Legion killed both Magneto and Xavier, and countless others when he went back in time. Governments panicked and set up concentration camps for mutants, and used Sentinels. Non-mutant superhumans would flourish in the world. Down in the Savage Land, Ka-Zar provided mutants with sanctuary.
Apocalypse amassed an army of mutant storm troopers, who were enraged at the injustices that humans had inflicted on them. He unleashed them on the world, and their assault was executed with swift and deadly precision. Soon there weren't any left to oppose the mutants. Huge slaughterhouses were established by Apocalypse, to exterminate what remained of the human population. All mutants and superhumans were forced to serve Apocalypse or be executed. Namor was one of those who pledge his allegiance, in exchange for Apocalypse sparing Atlantis. The Fantastic Four were among those who refused to serve him, and they were killed (except for the Thing, who survived and fought on in the resistance).
For decades afterwards the Savage Land remained untouched by Apocalypse's brutal rule, and flourished. Then his forces arrived and slaughtered the the community of mutant refugees (including Jean Grey and Scott Summers). Only their son Nate Summers escaped with the assistance of Sauron. He was found in the freezing interior of Antarctica by Wolverine who took him to the ruins of New York City.
Where there was a group of super heroes, whom still resisted Apocalypse's rule. Nate wants Brother Voodoo who became the Sorcerer Supreme after Doctor Strange's death to take them to the past so they can stop the rise of Apocalypse. He refused because the danger to the timeline would be too great, and told him they had to stop Apocalypse in the present. Under the leadership of Captain America, the small resistance team of superhumans and mutants turned into a formidable combat unit, the Defenders.
Within months after its formation they assaulted Apocalypse's fortress in NY City. They were attacked by Holocaust and clones of Peter Parker, and lose two team members. Brother Voodoo opened a portal through Dormammu's dimension to bypass the defenses and take them straight to Apocalypse. They encountered Dormmamu and Voodoo stays behind to hold him off to give the rest of the team time to get back to the material realm. Nate betrayed him and tok his Eye of Agamotto, dooming Voodoo.
The remainder of the team made it through the interdimensional portal and ended up inside Apocalypse's temple where they were immediately engaged by the Horsemen of Apocalypse. Lethal combat ensued between the two teams, resulting in deaths on both sides. Nate Summers whom is obsessed with revenge against Apocalypse and changing the past, takes the Molecule Man with him and abandons the Defenders at their time of need.
Using Owen's powers, Apocalypse is killed and so is the Molecule Man. When the rest of the Defenders arrive they discover that Nate has put on Apocalypse's armor and opened a portal to the past with the Eye of Agamotto. Captain America tried to stop him using Mjolnir but was unsuccessful. Using Owen's powers and the Eye of Agamotto, Nate went into the past but not to the one of his own world but an alternate reality.
The lighting bolt that was fired from the hammer went through the portal and killed thousands in the past, which set in motion the tragic events that would lead to the rise of Apocalypse in their world. Unfortunately Nate's obsessive need to fix the past, created an anomaly. One that spread across the Multiverse like a cancer. His action robbed countless realities of the contributions of Eric Magnus and Charles Xavier, thereby perpetuating the horrors that he tried to prevent.