message, Lilandra informs them they have only an hour left and the various X-Men contemplate what they have done with their lives and spend some time with loved ones. Xavier gives them one final lesson before the crystalline wave hits earth and shatters.