When Kitty Pryde's group of time displaced X-Men (The 05 X-Men) and Cyclops Uncanny X-Men are forced to team up to stop an out of control new mutant, when Young Cyclops is killed by a Sentinel. He is resurrected moments later by one of Cyclops' recruits, Christopher Muse, who is a healer. However, in the brief moments that Young Cyclops was dead, the adult Cyclops blinked out of existence and the world around the two groups suddenly began to shudder and shake, as if reality was collapsing from the time paradox.
This causes another round of debate from Wolverine's X-Men about returning the 05 to their proper place in the timeline. The debate is suddenly interrupted by the arrival of a group of older X-Men led by an aged Kitty Pryde, the grandson of Charles Xavier, and an adult Jean Grey (the time displaced 05 Jean Grey, having never returned to the past), dressed as the new Xorn. They seek to force the X-Men to go back to the past.
Realizing that something doesn't seem right, 05 Jean escapes with 05 Cyclops. The X-Men and "Future X-Men" pursue, with Xorn explaining that a catastrophe will soon befall the X-Men if the 05 do not return to their original place in the timeline. The exact nature of that catastrophe is left ambiguous.
05 Jean & Scott eventually make contact with Cyclops team of Uncanny X-Men, and after some consideration Scott agrees to help his younger self and young Jean. Realizing that Scott's thinking on the matter is compromised, Emma Frost telepathically alerts the X-Men and Future X-Men of Young Jean's and Scotts location. However, upon seeing Xorn attack her younger self, Emma has a change of heart and attacks Xorn with the Cuckoos and 05 Jean.
Xorn is able to defeat the combined powers of Emma and her Cuckoos, but 05 Jean is eventually able to defeat her. Xorn gives 05 Jean a glimpse of the future, a ploy on her part, which convinces 05 Jean that they need to go back to their proper place in the timeline. The three teams of X-Men part ways, with Cyclops unsure if this fight is really over. Magik, who is also suspicious of the motives of these new X-Men, travels to the future along with 05 Beast and 05 Iceman. It is discovered that these "Future X-Men" are really the "Future Brotherhood", and motives are purely self-serving. This new Brotherhood was created when Alison Blaire, also known as the X-Men Dazzler, is elected president and quickly assassinated, with the identity of the assassin unrevealed. The true "Future X-Men" agree to travel back in time and confront the Brotherhood.
Upon arriving at the X-mansion with 05 Jean, Scott and Angel, it is discovered that the 05 Beast and Iceman are in the future. The Brotherhood realizes that they will soon have to fight Cyclops team and the true "Future X-Men", and accelerate their plans. It is revealed that the "Future Kitty Pryde" is really Raze, the shape shifting son of Mystique and Wolverine. They attack the original X-Men, including Wolverine who is incapacitated. Raze is able to infiltrate Scott's team and capture 05 Iceman and Beast.
The 05 X-Men are brought to Beast's time machine and an attempt is made to send them back in time. However, an unknown force prevents this process from being completed. As the other Brotherhood members are overwhelmed by the Uncanny X-Men and the Future X-Men, the surviving Brotherhood members flee to Cape Citadel, the site of the first battle between the 05 X-Men and Magneto.
The Brotherhood attacks the military to attract the attention of S.H.I.E.L.D. The fully united force of the Uncanny X-Men, Wolverine's team of X-Men, and the "Future" X-Men arrive to stop them. Xorn is able to control the S.H.I.E.L.D. weapon systems on site and launch the government Sentinels, which were being created in secret. The X-Men defeat the government Sentinels, and turn their attention to Xorn. She is able to hold the combined forces off, but her powers overload and she explodes.
The exact catastrophe that befalls the X-Men due to the 05's presence is not revealed. The Future X-Men return to their proper place in the timeline with their casualties. The whereabouts of the Brotherhood member Raze is unknown. The 05 X-Men, due to being nearly forced to go back in time, decide to leave the Jean Grey School and join the Uncanny X-Men. Kitty Pryde, distraught that her input was disregarded during the ordeal, joins them to continue to mentor the 05 Team.
- The Future Brotherhood stay on The Present, as well as Kymera and her panther who join Wolverine's X-Men, in order to track them down.
- Charles Xavier II is crippled as his father.
- Shadowcat and the time-displaced X-Men quit Wolverine's X-Men and join Cyclops' X-Men.
- Wolverine wants S.H.I.E.L.D. to explain for their Sentinels.