Synopsis by Thunderbird III: Note: This story takes place many years before the events of X-Men Alpha. Magneto stands surveying the X-Men’s Mount Wundagore base. Quicksilver arrives to inform him that the X-Men are ready for their training session and Magneto orders him to go ahead and start a level one exercise before he arrives. He take a moment to reflect on how he is too harsh on his students, especially Quicksilver but that rigorous training is the only way they will be able to survive the trials that lay ahead of them. We are then introduced to the X-Men Iceman, Scarlet Witch, Colossus, Quicksilver, Jean Grey and Storm. They are taking part in a training exercise against simulated robots in the Killing Zone (Magneto’s version of the danger room) while Magneto comments to himself on their improving performances before joining their exercise. He thinks about how his only true place is fighting side by side with his X-Men and proceeds to instruct his students on the value of Teamwork. As Quicksilver and Iceman high five at the conclusion of the exercise Magneto berates the two of them for celebrating a minor victory and orders a level four exercise. Scarlet Witch protests but Magneto tells her that they need to learn to adapt and adjust in order to survive. Magneto then brings in the newest member of the X-Men who introduces himself as Weapon X but tells Jean he can call her Logan. Weapon X proceeds to take out several robots and in his berserker state nearly takes out Iceman as well before Magneto uses his powers to pin him against a wall. Jean Grey tries to telepathically calm him down but faints due to the strain. Logan tells her to be proud as many experienced telepaths have had their heads fried trying to poke around in his head. As Logan gets to know the X-Men Magneto goes off to greet another new arrival. We then skip to New York city where a giant floating image of Candra informs the cities humans that their time has come. Back in Wundagore Magneto looks at an old photo of Xavier wondering what the world would have been like had he survived when he is interrupted by Bova who informs him that Mystique and a young lady have been waiting to see him. Mystique introduces Magneto to Rogue and leaves her there bidding her a teary farewell. Magneto introduces her to the X-Men and she clobbers him as he tries to shake her hand saying that no one should try and touch her. Magneto calms her down telling her that her powers are a gift, not a curse and that the X-Men are now her family. Over Cape Citadel, Florida Apocalypse’s giant ship de cloaks and his horsemen Death, Candra, War, Sabretooth and Gideon prepare to attack. Meanwhile back at the school Scarlet Witch gives Rogue a tour of the facilities. She explains about Magneto’s goal as they pass a bust of Charles Xavier and Magneto himself joins them and explains Xavier’s dream to them. Quicksilver then interrupts and informs Magneto that Apocalypse’s troops are attacking Cape Citadel and Magneto orders him to assemble the X-Men in the Hangar. Apocalypses troops tear into the bases defence forces. Candra resents having to take orders from Sabretooth and as the giant ship holds off the ground troops the Horsemen proceed underground. Magneto having watched the events through a spy satellite travels to Cape Citadel with his X-Men. Scarlet Witch is left behind to watch the base and the other students. As the Blackbird flies away from Mount Wundagore, another mutant, Nemesis, watches from a nearby hilltop. As Sabretooth clears the last of the bases security the X-Men arrive at Cape Citadel looking for Apocalypse’s ship. They are unable to see the ship till it attacks and the X-Men abandon the jet break into teams in preparation for battle as Magneto reminds them that this is no training session. Meanwhile Nemesis is tearing up Mount Wundagore with energy blasts. As Scarlet Witch shepherds the remaining students to safety she notices Rogue has gone missing. Rogue attacks Nemesis but he repels her attack and prepares to strike. He is interrupted by the arrival of the Scarlet Witch whose hex bolts hurt him, enraging him further. Meanwhile at the base Gideon works towards launching the nuclear arsenal. Sabretooth protests at being mislead to the true purpose of the mission and Apocalypse mocks his ‘weakness’ and orders the rest of the Horsemen to deal with him. Candra encases him in a telepathic bubble and takes him outside to be executed but is interrupted by the X-Men before she can complete the act. Sabretooth convinces Candra to let him join the fight and takes charge as a battle erupts between the Horsemen and the X-Men. Magneto makes his way to Gideon. Gideon absorbs Magneto’s power and traps Magneto with them but Magneto uses power from the Earth's magnetic field to destroy Gideon and destroy the controls for the missiles before they can launch. On the surface Weapon X takes out Sabretooth as Strom knocks out Death and Iceman and Colossus team up to take out War. Apocalypse’s ship descends and he recovers his surviving Horsemen but leaves Creed behind. He trains the ship's weapons on the X-Men but Magneto appears from the rubble and takes out the weapon systems with an electronic pulse. Back on Mount Wundagore Scarlet Witch's battle with Nemesis has left her fatally wounded. As she dies she makes Rogue promise to always be there for her father. The last page shows Magneto kneeling over the body of his dead daughter with the X-Men watching.