Magneto stands on top of Wundagore Mountain and looks at the complex he has erected there. Sensing that the hatred towards mutants is growing stronger everyday, he has chosen to isolate himself from the rest of the world. Here, hidden from humanity, he can train the young group of mutants he has gathered from all around the world. Here they learn to protect themselves from a world that is not yet ready to accept them. A thunderous roar announces the arrival of one of his prize students - Quicksilver, the son of Magneto who is gifted with super speed. He tells Magneto that the X-Men are awaiting him in their training ground called Killing Zone. Magneto orders Pietro to run a Level One exercise until he joins them. Watching him depart, Magneto wonders if he is pushing his students too hard.
Somewhat later, Magneto watches his students' performance. Iceman, Storm, Quicksilver, Jean Grey, the Scarlet Witch and Colossus are fighting robots in the Killing Zone. They all have made progress in the use of their powers, and even Iceman is beginning to show signs of reaching his full potential. Magneto then joins the training session, for he thinks his place is not at the sidelines, but as part of the X-Men. He has to fight among them. Magneto reminds everyone of the importance of teamwork, and when Iceman and Colossus congratulate each other over their performance, he tells them of the danger of overconfidence.
Magneto then starts a Level Four exercise, much to Wanda's amazement, as they have never before trained under such hard conditions. Magneto says that in order to survive, they need to learn to adapt. Thinking that some of the X-men have become too lax, Magneto decides to introduce them to real danger. Magnetically raising a door at the far end of the room, he presents the team their newest and most dangerous X-Man: Weapon X. He immediately joins the battle and soon goes into a berserker rage. Pietro quickly pushes Iceman out of Logan's range and Magneto slams Logan into a wall. He then orders Jean to soothe Logan's mind with her telepathy. Although she is not very experienced with that power yet, Jean succeeds and finds a mental barrier of anger and hatred. Having calmed him down, Jean wonders aloud how anyone could stand such pain, but Logan doesn't answer. He congratulates her since more experienced telepaths have fried their brains trying around his head. Magneto orders the X-Men to show him around as he has another new arrival to tend to.
In New York City, a large ship appears in the sky, covering most of Manhattan in shadow. The people look up in fear, as a projection appears, even bigger than the ship. The image is that of Candra, who introduces herself as Herald of Apocalypse. She informs humanity that their day is over and that Homo Superior will soon rule the planet.
At Wundagore, Magneto thinks that Apocalypse is making his move sooner than he expected. All the planning and training will be put to the test now. Thinking of his friend Charles Xavier, Magneto wonders how he would have handled things differently. Magneto is interrupted by Bova, who reminds him of Mystique and a young Lady from the United States waiting in the other room. After being allowed inside, Mystique says that she has more important things to do than waiting for an audience, especially after what is happening in New York. Magneto tends to the young woman in her company, Rogue. She asks if he will help her learn to use her powers like Mystique said and he confirms it. Mystique interrupts; she has no time for all of this. Magneto already knows that Apocalypse tried to get Rogue, so he asked Mystique to find her for him, which she has done. Her task now complete, she wants to depart. Rogue panics, but Mystique says that she raised her to be stronger than that. Magneto is a good man and she will find friends among the X-Men soon. With tears in her eyes, Mystique says that she has grown quite fond of Rogue in their time together and then runs away.
The X-Men come to Magneto's office, and are curious about the new student. Iceman is happy that it's someone around his age, but when he tries to touch her, Rogue angrily pushes him away. After Jean catches Bobby with a telekinetic bubble, Rogue states that she won't be touched by anyone, and asks to be left alone because she is dangerous. Magneto denies this request. He says that he knows of her absorption power and how she retained a portion of Polaris' powers after an unsuccessful abduction attempt. He goes on to say that powers like hers are not necessarily a curse, and that together they will find a way to control them. Rogue softens up and they hug.
Cape Citadel is the stronghold of the United States' Nuclear Defense Arsenal. It is considered an impenetrable fort, however the army will learn different tonight. Apocalypse's giant ship de-cloaks above the fort and alarms immediately go off. The five Horsemen, Gideon, Candra, Sabretooth, War and Death, look down at the gathering troops with amusement. They are no match for them.
At the Wundagore complex, the Scarlet Witch is showing Rogue around and explains her the purpose of the school. Rogue wants to know why Mystique and Magneto apparently do not like each other. Wanda explains it with her father being a loner, who is perceived as cold and arrogant. He is difficult to reach. She goes on explaining that in his youth, one of Magneto's closest friends, Charles Xavier, died saving his life, and this event shaped Magneto. Standing in front of a bust of Xavier, they fail to notice that Magneto stands behind them and has overheard their conversation. Making his presence known, Magneto says that Xavier was a mutant, a visionary and a man of peace. Quicksilver storms in to inform them of the attack on Cape Citadel. Magneto tells Wanda to have the X-Men assembled in the hangar and rushes off to prepare for the upcoming battle.
At Cape Citadel, the Horsemen have started their attack. They easily defeat the first waves of tanks and soldiers, despite there being some dissention in the ranks. Candra doesn't like to be bossed around by Sabretooth who apparently is in charge. Gideon tells her to put aside their differences, because he needs to be online in the main complex within the next three hours - otherwise they will have missed a specific window of opportunity. Having entered the building, Sabretooth says that their objective is underground, and the group moves on.
Half a world away, Magneto follows the events on the satellite-fed monitors of the Ready Room. He regrets that the X-Men will be too late to help the many soldiers, but they will be avenged. Turning to his students, Magneto says they will leave for the United States in five minutes. While the X-Men board the jet, Magneto tells the Scarlet Witch that she will stay behind to take care of the school and the younger students, just in case they don't make it back alive. As Wanda and Rogue watch the jet depart, they are unaware of another figure observing too. On a nearby mountaintop stands a handsome stranger with long blond hair. His name is Nemesis, and although he is a mutant, he does not plan to enroll at Magneto's school.
The Horsemen reach the heart of the complex at Cape Citadel. After killing the remaining soldiers, Sabretooth orders Gideon to get to work, while he signals the boss that they are on schedule.
(Two hours later)
The X-Men's jet reaches Cape Citadel. They wonder where Apocalypse's ship is, as it doesn't show on their radar. Suddenly, the cloaking field of the craft drops, and they almost hit Apocalypse's ship. The Ship's defenses charge up and prepare to shoot the X-Men. Magneto orders Quicksilver to initiate autopilot and Storm creates a diversion with her weather powers. Magneto once more reminds his students that this is not a training session, and then the team moves into action. Jean levitates Logan, Magneto lifts Colossus, and Quicksilver rides down on Iceman's ice-ramp.
At Wundagore, the school is under attack by Nemesis. He hits parts of the building with his biogenetic microwave blasts, and some of the kids staying inside get injured and others killed. Nemesis laughs at the idea of so many mutants gathered in one place, yet none fit to survive. Elsewhere in the complex, Wanda is guiding some of the scared students to the underground shelters. She asks Rogue to help her with some of the youngest, only to find that Rogue is no longer standing behind her. The young woman has had enough, and decides to take the fight to Nemesis. With the magnetic might she permanently absorbed from Polaris, she is able to defy gravity and also to increase the power behind her punches. Rogue hurls herself toward Nemesis and knocks him over. After getting up, Nemesis uses his power on Rogue and the heat places her in agony. The Scarlet Witch attacks, and with her probability altering spheres, she actually manages to hurt Nemesis. He didn't think this was possible and promises to make Wanda pay ...
At Cape Citadel, Gideon has gained entry to the base's computer systems and has now access to all U.S. nuclear missile sites around the world. After contacting Apocalypse about the progress, Gideon starts the targeting and launching sequences, much to Sabretooth's surprise. He thought that the mission was only about controlling the missiles, not using them. Apocalypse predicted that Creed would oppose his plans at that point, but he needed him to lead the attack. Now Creed is useless and the other Horsemen stand ready. Candra is now in charge of the group, and with her telekinetic powers she quickly encases Sabretooth in a bubble that holds him in place. Not wanting to further disturb Gideon during his work, they take Creed outside to execute him but instead run into Magneto and his X-Men.
Although he is in deep trouble, Sabretooth convinces Candra that the Horsemen will need him in this fight. Candra agrees and releases him, though she announces that it will merely delay his execution. Sabretooth leaps towards Magneto who easily holds him at bay with his magnetism, though it was a set-up for a telepathic attack by Candra. Yet Magneto's will is strong enough to resist and he orders his X-Men to attack. Logan is more than willing to fight and jumps on Sabretooth and Candra. Creed, back in his leadership role, orders War and Death into the air, and then turns to Logan. He recognizes him as Weapon-X and says that Apocalypse thought of recruiting him, though then decided for Sabretooth. As they start slicing each other with their claws, Sabretooth says he has a need to side with the winners, which right now looks like it's going to be Apocalypse. He might even learn to live with the idea of nukes. All he wants is to survive. Logan has enough and goes into berserker rage.
Elsewhere, Magneto and Jean are making their way toward the base, while the other X-Men keep War and Death busy. They want to stop the missile launch, however Candra blocks their way to the building. Jean tells Magneto to move on, while she will deal with her. Reluctantly, Magneto moves on. He knows that Jean's decision is right, though he would prefer fighting alongside his team. In the basement, he finds Gideon at the computers and uses a magnetic pulse on him, unaware of the green haired man's amplifying and redirecting power. Crushing Magneto into a wall with his own power, Gideon intends to make the master of magnetism watch the countdown running down.
Outside, Storm uses lighting against Death, hoping that she didn't kill her opponent, and Iceman and Colossus easily defeat War. While Apocalypse's ship slowly descents, Sabretooth and Weapon X are still going at each other until Logan severs Creed's spine with his adamantium laced claws. In the computer room, Gideon taunts Magneto about the coming Age of Apocalypse and how the world will bow before him. Magneto summons all his resources and draws power from the earth's magnetic field, which he unleashes into one focused burst. It overloads Gideon's absorption power and he explodes, destroying the entire complex. The missile launch is prevented, and although the X-Men wonder if their mentor is still alive, they don't have the time to check as Apocalypse emerges in the hatch of his giant ship. He congratulates his foes, as they impressed him with how easily they defeated the Horsemen. Actually he would want to invite them to join him, but he thinks the X-Men are tainted by Magneto's righteousness. Apocalypse leaves Sabretooth to die among the X-men and after his ship takes off, the weapons prepare to blast the entire area. Suddenly, Magneto emerges from the wreckage and manages to create a magnetic pulse that shatters the ship's weaponry. The X-Men watch the ship fly away, and Magneto congratulates his students - today they have done well. However, this was only the first of many more battles to come and from now on they have to be prepared to oppose Apocalypse every single day.
Among the ruins of the school at Wundagore mountain lays the badly injured Scarlet Witch. Rogue tends to her and says that everything will be fine. Nemesis has left and the children are safe, but now Wanda needs to rest. However, the Scarlet Witch knows the end is near and says that she no longer feels any pain. She says that Magneto needs to know that they are no longer safe on Wundagore. Rogue repeats that Wanda should rest and not further strain herself, but the Witch has one more request. Her father's burden is too great and she knows that he needs a friend. She asks Rogue to be that friend since she will no longer be there for him. Rogue promises, but tells Wanda that they both can be there for Magneto. Wanda knows differently, and after saying "No Rogue ... I'm tired. So tired.", she dies.
When the X-Men return home, they all gather around Wanda's dead body. Magneto has paid the highest price this day and he knows that the X-Men's course is clearly set. For Wanda and for the world, they will fight on to make the world a better place.