X-Men of the future come to the present to make sure the original X-Men return to their proper timeline to prevent a supposedly bad future.
When the young Cyclops was apparently killed by Sentinels while on a mission, the older Cyclops disappeared. The young Cyclops was healed by the young mutant Triage and the older Cyclops reappeared. Wolverine's X-Men believed that it is dangerous for the young original X-Men to stay in the present and wanted to send them back. The future X-Men arrived and wanted to send the original X-Men back too. Young Cyclops and Jean Grey escaped from the Jean Grey School. The present and future X-Men hunted the two mutants down but with the distraction provided by Kitty Pryde and Rachel Grey who wanted the original X-Men to make their own choices, they escaped. They seek the help of older Cyclops' X-Men. Wolverine's X-Men and the future X-Men arrive and a fight ensued. Magik seek out young Iceman and Beast in the Jean Grey School and traveled to the future where they found the real X-Men. They convinced the future X-Men to travel to the present to help them stop the fake future X-Men, actually the future's Brotherhood.
In the present, with their cover about to be blown, the Brotherhood revealed their true natures and attacked the present X-Men. They managed to capture all the original X-Men and attempted to send them back. However, they discovered that something prevented the original X-Men from being returned to their proper time. Cyclops' X-Men and the real future X-Men aided Wolverine's X-Men. The Brotherhood traveled to Cape Citadel, where the original X-Men first fought Magneto. The combined forces of Wolverine and Cyclops' X-Men and the future X-Men fought the Brotherhood when S.H.I.E.L.D. arrived. Xorn, revealed to be the future Jean Grey, unleashed S.H.I.E.L.D.'s anti-mutant munitions and Sentinels. In the final fight against the original X-Men, Xorn unleashed her full power and was consumed by it. The X-Men escaped with Magik's teleportation powers while the surviving Brotherhood escaped in their own way.
In the aftermath, the future X-Men returned to their own timeline with Kymera staying behind to hunt down the remaining Brotherhood.
[Cyclops, Marvel Girl, Iceman, Beast, Angel]
[Cyclops, Emma Frost, Magneto, Magik]
[Wolverine, Storm, Beast, Iceman, Kitty Pryde, Rachel Grey]
[Storm, Kitty Pryde, Rachel Grey, Rogue, Psylocke, Jubilee]
Later revealed as the Brotherhood
Beast, killed by Sentinel
Deadpool, killed by Magik
Ice Hulk, created by the real Iceman and taken over by Xorn
Kitty Pryde, a disguise of Raze, daughter of Wolverine and Mystique
Xavier, grandson of Charles Xavier
Xorn (Jean Grey), future version of the young Jean in the present, consumed by own power
Colossus, killed by Xavier
Ice Master, future Iceman
Kymera, future daughter of Storm
Phoenix (Quentin Quire)
Sentinel-X (Shogo), adopted daughter of Jubilee
Wiccan, Sorcerer Supreme
Wolverine (Jubilee), killed by a Sentinel
More crossover info + cover gallery: http://marvel.wikia.com/Battle_of_the_Atom