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En Sabah Nur was born nearly five thousand years ago in a lone settlement on the very edge of the Amentet and the very edge of the Valley of the Kings, in Ancient Egypt, as a member of a tribe in Akkaba. Even as an infant, the child inspired fear, being born with gray skin and blue lines running across his lips and face. Ugly and malformed, the infant was abandoned by the tribe, to die in the harsh desert sun. However, out of the desert, the Sandstormers, a roving band of feared nomadic raiders, slaughtered the citizens of Akkaba. Their leader, Baal of the Crimson Sands, found the infant crying and recognized the potential power in the child. Baal named the infant En Sabah Nur, literally meaning "The Morning Light", and raised him as his own son.

As Nur grew, he surpassed the other tribesmen in intelligence and strength. Everyone in the tribe, except for Baal, hated and feared Nur for his inhuman looks and great abilities. Nur did not understand their fear, but hardened his heart against it. Moreover, Nur believed in the principle that Baal and the tribe lived by, that only the fittest, toughest, most ruthless, and pitiless, tested by hardship, would and should survive.

At a time when many time-traveling super-heroes, including the Fantastic Four, West Coast Avengers, and Dr. Strange, arrived in Rama-Tut's Egypt, the Pharaoh finally came face to face with Nur. In actuality, Rama-Tut was a time traveler from the far future, who would later become known as Kang the Conqueror. Tut knew that Apocalypse, one of the most powerful mutants who ever lived and the one who was destined to rule the world, had been born in ancient Egypt. Hence, Rama-Tut had gone back in time to find Apocalypse as a child, raise him, and thereby become the master of the most powerful being on the planet. Rama-Tut offered to make Nur his heir, if he would swear his loyalty. At that time, Nur revealed his face to Nephri, who rejected him for his appearance. Rama-Tut then tried to kill Nur, when he refused. Nur was then shot, by the Pharaoh, with the same weapon he used to de-power the Fantastic Four, and was again left to die, but survived with the sudden emergence of his mutant immortality and mass shifting. With his powers flaring, Nur defeated Ozymandias and Rama-Tut himself, who finally escaped back into the future, eventually to take on the identity of Kang. The Fantastic Four went back to their era, thinking the explosion a booby trap. Nur attacked Ozymandias and he was thrown into the technology on Tut's Sphinx, which turned him into a sand-like being, who could see the future almost right before it happened and would record Nur's accomplishments throughout time, as his scribe. Nur then claimed Tut's sphinx.

In 2620 B.C., Apocalypse joined forces with Imhotep and the Moon Knight of Khonshu (forming a protectorate who would become the Brotherhood of the Shield) to successfully fend off a Brood invasion. Other accounts stated Apocalypse only helped Imhotep against the Brood, but did not join the Brotherhood created afterwards.

When Nur fully realized his power and defeated the Pharaoh and his army, Egypt entered a new age, one in which his children walked among them. Offspring of Nur received a portion of his power, those closest related having near identical abilities. Nur forged his clan, now called Clan Akkaba after his birthplace and those who had abandoned and left him to die. During this time, the site of Akkaba reached somewhat of a renaissance as great monuments were erected there, whether by Nur, his descendants, or by the new Pharaoh no one knew. Egypt peaked, and so too did the clan’s influence on the world. With attacks by Alexander the Great and his Persian armies, Nur and his kin fought valiantly in a battle he would never forget. This battle helped Nur winnow out the weak in his clan and, as Egypt became nothing but a distant memory to the clan’s influence, Nur moved on to Ancient Rome. Before leaving, Nur revisited Nephri, now an ancient Egyptian Queen, and mocked her dying beauty, as he was still as he had been years before.

From then on, Nur plotted the conquest of the planet, through bringing about wars and conflict, in which the strong would defeat and destroy the weak. Over the centuries, Nur was worshiped by many civilizations, under a variety of names. Nur also founded a group of fanatics devoted to the Darwinian ideals that the strong ("fit") should inherit the Earth and the weak ("unfit") should be culled, named the Riders of the Dark.

t an uncertain point in the distant past, Apocalypse and his wife Genesis made their children his first Horsemen. When Okkara was split by a force wielding the Twilight Sword, Apocalypse and these horsemen fought the invaders. In the end, they were responsible for the sealing of the chasm. The horsemen were sealed on the other side of the chasm alongside Arakko, to the sorrow of Krakoa.

By 281, Apocalypse was already recruiting for his "Final Horsemen", collecting Decimus Furius and storing him away to awaken later. In 325, he recruited Sanjar Javeed for the same purpose.

Later, Professor X sent out a telepathic message to everyone on Earth, declaring the foundation of Krakoa, a new mutant nation. Xavier sent out another telepathic call to all mutants, offering amnesty and a place in Krakoa. Two days after Krakoa was officially recognized by the United Nations, Apocalypse traveled to Krakoa alongside many other former enemies of the X-Men. He revealed to those present his past history on Krakoa. When pressed by Magneto, he declared that he was proud of what they had accomplished, agreeing to submit to all the laws of Krakoa. He was given a place on the ruling body of Krakoa, sitting alongside Xavier and Magneto on the Autumn wing of the Quiet Council.

Later, the Arak Coral emerged, and bonded with Krakoa. Apocalypse met the High Summoner of Arakko, who was revealed to be the son of Apocalypse's first Horsemen of War. The Summoner pleaded to Apocalypse to save them from their enemy. Alongside Xavier and Magneto, Apocalypse attended the World Economic Forum in Davos.

As depowered mutants joined the nation of Krakoa, a problem emerged. The Five possessed the capacity to resurrect these former mutants in mutant bodies; however, this requires them to first die. In part to ensure that the Five were not overwhelmed by such resurrections, Apocalypse proposed the "Crucible", a novel ritual of combat to earn the right to die and be resurrected as a mutant once more. The Quiet Council assented to the proposal. The first to undergo the trial was Melody Guthrie, who faced Apocalypse himself in a sword-fighting duel. Melody refused Apocalypse's offer to surrender, and thus was slain at his hand. She was then resurrected with her powers restored and resumed her mutant name of Aero, much to the pride of Apocalypse.

When a Gateway to Otherworld formed, Apocalypse sought to harness the mutant magic of the dimension, but was blocked from the other side. Apocalypse asked Betsy Braddock to bring her brother Captain Britain to Krakoa, hoping to use his power to unlock the gateway. However, the Braddock siblings ventured to Otherworld on their own, only to be ambushed by Morgan le Fay, who had gained control of Camelot. Meanwhile, Apocalypse had Trinary bring Gambit and Rogue to the gate, seeking to have Rogue absorb the power of the gate and thus weaken the magical ward upon it. The sorceress enslaved Brian with her dark magic, and Betsy escaped to Krakoa using the Amulet of Right.

Betsy, now Captain Britain herself, arrived on Krakoa, discovering that Rogue had entered a magical coma as a result of her interaction with the Gate. When Betsy traveled to England along with Gambit, Jubilee, and a comatose Rogue to rebuilt the Braddock Lighthouse, they were attacked by the Coven Akkaba, servants of le Fay. Apocalypse arrived and promised them he would protect the Lighthouse and Rogue while the others went to Otherworld. Lacking the proper material to both create a stable gateway to Otherworld and to awaken Rogue, Apocalypse recruited Richter, to serve as a master of Earth and retrieve the bones of ancient mutants. While the rest of the newly reformed Excalibur were away, Apocalypse watched as monsters from Otherworld emerged to attack the Lighthouse. Apocalypse revealed that what happened with Rogue was not an accident, but the latest step in a ritual eons in the making. However, when Prestige made telepathic contact with Rogue at Gambit's request, the ritual's progress was accelerated. Enraged, Apocalypse beat Gambit into submission. As he went to complete his ritual, Apocalypse discovered that Richter had already spent the energy of the crystals he'd been sent to retrieve. At that moment, Rogue awoke, infused with power, and attacked Apocalypse. He allowed Rogue to absorb his life, realizing that in death his bones would have the power required to complete the ritual and access Otherworld.

Apocalypse was quickly resurrected, a privilege afforded to him due to his place on the Quiet Council. He was then greeted by Jamie Braddock, whom he appeared to be in league with. Apocalypse challenged le Fay for the throne of Avalon; in place of a war, the dispute would be solved by a duel to the death between their champions; Betsy and the possessed Brian, respectively. After Betsy involuntarily defeated her brother, Apocalypse officially announced Jamie Braddock as Avalon's new king. Jamie, also known as Monarch, then imprisoned le Fay and resurrected Brian. This, it seemed, had been Apocalypse's plan from the start. Following their victory, Apocalypse began vivisecting le Fay, seeking to study the physical and biological components of magic.

He then tasked Excalibur with retrieving the skulls of five Warwolves, which were needed for expanding their coven between dimensions. After finally getting the components he needed, Apocalypse and Excalibur were able to access the Starlight Citadel. As Betsy confronted the Omniversal Majestrix Saturnyne, Apocalypse gathered all of the High Lords at the volcano of Arak Maw and told them that it was time for the entire mutant population to become equal to them. He and Rictor then proceeded to kill Crule, Saul, Nicodemus and Candra in order to turn their life force into crystals that would serve as a portal to Otherworld. However, Candra prior to being killed left her gem containing her life force at the Citadel which was picked up by Gambit. Apocalypse contacted Betsy and told her about the gem, and then after seeing it at the hands of Gambit she told him to give it to Apocalypse and he complied, throwing it at the Krakoan portal where Apocalypse got it and finally completed his own portal. Following that, Apocalypse went to his grandson, the Summoner, who explained to him what happened to his horsemen, his wife, and the other mutants who remained on Arakko. After that, Apocalypse directed his grandson to the portal to Otherworld where he could return to Arakko, while being accompanied by Unus the Untouchable and Banshee, where the Summoner declared that he would "greet [him] in the manner befitting not just a hero of Krakoa, but as the father and true heir of Arakko."

After the Summoner and a injured Banshee returned to Krakoa after "being ambushed by the Daemons", Apocalypse brought the situation to the council of Krakoa. The Council was angry at Apocalypse for creating the External Gate without their knowledge and permission, but Apocalypse found support from Krakoa itself who wanted to reunite with its long lost half and didn't allow the Council to destroy the gate. Instead Apocalypse and his grandson, went alongside some volunteers to Otherworld in order to face the threat. Apocalypse was then reunited with his long lost children, and tried to reconnect with them, but instead they and the Summoner assaulted him. He and Rictor were taken to the Healing Gardens in order to cure them from Pestilence's poison arrow , but the poison proved to be too strong. As Rictor began succumbing to the poison, Apocalypse demanded Healer save him, but the Healer refused stating that Apocalypse needed it more and Rictor would just be resurrected. This caused Apocalypse to attack Healer, but he was then himself attacked by Rachel Summers in retaliation, leaving Apocalypse even more damaged. Magneto then told Apocalypse that following the grave accident revolving around Rockslide's failed resurrection, all of the eggs in the Hatchery had been destroyed and they would need time before Apocalypse would be resurrected, while also berating him for his failed experiment.

Apocalypse eventually recovered from the infection and alongside Gorgon returned to the Temple of the Horsemen. There he destroyed the tombs that represented his children and retrieved the four pieces of the Scarab, since he was one of the Champions of Krakoa who would fight in the Ten of Swords tournament.