Chapter 1: War
The Avengers attack Magneto's Utopia, and SHIELD fighter jets begin shooting up the place. As the X-Men rush into the battle, there is a flashback to the day before. SHIELD has gathered every living member of every version of the Avengers, from Captain America to Rocket Raccoon. Nick Fury tells them that several mutant terrorists have been causing chaos, and they all work for Magneto's Brotherhood of Supremacy, an infamous mutant terrorist group. Now, Magneto has awoken one of the most powerful mutants ever, and they need to stop his evil plan.
The Avengers and Nick Fury get in the Quinjet and head for Utopia, as several SHIELD soldiers follow. They arrive at Utopia and begin attacking. The X-Men rush out from Magneto's palace and see the chaos. Cyclops approaches Nick Fury and tells them to stop, but Nick Fury says that Magneto is dangerous and unpredictable. Fury accuses Cyclops of turning against humanity as well. After all, he did leave the government and form his OWN mutant team recently. Cyclops tries to tell Fury that all Magneto wants is peace, but Fury says that if he wanted peace he would've told his mutant henchmen to stop destroying things.
Suddenly, En Sabah Nur turns giant and comes crashing through the front of Magneto's palace. En Sabah Nur tries to tell the humans what happened in his vision, but he is repeatedly shot at by SHIELD fighter jets. En Sabah Nur tells them they must stop for the good of mankind, but Magneto's children, Quicksilver and Scarlet Witch, command the Brotherhood of Supremacy to fight back. The mutants charge into battle, and so do the Avengers. Hulk and Juggernaut begin punching each other repeatedly, but Hulk proves he's stronger by tearing off the Juggernaut's arms and smacking him with them. Hulk begins destroying everything, as Juggernaut lies on the ground, writhing in pain.
Chapter 2: The Battle Begins
Havok tries to tell Cyclops to join the Avengers and fight against Magneto, but Cyclops tells his brother that Magneto doesn't WANT war. Havok realizes his own brother has turned evil, and he must stop him. Havok knocks Cyclops out with an energy blast, but right after he is attacked by the X-Men, who must defend their leader. As the X-Men take on Havok, Magneto comes out of his palace, sitting on a metal sheet which he is levitating. He tells the humans that this war is meaningless, but Rocket Raccoon fires a bazooka at him. Magneto stops the missile in midair and tells the humans that if this is how it has to be, Magneto will not just sit back and watch them destroy his kind. Magneto shoots the missile back at Rocket Raccoon, who jumps out of the way as it hits the ground and causes an explosion.
Iron Fist battles Toad, who manages to avoid his attacks by hopping around repeatedly. Toad spits out some green, adhesive slime right at Iron Fist's face, keeping him from seeing anything. Toad begins punching and kicking the blinded Iron Fist, and finishes him off by wrapping his tongue around him and flinging him up into the air. As Iron Fist falls to the ground, Thor battles the adapting mutant Darwin. Thor fires a bolt of lightning at Darwin, but Darwin adapts to it by turning into metal. Instead of being fried by the electricity, he is now able to conduct it, and grabs Thor's face, shocking him with his own electricity.
The armless Juggernaut begs the X-Men for help, and Elixir uses his healing powers to grow Juggernaut's arms back. Elixir tells Juggernaut not to fight the humans, but Juggernaut is confused. Elixir reveals that Magneto and En Sabah Nur wanted to bring peace to the world, not war. The humans and mutants must co-exist peacefully. Juggernaut understands, and goes to tell his fellow mutants not to fight back. Meanwhile, Quicksilver and Scarlet Witch are killing several SHIELD soldiers when their father approaches them. He tells them that he wanted peace with the humans, but Scarlet Witch tells them that it's pointless. Humans will always remain hostile toward mutants, so mutants should just be the same way toward humans, and this is the way it was always meant to be. Magneto decides to join in on the war, and fight for his kind once again.
Iron Man flies past, and shoots Scarlet Witch and Quicksilver with repulsor blasts. Magneto pulls Iron Man's armor off using magnetism, and pulls it apart in midair, turning it into a huge blade that he uses to impale Tony Stark with. Tony Stark drops to the ground, and coughs up blood as Magneto laughs maniacally. Quicksilver runs up to the rampaging Hulk super-fast, and blows him back with a sonic boom, knocking him out and causing him to revert back into Bruce Banner. Scarlet Witch levitates Bruce and rips his body in half. She then disintegrates both parts of him into piles of dust.
Elixir sneaks up on the Scarlet Witch and drains out some of her life energy, putting her to sleep. Elixir heals Bruce Banner and Tony Stark, bringing them back to life. Quicksilver charges at Elixir and tackles him, but as they both fall to the ground Elixir drains some of Quicksilver's life energy, putting him to sleep as well. En Sabah Nur, in his giant form, fights off several SHIELD agents at once, when Goliath turns giant and approaches him. Goliath tells En Sabah Nur that things are becoming just like his vision. En Sabah Nur tells him that the time for peace is over, and he has finally accepted that. Goliath battles En Sabah Nur, but is too outmatched. Nur blasts Goliath with fire, and Goliath is horribly burned. He falls to the ground in pain, and Nur tells him he will spare his life, since they are both mutants.
Cyclops is woken up by Armor, who transforms into her armored version and tells him they have to do something, and he has to pick a side. Cyclops hesitates, but finally picks a side. He decides that the X-Men should fight with their fellow mutants, and when the battle's done, they can go through negotiations with the humans to achieve peace. Armor tells him there's no easy way out, but Cyclops tells her that he's aware. The X-Men gather behind Cyclops, who commands them to charge into battle.
Chapter 3: Avengers Vs. X-Men
The X-Men charge into battle against the Avengers. Cyclops takes on his brother, Havok, as Longshot fights Daredevil. Longshot shoots Daredevil in the leg, crippling him, and then knocks him out with a swift kick to the face. Wonder Man sneaks up on Longshot, but Longshot quickly turns around and throws a smoke bomb into his face, blinding him. Wasp flies into battle against Goliath, who turns huge and claps at her, shooting out a burst of wind. Wasp goes flying through the air and turns back to normal size as she falls to the ground.
Juggernaut is puzzled to see the X-Men battling the Avengers, but Armor tells him that they've decided mutants must stand up for themselves. Juggernaut and Armor are attacked by the Hulk, but they manage to work together and knock him out. Wolverine battles the mutant Omega Red, who has metal tentacles coming out of his wrists. Wolverine gets tangled up in one of the tentacles, which Omega Red charges with electricity, shocking Wolverine. Omega Red calls Wolverine a traitor against his kind, and tells him that even if he were on the mutants' side he still wouldn't be worthy of joining the Brotherhood. As Omega Red monologues, Wolverine's healing factor kicks in and he gets back up, stabbing Omega Red in the face.
Storm and Shadowcat ambush Jubilee, who fires explosive blasts at both of them, but Shadowcat turns intangible and the blast goes right through her, while Storm flies out of the way and fires a lightning blast at Jubilee, severely injuring her. Elektra challenges Spiral in a martial arts dual, but Spiral manages to outmatch Elektra with her six arms. Elektra is knocked back and hits the side of a building, falling to the ground. She tries to get up, but Spiral is about to chop her head off. Suddenly, Rocket Raccoon shoots Spiral with a machine gun and kills her.
Cyclops is taking cover behind a pile of rubble as Havok shoots a beam of energy at him. Cyclops looks around, seeing all the death and destruction, and realizes the mistake he's made. Cyclops gets out of cover, and tells Havok he surrenders. Havok believes this is just another trick, but Cyclops tells him it's for real. The X-Men peacefully surrender, and leave Utopia. En Sabah Nur, seeing the X-Men surrender, realizes they were right. His vision has come true. Nur approaches Magneto and tells him they must surrender. Magneto tells Nur that humanity's time is done, but Nur tells Magneto it's just making things worse. Magneto tells Nur that the two of them could take over the Earth and make mutants the dominant species, but Nur doesn't listen.
En Sabah Nur kills himself using his telepathic powers to destroy his own brain. Magneto tells Scarlet Witch and Quicksilver that they must continue to fight back, but the two are in too bad of a condition to continue fighting. Quicksilver tells his father they must surrender with the X-Men, and Magneto snaps. Magneto attacks Quicksilver, and nearly kills him. Selene creates an illusion to trick everyone as Magneto and his mutants leave, all except for Nightcrawler, Darwin, Kid Omega, Quicksilver, and Scarlet Witch, who decide to turn themselves in. However, instead of imprisoning them, Nick Fury decides to give the five of them a second chance, and he sends them to the Academy of Tomorrow so they can join the X-Men.