Salem Center, New York, a young Jean Grey rides inside a taxicab. She wonders to herself why her life had to change. She used to be normal. Then one day, as she held her dying friend in her arms, she unintentionally used her mutant power for the first time. This is why she’s in the taxicab. She’s on her way to a new school, to Xavier’s School For Gifted Youngsters.
The taxi drops her off and as she makes her way to the door it all seems oddly familiar. She enters the school and is greeted by Professor Charles Xavier. He tells her that he can read her thoughts and he knows about her talent. He continues to tell her that she’s a mutant and he has formed his school to teach mutants how to best use their powers to benefit humanity. Professor then summons the rest of his students.
Bobby Drake comes in swinging on an ice rope. Jean realizes she already knows a lot about him even though she’s never met him before. Next in is Beast, in a human state. She senses something amiss with him. Storm walks in, the leader of the team. Jean can’t explain it, but she knows the black and gold uniform isn’t right on Ororo. Last but not least, Gambit enters and kisses Jean on the hand. He’s wearing red shades. He lowers them and Jean notes he has red eyes, but not the right red eyes.
Professor asks her how she’s doing and she tells him fine. They’re interrupted by an alarm from Cerebro. Surprisingly, their newest member knows the meaning of the alarm. A new mutant has been found. They make their way to the study and on a screen they see Magneto and Polaris. They are trying to take over Cape Citadel. Professor explains to Jean that there are also mutants out there bent on proving their so-called superiority over regular humans. Put simply, there are evil mutants out there.
The X-Men are excited. They finally get to test their skills on an opponent. The Professor tells them to wait. As they watch, Magneto and Polaris leave with a final warning: surrender next time, or they all die. As they fly off the screen, Gambit complains that they haven’t been able to fight anyone. Professor tells him that fighting is a last resort. He would never place any of his pupils in danger unnecessarily. Jean thinks to herself that what the Professor says is true, but everything else seems wrong.
Up above Earth on Asteroid M, Magneto and Polaris debate the actions of the day. Mags is upset because he wanted to show them his full force. Polaris tells him that although she believes in his cause, she will not kill innocent people. Magneto gets angry and starts off on a rant. He’s cut short by Rogue who’s standing nearby. She tells him about a news report she heard. It featured Charles Xavier, expert in human genetic mutation. He believes that humans and mutants can live together in peace. A grossly disfigured Marrow argues the point. Magneto backs her up and says that mutants who look different than humans will never be accepted. He reaffirms his belief that the world should belong to mutants. At this time, Sunfire flies in and reports to Magneto that he has found more mutants who might join up his cause.
Back in Salem Center the X-Men are training in the Danger Room. Charles is coaching Jean in perfecting her skills. He asks her what’s been bothering her since she’s arrived. She tells him that he probably won’t believe her, but she knows something’s missing, something important. He psi-probes her mind and comes up with nothing. However, now he senses something amiss as well. He starts to doubt his crusade. Does he have the right to put his students in harm’s way? Storm comes by with a message. Cerebro has spotted another mutant nearby, 32 miles north at the Monolith circus.
At the circus, the X-Men search for their mutant. Dressed in regular clothes, they walk around unnoticed. Jean passes by a poster advertising “Robo Man”. The man pictured has a metallic arm and a flash in his eye. Jean thinks to herself that he looks familiar. The team stumbles upon the main attraction. A metallic man is holding an elephant above his head using only one arm.
Inside a small tent, Bobby and the Professor explain to the metallic man their cause. Suddenly, the tent is ripped off the ground and we see Magneto and his Brotherhood. They have come to recruit the mutant as well. The rest of the X-Men rush over in case a battle starts. Professor and Magneto try to convince one another that their way is the right way. Jean can’t help but cringe at their words. The Prof tells Magneto that they should be on the same side; too many lives have been lost. He says he won’t let another X-Man die. At this point, the team wonders aloud “Who died?” Nearby, a shadowed figure runs from a mob.
Professor X doesn’t understand why he said what he just said, but he knows something is wrong. Magneto is confused at this point as well. The shadowed running man trips over a rock and falls to the ground, losing his red shades. He looks up and weakly calls out Jean’s name. “Scott”, she cries and suddenly remembers everything. She telekinetically knocks the mob back. Scott, lying in her arms, warns her that Apocalypse is manipulating time.
The X-Men and the Brotherhood take on the crowd, beating them senseless. Scott tells Jean that she has to stop the fighting. He reminds her of what happened, the sacrifice he made and the merge of their bodies into one. He tells her that his body can’t contain the powers; that he’s failed. The crowd was supposed to contain him, to stop him from contacting his teammates. Now that he has done so, Apocalypse won’t hold back. At this point, the people in the mob start reverting into the Monolith cultists. Scott tells Jean he’s under attack by Apocalypse now. Jean starts crying and tells him she’ll protect him. Sensing trouble, Scott tells her he loves her. He then metamorphoses into Cyclopalypse and knocks Jean away. Professor sees this and yells for everyone to attack Cyclopalypse. Slowly, everyone remembers what really happened. They all fight their hardest, but it doesn’t do anything against the power of Cyclopalypse.
Jean yells for everyone to stop. She tells them that Cyclops is still alive inside, unable to control the massive power of the Twelve. Cyclopalypse starts fizzing and seemingly explodes. Everyone is thrown backwards and reverts to their true forms. They find themselves back at the chamber of the Twelve. They find the power circuit is badly damaged.
Nate asks where Apocalypse is and the Professor does a mind scan. He can’t find any trace of Apocalypse, Cyclops, the Skrull warriors or the Living Monolith and his followers. Professor thinks that Apocalypse might have failed because Scott couldn’t contain the power. Jean tells the Prof off. She says that it was Scott fighting from the inside that caused Apocalypse to falter. Professor tells her that he didn’t sense Scott at all during the fight. He suggests it was a ruse by Apocalypse. He tells her that Scott is gone. Jean starts crying again and she yells at Xavier. She brings up how he came out of retirement for him. He gave up a chance at a normal life for him. She walks off and we see the rest of the X-Men’s downcast faces. Professor tells them to let her go for now. There’s nothing more to do.