The Horsemen of Apocalypse take off for Manhattan. Apocalypse watches them from his view-screen, allowing X-Factor to see as well. Mayhem ensues immediately as Pestilence and Famine lay waste to a bunch of humans. Beast, Iceman, Cyclops and Marvel Girl watch in horror from their restraints. Cyclops yells at Apocalypse for manipulating his Horsemen and especially Warren to the dark side. En Sabah Nur explains that the humans are mutants’ natural enemies. He points out that Cameron Hodge understood that. That’s why he prompted Warren to form X-Factor, a group posing as mutant hunters and when he no longer wanted X-Factor around he had Warren’s wings amputated and blew up his plane. Apocalypse rescued him, however, and gave him new wings and a new purpose; to exact revenge on those humans who would rather see him dead.
Apocalypse claims that he will save mutantkind. He offers X-Factor another chance to join him, to oppose the Mutant Registration Act (which requires all mutants to register their powers with the government). He suggests the next step from the humans may be to send them off to camps, use them as weapons, or even exterminate them.
All of Apocalypse’s talk is making Beast angry. He uses his newfound strength and manages to rip off a scrap of metal from his restraints. He looks over at Iceman and tosses the hunk of metal at his inhibitor belt. It does the trick and Iceman’s free to use his powers. He ices up and breaks free, simultaneously icing up everyone else’s shackles, setting them free as well.
Apocalypse mocks their continuous attempts at stopping him. He enlightens them to the fact that he is benefiting the world by ridding it of the humans. Cyke doesn’t buy it and orders Jean to telekinetically lift them up towards Apocalypse. En route, Jean tells the Evil One to stop the madness. Apocalypse tells her that the real madness is their expectation of victory.
Apocalypse reaches out to Caliban who’s trapped in some sort of bubble. He tells him that he’s not quite ready to join in the fight, and moves him out of harm’s way. X-Factor attacks. Iceman freezes the platform beneath En Sabah Nur’s feet, causing it to fall apart. Apoc’s arms form into wings and he flies away. Scott takes a shot at him with his optic blast and misses. His shot blasts through the ships’ walls and into a New York city transformer. Somehow, thanks to that blast, Apocalypse’s ship is able to draw power from the transformer.
Iceman is upset and wonders aloud if they can ever go without causing destruction. Jean tries to calm him, but is cut off by Apocalypse. He reminds them of how much the humans despise them, despite their best efforts. He once again asks them to join him and stop their aggressions.
Cyke tells him to forget it, and X-Factor moves in for another attack. Apocalypse grabs a nearby lever, opening up a bay door beneath them sending them out into the city. He tells them to go ahead and try and stop his Horsemen. Cyke and Jean are sucked out, but Hank grabs Bobby and a nearby pole and manages to stay inside. Once outside, Marvel Girl uses her telekinesis to keep herself and Cyclops afloat. They notice that Iceman and Beast managed to stay in the ship. Unfortunately, the ship is invisible and they’re not sure where it’s located. They decide to head down to the ground where they notice a bunch of bodies lying on the ground.
Scott immediately realizes it as Pestilence’s work. Jean spots her in the subway knocking over a few more humans, before racing off into the tunnels. For some reason Jean’s powers can’t affect her and they lose her. They hear a scream above them. Cyclops blasts an opening through a nearby grate and Jean lifts them up. They’re in Central Park, with War off to the right, and the screams coming from the left. Scott and Jean share a passionate kiss before splitting up in both directions.
Jean arrives in time to find Famine harassing a bunch of humans at a hot dog cart. She emaciates the three customers and vendor before Jean can get to her. Jean goes after her and tries to talk some sense into her. Famine knocks her away, touching her, and explaining to Jean that her parents were ashamed of what she could do, but not Apocalypse, he loved her. Jean asks her what her real name is, and Famine tells her it’s Autumn.
Jean tries to convince her that she needs help, and offers it. While speaking, Jean telekinetically lifts up the hot dog cart and throws it at her. It connects and Famine goes flying off her horse. As she falls, she yells out to Apocalypse, telling him that she won the fight with Jean and that he should give her what he promised. He promised to send her to America’s Bread Basket where she could melt the fat off of everyone.
Suddenly, Famine and her steed disappear in a teleportational burst. Jean wonders aloud where Apocalypse would have sent her. Jean’s focus shifts back to herself as she’s starving from Famine’s touch. She reaches for some knocked over hotdogs and sodas.
Meanwhile, Cyke spots War flying overhead. War talks about how the government wastes its money on War monuments when they should be spending it on those soldiers who were wounded in the wars. He blasts a nearby statue, much to Cyclops surprise. Cyke blasts him, but it ricochets off of War’s armor. Cyke tries to assuage him by mentioning the civilians in the area and how they could get hurt like he was. War doesn’t care anymore, though. He tells Cyclops that civilian casualties are the main by-product of war. Cyke dodges one of War’s blasts and somersaults onto his ride. He fires an optic blast directly into his steed’s mouth. The mechanical beast’s head explodes and both War and Cyclops go flying towards the ground. Despite all of Cyke’s attempts at convincing War to stop his madness, he stays with Apocalypse who saved him from his paralysis.
Jean arrives on scene and stops Scott from smacking into the ground. War, though, disappears in a teleportational burst. Scott explains to Jean that War is as loyal to Apocalypse’s cause as they are to Xavier’s. He admits that with mutants like Apocalypse, you can’t really blame the humans for hating them.
Back on Apocalypse’s ship, Iceman pleads with Beast to take it easy. He doesn’t want Hank to overtax his brain. Bobby fires a volley of ice balls at Apocalypse, who morphs his arm into a shield and deflects them right back at him. Several of them come back and knock Hank off his feet. Apocalypse ‘ports and reappears behind Iceman. He clocks him in the back of the head, knocking him unconscious. Apocalypse stares down Hank. He morphs his legs into elongated poles. Hank rips out a piece of the wall and tosses it at him. Bobby awakens just in time to see Hank overexert himself again. Apocalypse disappears before the debris can hit him and reappears on a nearby floating platform.
Lightning starts surging around the ship. The ship itself starts to turn on its side. Hank wonders what he did. From the outside, the ship becomes uncloaked. Somehow Hank really messed things up and everyone in the city below is panicked. The ship starts to slowly sink and runs into the top of a building, knocking it over. Inside, Beast is still clueless as to what’s happening. Apocalypse informs him that the cloaking mechanism malfunctioned and the ship’s stabilizers went offline. He then starts laughing like a madman. Beast leaps at him, but Apocalypse just teleports elsewhere. He continues to tell Beast that everything that’s going on is his fault.
Back outside, Scott and Jean watch as the ship tumbles entire buildings. Despite her weakened condition, Jean tells Scott they need to do something. They fly towards the ship to try and stop the destruction. On their way they run into Warren, now known as Death who is adding to the destruction. Scott fires a blast at him and misses. Angel turns around and mocks Scott for still „hunting" mutants. He talks of his contempt for the humans for what they did to him. Jean can understand his situation, but doesn’t know why he would attack them. They were good friends.
Death soars towards them, making contact with Scott and knocking him loose of Jean’s hold. Jean goes after Cyke and regains control of him. She mentions how Warren had the chance to kill them and didn’t take it. She thinks they have a chance to break him of Apocalypse’s influence. Scott is doubtful, however. He believes Warren is just toying with them.
The ship hits another building and Jean and Scott realize they have more important matters to attend to. They take notice of the ship’s path and realize its next stop is the Empire State Building with no time to prevent it. The ship makes contact with the building’s antenna and Jean tries her best to hold it in the air. She isn’t sure how much longer she can hold it when Power Pack shows up to assist. Unfortunately, they’re followed by Pestilence who zooms in on Scott and Jean. Luckily, Molecula comes to the rescue knocking Pestilence off her horse.
Warren comes back on scene and slices the antenna in two pieces. Jean can’t hold on to both pieces and one of them falls to the city below. Meanwhile, Katie Power swoops down to save Pestilence before she hits the street. Once she grabs hold, however, the debris from the sliced antenna comes falling all around her. She loses her grip on Pestilence as she maneuvers through the air. Both the debris and Pestilence slam onto the ground.
Back on the ship, Beast dives once more towards Apocalypse. He teleports once again and laughs at Hank’s futile attempts to stop him. He knows Hank’s brain power is shrinking with every feat of strength he makes. Unbeknownst to En Sabah Nur, Iceman is conscious and he freezes the platform Apocalypse is standing on and encases him in a block of ice. Apocalypse manages to break free, though, and informs them he’s taking it up a notch. He pulls another lever.
Back outside, Death heads toward Power Pack, Scott, and Jean. He disappears suddenly as he is teleported away by Apocalypse. They head to the city below and find Pestilence’s dead body. Her steed, however, is in good condition. Scott suggests he and Jean ride it back to Apocalypse’s ship. Power Pack wants to know who Apocalypse is. Jean fills them in and they tell her they want to help. Scott tells them that they can help by watching over the city, and they take off.
In Apocalypse’s ship, War fires a clap-blast at Hank. Hank dodges it, and Iceman takes his turn, throwing a huge block of ice at War. War takes the hit, which shorts out his armor. Death makes his entrance and tells Iceman to surrender. A blast opens a hole in the wall behind Bobby and luckily for him it’s Scott and Jean. Warren takes the opportunity and lays down a volley of blades at his former friends. Jean redirects the blades, so Warren fires some at Hank who’s located elsewhere. Beast manages to somersault out of the way coming out unscathed.
Cyclops blasts away at Death. Jean and Scott debate whether Warren is able to be saved or not. Jean thinks so, but Scott still has his doubts. Iceman comes up with a plan and tells Jean to cover him. He heads off behind his teammates and warns them that if his plan fails, they might have to kill Warren to stop him.
Speaking of Warren, he comes flying in towards Jean. He asks her why she sticks up for the humans. She tells him that their powers give them responsibilities and they use theirs for justice. Nearby, War tries to get his hands together for one more clap. Jean notices him and tosses him in the air towards Warren. Warren tells him he’s outlived his usefulness and sends War flying into a wall.
Warren speaks of the injustice that was wrought upon him by the humans. His wings were amputated, and now Apocalypse has made him the judge, jury, and executioner. He spots Iceman near him and dive-bombs him, breaking his ice-form in half. Apocalypse congratulates him, while Jean and Scott yell out in horror. Warren, himself, yells out in anguish. He suddenly realizes what he’s done. He looks at Apocalypse accusingly, asking him what he’s done to him. En Sabah Nur tells him that he passed the final test, and that he is truly strong. Warren takes off his mask and tells Apocalypse that he is no longer his master. He immediately flexes his wings and lays down a volley of blades at his former boss. Apocalypse forms a giant shield with his arm and blocks the attack.
The rest of X-Factor join in the fight now that Warren is back on their side. From around the corner, Iceman comes in on an iceslide, much to Angel’s surprise. Warren asks him what happened. Bobby explains that he made an ice replica of himself, hoping that if he destroyed it, it might snap him out of Apocalypse’s hold.
Apocalypse goes on the defensive with the combined might of X-Factor on his trail. He manages to bash Warren in midair knocking him towards Beast. War sneaks up on Beast and Angel intent on killing the traitorous Horseman. Beast snatches Warren up and dodges the blast. Iceman comes in and freezes War up. Jean and Scott are left to tangle with Apocalypse. Apocalypse brings Caliban forth, still inside his bubble. He asks Caliban if he is still on his side. Caliban tells him that as long as he keeps his promise to make him strong, he is. Scott attempts to break up their conversation with an optic blast. Apocalypse creates a shield, using the brunt of the force to knock him, War and Caliban through the ship’s wall and out to safety. He yells to X-Factor that they can keep his ship. He morphs his arms into wings and flies away.
Jean attempts to go after him, but Scott tells her not to. The ship continues to flip over and Iceman decides to freeze one end and see if it stabilizes it. A sudden explosion occurs and the ship swings down into the water, narrowly missing the Statue of Liberty. Unfortunately, the ship’s not down and it topples over heading straight for X-Factor’s headquarters. It comes to a stop smashing stop, crushing their base of operations.
Inside, everyone’s excited that they managed to save New York City. In fact, they’re even happy that they destroyed their former headquarters. Warren’s the only one not celebrating. He tells them what happened to him. How he had survived the plane crash and that his friends never looked for him. Apocalypse found him, though, and twisted him into what he is now.
Warren’s story is interrupted by some knocking on the ship’s roof. It’s a bunch of reporters and the team decides they’re ready to face the music. They tell Warren to join them, but he refuses. He’s ashamed and worried at what Apocalypse’s changes have done to him. Cyke opens the hatch anyway and the team meets with the press. The reporters bicker over whether they’re heroes or enemies. Cyclops informs them that they’re the ones who saved the city and that it was Apocalypse and his Horsemen that were the bad guys. One of the reporters spots Warren and claims that he was one of the villains. This opens a debate where X-Factor discusses the fact that there are evil humans and mutants alike, and that they shouldn’t judge all mutants as evil. They confess to what they were really doing as X-Factor; taking mutants and training them so they were no longer a danger to themselves or society. Unfortunately, their cover as mutant hunters further fueled the humans’ fear of mutants. Cyclops calls on everyone that is good in the world to work together as humanity’s children, or else the evil people of the world "will make the Earth a battleground... and ultimately a graveyard."