Battle of the Atom

Before

• A philosophical debate between Cyclops and Wolverine on the future of the X-Men split the team in two. In the resulting Schism, Wolverine left Utopia and set his own school up in New York, the Jean Grey School, taking a number of students and X-Men with him. [X-Men: Schism, Wolverine and the X-Men (1^st series) #1]
• Under the influence of the Phoenix Force, Cyclops killed Charles Xavier. Cyclops was arrested but escaped prison and set up a new school, the Xavier School, in an abandoned Weapon X facility. [Avengers vs X-Men crossover, Avengers vs X-Men: Consequences, Uncanny X-Men (3^rd series) #1]
• Hoping to undo Xavier’s death and prevent Cyclops’ choices that led to it, Beast settled on an unorthodox solution. Traveling back in time to a point a few months after the X-Men began their adventures, Beast convinced the young, original five X-Men to accompany him to the future, intending to show them how bad things had become in order to inspire them to avoid them. To everyone’s surprise, the original five refused to return home. After much deliberation between the various X-Men groups, it was decided to allow the five to stay in the present at the Jean Grey School, under the tutelage of Kitty Pryde. [All-New X-Men (1^st series) #1-3]
• Teen Angel would leave the Jean Grey School and join Cyclops’ school instead. [All-New X-Men (1^st series) #11]

Crossover

When Kitty Pryde is alerted to a large spike on Cerebro, she takes the original, time-displaced X-Men to investigate. They indeed discover the newly emerged mutant but moments later are attacked by Sentinels. Fortunately, Cyclops and his own group of X-Men, who were also alerted to the new mutant’s presence, arrive and join in the skirmish. During the battle, teen Cyclops is killed, removing the adult version from existence and horrifying all. However, when teen Cyclops is revived by Triage, the adult version reappears.

Afterwards, Kitty and the other X-Men are adamant that the time displaced X-Men need to go back to their own time before anything else goes wrong. The heated discussion is interrupted by the arrival of a group of mutants, claiming to be the X-Men of the future and led by the grandson of Charles Xavier. They agree that the teens should go back to their own timeline and have travelled back to make sure it happens.

Despite the arguments from the X-Men teams, both present and future, young Jean and Cyclops are determined not to return and devise their own plan while everyone else is distracted. Jean uses her powers to start a fight between Wolverine and the future X-Men, causing a diversion during which she and Cyclops slip away. After taking the Blackbird to get far enough away, they ditch the jet and continue on foot. Nevertheless, the two groups of X-Men quickly catch up with the fugitives and the two are reluctantly made to see that everyone needs to go back to their own times. However, with the help of a sympathetic Rachel Grey, young Jean and Cyclops again give everyone the slip.  

Turning to the only people they believe can help them, the two seek the aid of the adult Cyclops and his own group of X-Men. To understand the situation better, Emma Frost and the Stepford Cuckoos read Jean’s mind and project her memories for all to see. During the process, Magik becomes alarmed upon learning of the future X-Men and teleports away before anyone can ask why. In the end, the adult Cyclops decides to help his teen self and Jean stay in the present, though the rest of his team do not agree.

Meanwhile, Kitty Pryde is facing a similar situation as she begins to fall out with her own group of X-Men over the fate of the teens. They eventually catch up with the two fugitives and Cyclops’ team but the reunion doesn’t go smoothly. Emma, the Cuckoos and Jean get into a telepathic battle with Xorn, one of the future X-Men, who turns out to be the future version of Jean Grey. As Xorn beats all the other psychics except for her teen self, all the onlookers start squaring up to each other. A fight breaks out but it is soon stopped by the young Jean Grey, who has read her adult self’s mind and seen the terrible consequences of the original five remaining in the present. She reluctantly tells everyone that they need to go back to their own timeline and the various groups accept her decision.

Elsewhere, Magik takes the young Iceman and Beast into the future to corroborate the future X-Men’s claims. They land outside the X-Mansion and are immediately met by a group of X-Men led by Jubilee. Jubilee is angry to see the visitors from the past and does her best to ensure no vital information is passed to them. Magik explains the situation going on in the past and pleads with her to help fill in the gaps. Jubilee finally relents and explains the series of events that caused a rift within the X-Men. Dazzler had been elected president of the United States but, as she was giving her victory speech, she was brutally murdered. In the aftermath, Beast realized that mutants would never be accepted and decided to do something about it. Upon hearing all of this, Magik teleports the future X-Men back in time to the present day to help clear up the mess. She arrives at Cyclops’ school, just as his group is getting back from their altercation with Storm’s team.

At the Jean Grey School, Wolverine’s team and the other team of future X-Men are escorting teen Angel, Jean and Cyclops inside. They discover that teen Iceman and Beast have gone missing, much to the anger of Charles Xavier Jr. During the argument between the groups, Rachel picks up on some stray thoughts and realizes that Charles’ team are not the X-Men after all, but actually the future Brotherhood. With their façade broken, Charles orders his team to attack the X-Men and ensure the original five go back to the past. The future version of Kitty then reveals herself to be Raze, the shapeshifting son of Wolverine and Mystique. Catching his father off guard, Raze stabs Wolverine, just as Xorn unleashes a telepathic attack on the other X-Men. The present-day X-Men are eventually subdued and Charles’ team readies Jean, Angel and Cyclops to be sent to the past.

Cyclops’ team arrives at the Jean Grey School with the real X-Men of the future to find a scene of destruction. The future Brotherhood manage to ambush them and kidnap teen Iceman and Beast, taking them into the school. Charles Jr then uses his telepathic powers to take control of Krakoa and subdue the rest of the X-Men, whilst the rest of the team work on sending the teens back to the past. The original five X-Men are loaded on to the time machine and future Beast starts it up. However, despite the machine working properly, the teens stay in the present, much to the confusion of the Brotherhood. To test the device Beast successfully sends Raze back in time and brings him back, proving the problem does not lie with the machine. Reluctantly, Beast deduces that the original five can no longer be sent back to the past because they have created a time/space paradox.

Cyclops, having broken free from Krakoa, catches up with the Brotherhood but Xorn telepathically distracts him long enough for them all to escape with the teen X-Men. Afterwards, Cyclops’ and Wolverine’s teams of X-Men meet up again and join forces with the future X-Men.

Elsewhere, the future Brotherhood use one of the X-jets to fly to Cape Citadel, so that they can go through with their “Plan B.” They attack the base, triggering an alert on Maria Hill’s SHIELD helicarrier. The X-Men also pick up on the alert, teleport to the base and engage the Brotherhood in combat. An adult Quentin Quire, the Phoenix-empowered version from the true, future X-Men, breaks the kidnapped teens free so they can join in the fight. The Brotherhood is quickly beaten but the X-Men realize that this was their plan all along, as the SHIELD helicarriers show up. Maria Hill demands the X-Men stand down but Xorn and Charles Jr. take control of the weapon systems on board and fire an array of missiles at the mutants on the ground.

The various groups of X-Men leap into action and disarm a number of the missiles before they hit the ground. However, the ones that do make it down don’t explode; instead turning into Sentinels. The X-Men suddenly find themselves fighting against SHIELD’s own anti-mutant ordinance, as well as the Brotherhood. The future versions of Beast, Jubilee and Colossus are killed in fight as the carnage continues. After neutralizing the future Quentin, Xorn turns her attention to Wolverine and Cyclops. Blaming them for the state of her future, she attacks them and eventually defeats them. However, before she can celebrate, the teen versions of the original five prepare to take her on. The fight is brief and, in the end, only the past Jean is left standing against Xorn, her future counterpart. Xorn begins to lose control of her powers and glows with energy as everyone else begins to back off. Unable to contain her powers, she dies in a huge explosion that damages many of the Sentinels and the helicarrier. As the dust settles on Cape Citadel, Maria Hill lands on the ground to arrest the X-Men but finds no trace of them, excepting Xorn’s faceplate.

Magik managed to teleport the X-Men out of the area before anyone was killed in the explosion. Back at the Jean Grey School, the future X-Men mourn their dead and prepare to travel back to the future. Rachel psi-scans Cape Citadel and discovers no bodies were found, indicating the surviving members of the future Brotherhood also escaped. With the drama over, Cyclops and Wolverine’s groups of X-Men return to their state of distrust and go their separate ways. Kitty Pryde, angry at Wolverine and Storm over the treatment of the original five, quits the X-Men. The teen X-Men also decide they want to leave the school, so they join her and meet up with Cyclops’ group of X-Men.