In Madagascar, Wolverine, Nightcrawler, Storm, the Proletarian, and Magneto lead an army of mutants against 200 Sentinels. They meet at the beach, trying to push back the Sentinels at the border. Apocalypse uses a S.H.I.E.L.D. satellite laser to terribly injure Magneto, and Wolverine is thrown into the ocean where the metal in his bones causes him to sink out of sight. The mutants fight together to defeat one Sentinel. Magneto gets back up and pulls the satellite out of orbit to take out another Sentinel with it, the mutants fight together to take out another Sentinel, Magneto helps mop up the remainder. There are some casualties among the defending mutants, but the sentinel invasion is stopped. By leading an army against an unprovoked invasion, Magneto has cemented his reputation as the hero of Madagascar and the savior of its mutants.
Elsewhere the Soviets launch an invasion of the United States through Alaska, halted only by the actions of Steve Rogers. There is intense confusion in the United States’ political and military structure as some obey the President’s order to submit to Apocalypse, others rebel, and the remaining Hydra agents foment chaos.
Emma reveals that Professor X was taken out by the amalgamated personality of his shadow, Cassandra Nova, formed when Scott, Jean, and Hank left. Nova has chosen this moment to strike when Xavier is needed the most. Scott proposes a dangerous plan. Rogue will absorb Xavier’s telepathy and use it to attack Apocalypse’s self-image when he shapeshifts to use different powers in response to the X-Men’s attacks. But in order to get past Apocalypse’s defenses, the mental damage will be equally inflicted on Rogue’s own mind as she suffers with him. Bobby protests sacrificing Rogue in this way, but she volunteers to carry out the plan.
Rogue absorbs Xavier’s telepathy and at Scott’s insistence also Polaris’s magnetism to give her a power to protect herself in a physical fight. Something that conveniently excuses Polaris from combat… Curious, Rogue peeks into the minds of those around her. She sees Xavier’s struggles with Cassandra Nova, Iceman’s concerns about her well-being and doubts about the plan, and Beast’s spirit of scientific curiosity. When she looks into Scott’s mind, a bird made of flame lunges at her and shocks her out of the psychic realm.
In Washington, D.C., Apocalypse carves out the Lincoln Memorial to make a throne for himself as he awaits the X-Men in the National Mall. Cyclops, Rogue, Beast, and Iceman confront him, with Iceman’s irreverence giving the others courage in the face of such power. The city has been evacuated… or rather, Apocalypse has allowed the ants to flee.
Before battle can begin Namor the Submariner, called by some the First Mutant (however inaccurate that is now known to be), makes a dramatic appearance and steals the initiative with a great punch to Apocalypse. Rogue establishes a link with Apocalypse to make him lose his sense of self, enduring constant assaults and taunts from his powerful personality as she throws the collective worst of the world against him. Beast uses a prototype power-canceling net to inhibit Apocalypse’s abilities and slow his shapeshifting.
As per Cyclops’s plan, Iceman and Cyclops combine attacks of ice and fire to catch Apocalypse in an explosion that Rogue uses to weaken him. Apocalypse first tries to energy blast everyone, but realizes that the X-Men are used to such tactics. So instead he grows to giant size, in the process shrugging off Namor’s attempts to pin him. Ripping the Washington Monument out of the ground, Apocalypse uses it as a giant club to sweep the entire mall. Rogue mostly manages to evade with the magnetic powers she took from Polaris, but is clipped hard enough to knock her out. Iceman is crushed, and even Namor is hurt. Beast manages to avoid the blow by riding the monument as it swings, and Scott draws deeply on the Phoenix power to transmute the very rock of the monument to water and push it out of his way a split second before it impacts him.
Beast rushes to Rogue’s side and injects her with a massive shot of adrenaline, determined to bring her back on her feet long enough to complete the plan no matter what. Apocalypse seems unstoppable, shrugging off all damage and winding up for another swing to kill them all.
Inside his mind the strain is beginning to tell, however, as Rogue continues to search for the core of Apocalypse’s self-image. She finds it in the center of the horrors she has conjured, a lost and neglected child in the desert who has only one thought- I will survive. As Beast rams a car into Apocalypse, he transforms himself into diamond to take the impact. Rogue seizes the opportunity to shelter the child from the dust storm and promises not to abandon him, taking away Apocalypse’s core imperative that he must survive alone. Unable to transform any longer, he is left as a giant diamond statue dormant in the National Mall.
As Madagascar is repaired, Kurt becomes engaged to Wanda and decides that he can no longer overlook what he considers to be the violent and evil members of the Brotherhood. He confronts Erik, promising that if the Brotherhood’s leader does not purge psychopaths like Sabertooth and Azazel, Kurt will call upon the X-Men to force the issue. X-Men like the violent murderer Wolverine, asks Magneto?
Believing he is coming ever-closer to understanding the source of mutant powers, Beast begins constructing his own version of Cerebro. He is still uncertain how to overcome the need for a powerful telepath to operate it but confident that he will find a way.
Receiving the thanks of the world from her hospital bed, Rogue asks Professor X to lock away the fragments of her mind and give her relief from the voices she has accumulated. Professor X tells her the tragedy that will unfold, how she will inevitably grow curious and seeks out for herself what has been sealed away restoring all the old problems and blaming Xavier for it. She asks for it anyway. After she leaves the hospital, Logan takes her away for a long training trip to teach her how to protect herself without powers and perhaps develop the mental discipline to control the personalities she absorbs.
Scott talks to Professor X, having come to understand why he did what he did, and how Scott came to the same place in his own life. Scott manipulated everyone in order to take down Apocalypse and used Rogue as a tool and he does not regret any of it. Xavier tells Scott that he is proud Scott has learned to see the big picture and that it should never be easy. If they ever stop hating themselves for it, then they will truly be lost. Bobby’s opinion on the matter is best communicated by the giant block of ice encasing Scott’s car.
Elsewhere, the various organizations that Apocalypse manipulated find themselves being brought under the control of a new group emerging from the shadows. It is a group that controls great wealth and power, from the wealth and clout of America’s richest social elite, to the technological secrets of the world’s most advanced nations, to the secrets hidden in the head of the powerful, to the armies of Atlantis and strength of a mutant who went toe-to-toe with Apocalypse. A group calling themselves by a name from old conspiracies… the Illuminati.
The last scene is Rogue walking in the desert in her dreams, hand-in-hand with a toddler En Sabah Nur.