Charles Xavier believed in the possibility that humans and mutants could co-exist with one another but his best friend, Erik, believed otherwise. That was all to change on the day Xavier was accidentally murdered at the hands of Legion. Erik changed his views on human/mutant relations and chose to honor his best friend by continuing on with his dream instead. However, people's intolerance against those who were different prevailed and Erik isolated himself from the world, acquiring a base in Wundagore Mountain to reside in. Unfortunately Apocalypse was beginning to make a play for world domination with nobody to stand in his way. Dubbing himself Magneto, Erik founded the X-Men as a means to reinforce the dream and to fight Apocalypse to a standstill. His first two recruits would be his own children, Quicksilver and the Scarlet Witch, who embraced the dream and helped Magneto gather other members to the cause. Magneto announced that he would help mutants train in the use of their powers. Jean Grey's parents began to fear for her safety and turned to Magneto for help, who took the young girl in. As a result Jean Grey would become the third X-Man to be recruited to the cause. Eventually Magneto would gather other mutants such as Colossus, Iceman and Storm to the X-Men as well as younger mutants to train in their powers and use as possible future X-Men one day.
Due to the harsh reality under Apocalypse's rule, Magneto would push his X-Men to their limit in the Killing Zone, the combat training room in their Wundagore base. Nonetheless his X-Men proved themselves formidable in their exercises. The X-Men were soon to get two new recruits-Weapon X and Rogue, who was brought to the base by Mystique. At the same time however, Apocalypse's Horsemen were to make their presence known by attacking Cape Citadel and launching all U.S. missiles located around the world. The X-Men were called into action, with Magneto asking the Scarlet Witch to remain behind to look after the younger students. As they left, the X-Men were unaware of another, more deadly mutant approaching the base-Nemesis. Nemesis began attacking the base, with the Scarlet Witch trying her best to protect the students. The more assertive Rogue however chose to attack Nemesis rather than wait for help to arrive. Wanda went outside to try and protect Rogue and used her hex powers on Nemesis, which actually hurt him. As an act of revenge, Nemesis killed the Scarlet Witch before departing. Before she died, Wanda begged Rogue to look after her father after she was gone. When the X-Men returned from a successful mission, they were greeted by a destroyed base and a dying Scarlet Witch, the first casualty in the war against Apocalypse.
The death of Magneto's daughter initially made the master of magnetism want to give up but his X-Men gave him the strength to carry on. Acquiring more X-Men to the fold such as the shape-changing mutant Morph, Nightcrawler, the son of Mystique, and former Horseman Sabretooth, helped to strengthen Magneto's side. The X-Men were also forced to move location knowing that Apocalypse knew about their base in Wundagore Mountain. On one occasion, during a raid on Sinister's pens, Sabretooth rescued a young mutant girl named Clarice. Under his tutelage, Clarice would become a formidable fighter and X-Man, choosing the name Blink because of her teleporting abilities. The X-Men would later fight the Horseman known as Death during which the X-Men would team up with Cyclops, a member of Sinister's elite mutant force. The X-Men also rescued a mutant named Sunfire, whom Death was keeping prisoner. Defeating Death, the X-Men also acquired a new member in Sunfire.
Jean Grey was captured by Cyclops and sent to Sinister's breeding pens where Sinister took a sample of her DNA, later combining it with a sample from Cyclops to create the mutant known as X-Man. Weapon X stormed the compound and freed Jean, battling Cyclops along the way and losing his left hand in the process. Weapon X and Jean decided to leave the X-Men altogether leaving Magneto devastated by the news. Rogue began to date fellow X-Man Gambit but she was also burdened with feelings for Magneto. During a battle with Wolverine, a mutant altered by the Beast, Rogue was forced to choose between the two when both were attacked by Wolverine. Choosing Magneto over Gambit, the Cajun mutant was left heartbroken and, after defeating Wolverine, left the X-Men. Magneto and Rogue would later marry and have a son named Charles, named after Magneto's long departed friend.
Soon afterwards, the X-Men would meet a man that would give them a new purpose in life-Bishop. Bishop was a witness to the murder of Charles Xavier twenty years earlier and, as he claimed, this event altered reality. To see if there was any truth to Bishop's claims, Magneto asked Rogue to absorb the strangers memories, with him extending the bio magnetic shield that protected him from Rogue's ability, thus acting as a buffer between the contact. At the moment Rogue touched Bishop, Magneto's mind was filled with images that proved Bishop's claims. Magneto formulated a plan to make things right and ordered Nightcrawler to find his mother and bring to him the mutant seer called Destiny. Colossus and Shadowcat were to rescue Illyana Rasputin from the Seattle Core. He also requested Gambit's aid, who at the time had formed his own team called the X-Ternals, and asked him to bring a shard of the M'Krann Crystal to help in his plan. In the meantime the other X-Men would continue with their mission to rid the world of Apocalypse. The X-Men broke into two separate teams with Rogue's team trying to prevent the human cullings from happening in Chicago while Quicksilver's team helped the Sentinels with the human evacuation in Maine. Despite Quicksilver's team having to face opposition from both the Brotherhood of Chaos and the Horseman known as Abyss, the evacuation proved a success. Rogue's team faced a tougher time, with Sabretooth been captured by Holocaust and almost killed. Nevertheless, the X-Men did manage to break into the Infinite processing plant, rescue Sabretooth and defeat Holocaust. To top it all off, they also managed to destroy the processing plant itself, thereby preventing more Infinites from been created. Unfortunately, Apocalypse found out the location of the X-Men base and, accompanied by an army of Infinites, made his way to the Xavier estate in Westchester. With the X-Men still on their various missions, it was up to Magneto and Bishop alone to stop Apocalypse's forces. However, the army proved too formidable and Apocalypse managed to defeat Magneto with the Infinites capturing Bishop.
When the X-Men returned home they discovered the mansion was empty with signs of a struggle. Quicksilver ordered Dazzler and Exodus to enter the tunnels and locate his little brother, who was in the care of his robotic Nanny. In the meantime, Bishop was been interrogated by the Madri. When Shadow King entered the time traveler's mind, he discovered the existence of a timeline in which Apocalypse did not rule. Back at the mansion, Quicksilver decided that his team would go to Quebec to rescue Bishop as he was integral in his father's plans. Gambit had returned from outer space with a shard of the M'Krann Crystal in tow, Unfortunately he was betrayed by his X-Ternal teammate Guido and the shard was given to Apocalypse. Guido also destroyed Nanny and delivered young Charles to the dictator as a means to gain freedom for himself and Lila Cheney, the woman he secretly loved. The X-Men managed to free Bishop from the clutches of the Madri and encountered Jamie Madrox, the host body from which the Madri duplicates originated. Abyss chose this time to make his presence known and attacked Quicksilver and Banshee. Banshee sacrificed his life to defeat Abyss once and for all. Jamie Madrox begged Quicksilver to end his life but when the X-Man showed he could not end an innocent life, Madrox chose to end his own, thereby stopping the Madri once and for all.
Rogue and her team returned from their mission and found out that her husband and child were captured by Apocalypse. Initially blaming Gambit, Rogue soon came to her senses and vowed to get her family back. Colossus and Shadowcat returned with Illyana. Nightcrawler also arrived with the mutant Destiny and Quicksilver's team returned with Bishop. With the team back together once more, they decided to rescue Magneto and take out Apocalypse once and for all. Blink teleported the team to Apocalypse's fortress while X-Man, the mutant created by Sinister, rescued Magneto. Illyana and Destiny entered the M'Krann Crystal and used their powers to allow Bishop to go back in time and prevent Legion from murdering Charles Xavier, thus preventing this timeline from ever happening. When Colossus learned that the timeline Bishop was trying to restore was one in which his sister was dead, he became angry and deranged. Trying to enter the M'Krann Crystal to prevent this from happening, he accidentally killed his wife Shadowcat by stomping on her. Gambit used his powers to stop Colossus and killed him. Bishop succeeded in his mission in preventing Xavier's murder while Magneto and Apocalypse fought one another. Magneto used his powers to rip Apocalypse in half, thus ending the Age of Apocalypse once and for all. Standing side by side with his wife, Magneto watched as the Human High Council's missiles rained down on New York City.