Chapter IX : The Age of Apocalypse
As the battle on the Moon was still a recent event, and as the destruction of his fortress apparently interrupted his latest hibernation cycle, Apocalypse most likely journeyed to another of his bases, and began his regeneration cycle anew. If this is the case, then Apocalypse most likely slumbered obliviously through the chain of events that, for the briefest of moments, transformed the world into all that he wished it to be.
When David Haller, the powerful mutant known as Legion, informed his father, Professor Xavier, that he wished to travel back in time to prevent Magneto from ever becoming a threat to his dream of human/mutant coexistence, Xavier sent his X-Men back in time to stop him. Four X-Men (Bishop, Iceman, Psylocke and Storm) followed Legion to Israel of 20 years ago, where the younger Xavier had first met the mutant who would eventually be called Magneto. Easily besting the X-Men with his mental powers, David attempted to kill the much younger and inexperienced Magneto. David's plan backfired, however, when his father, there in the past, jumped in front of a psi-blast meant for Magneto, killing the young Xavier instead. The act of David killing his own father before he was born resulted in a paradox, after which he and the rest of the X-Men (save Bishop) disappeared in the resulting tear in reality. Bishop, already a time-traveler from the late 21st century and thus a temporal anomaly, alone was unaffected by what happened next. [Legion Quest]
While the youthful Magneto attempted to understand what had just happened and wonder who had killed his good friend, Charles, other eyes drew different meanings from these events. In one of his secret fortresses, from which he watched and monitored world events, Apocalypse had witnessed a group of powerful mutants in battle. These mutants seemed to indicate that the emergence of mutants in the world was happening far sooner than he, or his associates, had anticipated. After his long wait, the time had come for Apocalypse’s long anticipated Time of Testing.
Having gathered his forces a decade earlier than in the original timeline, Apocalypse’s Celestial ship appeared above New York and informed the world population of his presence. In a sense, it was his declaration of war on the human race. The first battle in this war, however, occurred at Cape Citadel, stronghold of the United States' nuclear defense arsenal. Arriving on the scene at their master’s orders, Apocalypse’s Horsemen, consisting of Gideon, Candra, War, Death and Sabretooth, took control of the base and prepared to launch its arsenal against U.S. cities. The plans were thwarted by the arrival of the X-Men, a group of mutants gathered and trained by Magneto, trying to follow in the dream of his closest and now deceased friend, Charles Xavier. Magneto’s X-Men turned back Apocalypse’s Horsemen, but suffered a heavy price. During the conflict, Apocalypse had sent his son, Nemesis, to the X-Men’s mountain headquarters, where he murdered some friends and allies of Magneto, including his daughter, the Scarlet Witch.
Over the next several years, En Sabah Nur attempted to reshape the world to his own vision of the future. By the date David, in the original timeline, traveled back in time, Apocalypse's forces controlled all of North America. Through nuclear warfare, he had made South America a wasteland and was preparing to move against human-held Europe. His genetically engineered mutants, called Infinites, herded humans and weak mutants through culling pens, eliminating the unfit. His genetic biologists, the Dark Beast and Mister Sinister, performed horrific experiments on the remaining populace, attempting to breed more powerful mutants. For any humans still on the North American continent, it was only a matter of time before they would be culled. For the mutants who would not submit to Apocalypse's rule, they also faced certain death. Headquartered in the former city of New York and overlooking the Hudson River, which he had renamed the New Nile, the ancient En Sabah Nur had finally reached the time of testing. This was the Age of Apocalypse.
The only two things standing in Apocalypse’s way were the Human High Council, the elected body of humans governing over free Europe, and the X-Men. Although Magneto and his X-Men had attempted to resist Apocalypse at every turn, for the most part they had failed. Apocalypse’s forces had multiplied and grown stronger, while Magneto’s resources and allies were few and insignificant in comparison. 
More so, they were running out of time. Having nearly solidified his stranglehold over the North and South American continents, Apocalypse had set his sights on the rest of the globe.
The world was not without hope, however. During a mission in Seattle, Magneto and his X-Men came across the now elderly mutant known as Bishop. After rescuing the mutant from the Infinites, Magneto learned his story of being from an alternate timeline, a timeline which sounded much better than the one in which they currently lived. Convinced of Bishop's claims, Magneto set in motion a plan which would restore the previous timeline, by undoing the event that caused it. Ordering a team of thieves to journey to the Shi'ar Galaxy, Magneto charged Gambit and his "X-Ternals" with recovering the M'Kraan crystal. After meeting the crystal's guardian, Jahf, the team recovered a sliver of the crystal which, due to the nature of the artifact, would serve as well as the crystal entire. Their success was short-lived when they were betrayed by Guido, an unwilling operative of Apocalypse, who stole the shard and returned it to his master.
The X-Men's plans were further thwarted when Apocalypse managed to capture their leader, Magneto, and his son, Charles. Beaten and tortured by Apocalypse, Magneto's will was all but gone, as he learned that Apocalypse now had possession of the M'Kraan crystal shard. 
To both his and Apocalypse's surprise, though, they were informed that the Eurasian Human High Council had launched a final assault on Apocalypse's strongholds, using nuclear weapons that had, no doubt, killed millions. Enraged, Apocalypse commanded his forces to expand the Atlantic Sea Wall, expecting to kill all of the inhabitants of Eurasia.
As Apocalypse's forces scrambled, a strike team of X-Men stole their way into fortress. Finding the chamber that housed the M'Kraan crystal shard, Destiny, Illyana and the time-displaced Bishop entered the crystal. Through Illyana's disc-stepping teleportation power, the aged Bishop was transported through time, back to Israel twenty years ago. Arriving on the scene of the battle with Legion and the younger Magneto, the older Bishop managed to avert the horrible tragedy of Xavier’s death by turning Legion’s own energies against him, killing him. The timeline now corrected, the elderly Bishop disappeared from existence, followed by the four X-Men Bishop, Storm, Iceman and Psylocke, all of who return to their proper time in the future.
Back in the timeline of the Age of Apocalypse, the battle continued, all parties unaware that their existence was about to end. Having joined forces with Nate Grey, the genetic product of that timeline's Mister Sinister as a weapon against Apocalypse, Magneto fought tirelessly against Apocalypse. When Nate Grey disappeared into the M'Kraan crystal with Holocaust, the son of Apocalypse, Magneto found himself alone against the ancient mutant. Apocalypse managed to wrap his hands around Magneto's neck, intending to strangle his old foe, but found instead that it was a trap by the Master of Magnetism, who had been using the time to magnetically charge the body of Apocalypse. Crackling with electro-magnetic energy Apocalypse was literally ripped apart, ending his life.
Magneto's victory was a hollow one, as the Eurasian Human High Council had no idea that their enemy was now dead, they were still bombing the city. As the explosions grew closer, Magneto and his wife, Rogue, knew that even if the bombs were stopped, if Bishop was successful, the whole reality would be ending momentarily.
To their surprise, not only did the missiles not explode but reality continued. Though Bishop's plan had succeeded and the prior timeline was restored, this altered timeline continued as an offshoot. Thus were the victims of Apocalypse forced to pick up the pieces left behind by his reign of terror. Unfortunately for them, the populace of this timeline had to contend with others that attempted to take up the mantle of Apocalypse, causing as much terror and horror as he did. Though no more, Apocalypse's legacy nonetheless lived on.