Legion (David Haller), an extremely powerful psionic mutant and son of Professor Charles Xavier and Israeli diplomat Gabrielle Haller, travels back in time with the intention of killing the former best friend, now Arch-Nemesis of Xavier and his X-Men, Magneto. When he on the verge of ending Magneto's life, Xavier interspaces himself between the two, and Legion kills Xavier instead. Due to a "Grandfather Paradox", Legion then ceases to exist. His father, of course, has now died before he was even fathered.
Because of Xavier's sacrifice, Magneto comes to believe in his late and former friend's dream of peaceful co-existence between humans and mutants. Apocalypse, a nearly immortal mutant who has survived for centuries was monitoring the fight. In this reality, he chooses this moment as the perfect time to begin his "survival of the fittest" genetic war. In the regular Marvel timeline, this doesn't happen until 10 years later.
In this timeline Magneto establishes the X-Men, but not until after Apocalypse establishes himself as a major power. Apocalypse comes to rule all of North America; New York City is renamed Apocalypse Island and the Statue of Liberty is replaced by a gigantic statue of his visage.
Apocalypse initiates a worldwide genocidal campaign of "cullings" in which millions of humans die. The few that survive live on parts of Europe and Africa which are not devastated by nuclear weapons, a fleet of Sentinels remaining as their only defense.
Meanwhile, the disturbance of the timeline leads to a crystallization wave of the M'Kraan Crystal that is heading toward Earth...
X-Man is the son of Scott Summers & Jean Grey, forged from the DNA of Scott and Jean Summers by Mr. Sinister
The only major mutant character missing in the original Age of Apocalypse is Psylocke. Fans speculate that she was likely either killed in one of Apocalypse's cullings or that she is one of the members of the Brain Trust keeping control over the pens. When the Age of Apocalypse was revisited a decade later, she appeared in X-Men: Age of Apocalypse #4 (May 2005). Her origin remains unknown. There has been no explanation of what exactly she was doing during the original Age of Apocalypse.
Other anti-Apocalypse forces
Besides the X-Men and its many offshoots, the Human High Council remains as the other power opposing Apocalypse. Unlike the X-Men, however, the Human High Council considers the extermination of mutants as a viable option. Bolivar and Moira Trask, as well as Brian Braddock, are the major proponents for a mutant holocaust.
Secretly, the Human High Council supports a Human Underground Resistance.
Programmed to protect humans above anything else for which they are capable of not attacking mutants if it aids in the acomplishment of their Prime Directive
A activist of mutant-human peaceful coexistance, for which Apocalypse imprisoned him. Rescued by Magneto, Nightcrawler and Rogue. Later brokered the Kelly Pact, a no agression treaty between the Human High Council and Apocalypse.
A scientist of the Human High Council, secretly "bought" by Mikhail Rasputin, who supplies him with mutants for experiments in which Banner seeks to mutate himself
One of the many human prisoners aboard Mikhail Rasputin's ships.
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Timeline escapees
After the Age of Apocalypse story arc, Bishop travels back in time to prevent the timeline from ever occurring. This occurs simultaneously with a nuclear exchange between the Human High Council and Apocalypse. Most characters were seemingly killed by the nukes, but the fate of the remaining survivors remained unclear. It is presumed that they were erased from existence.
Some characters escape the Age of Apocalypse into the Earth 616 continuity. These include Nate Grey (the AOA version of Cable), Holocaust (one of Apocalypse's horsemen), Beast, and Sugar Man. Nate Grey allies himself with the X-Men a few times, but later "dies" by disseminating into every lifeform in the universe. Holocaust remains at large in the main Marvel Universe until he joins the Exiles and is killed by another universe's evil version of Hyperion (in Exiles #62). Sugar Man later died at the hands of the 616 Callisto. Dark Beast is the only one of these four still alive. Beast and Sugar Man are sent 20 years into Earth 616's past. This allows for major retconning that explains that the Age of Apocalypse's Beast (now known as Dark Beast) has a hand in the creation of the Morlocks. It also explains why Mister Sinister initiated the Mutant Massacre: he recognised his stolen handiwork, and ordered it exterminated, as a debasement of his art. Furthermore, Sugar Man gave genetic technology secrets to the Genegineer of Genosha, allowing this small nation to become powerful by enslaving mutants.
Blink escapes into the multiverse itself: she joins and leads the reality-hopping team of heroes known as the Exiles. Her counterpart on Earth 616 has been dead since the Phalanx Covenant story arc.
Sabretooth also survives along the same means as Blink. He joins a team of reality-hopping super beings known as Weapon X. During one mission, he opts to stay behind on a world to raise a child. Eventually, he is brought back into action and joins the Exiles. They have since visited the post story-arc Age of Apocalypse, the survival of which comes as a surprise to Blink and Sabretooth.
In 2005, Marvel published an Age of Apocalypse one-shot and mini-series to celebrate the 10th anniversary of the popular event.
The one-shot features stories set before the events depicted in the original "Age of Apocalypse" event, similar in focus to the Chronicles of the Age of Apocalypse issues: the one-shot contains the story of how Colossus and Shadowcat left the X-Men to train Generation Next, how Sabretooth met Wild Child, the first appearance of the Silver Samurai, and that the world survived the Human High Council's nuclear attack.
In the mini-series, we are introduced to several characters who weren't in the original storyline. Long time characters Psylocke, Cloak, Dagger, Wolfsbane and the Morlocks including Feral, Thornn, Leech, Marrow, Skids who where survivors of Mister Sinisters experiments are introduced. Newer characters X-23, Beak and Icarus are seen, along with the concept of Xorn.
The Exiles team, many of which are from the Age of Apocalypse universe, visited the world as well during this time.
X-Men Legends 2: Rise of Apocalypse, released the same year, was heavily influenced by the AoA storyline, including several characters and concepts from the storyline.