The story of Apocalypse begins in 3000 BC in Egypt during the First Dynasty. Born gray-skinned (although Apocalypse's skin colour is sometimes depicted with different human pigment variations) and blue-lipped with natural facial markings, in the settlement of Akkaba, he was abandoned as an infant, but found by a band of desert nomads called the Sandstormers, whose leader, Baal, saw the child's potential power and decided to raise him as his own naming him En Sabah Nur. Baal had perviously been visited by the Doctor during an invasion of Vashta Nerada in the Nile Delta region, and had been told not to accept him as his own. Nonetheless Baal takes him in. He is taught the philosophy that the tribe lives and dies by survival of the fittest. Nur and Baal are the only Sandstormers to survive on the day that General Ozymandias and his army destroy the Sandstormers tribe, as they find refuge in a sacred cave before it collapsed. Baal eventually dies from lack of nourishment after weeks of deprivation, but before he does, he admits to Nur that he had believed him to be a savior foretold in ancient prophecies who is destined to overthrow the pharaoh Rama-Tut. The TARDIS appears and the Doctor is at first angry with Baal but soon comforts him as he dies. He offers to take Nur as a companion, but Nur does not accept. The young Nur vows to take revenge on the pharaoh and claim his destiny. He hides himself as a slave in Tut's city, where he has visions of Egyptian gods who reveal his great destiny.
The pharaoh Rama-Tut, in actuality an earlier incarnation of Kang the Conqueror who had come back in time to locate the young Apocalypse and take him under his wing, tries to convince Nur to join him, but the young mutant savagely attacks the pharaoh only to be taken down by the conqueror's futuristic weapon. Nur survives, and tries to rescue Nephri, Ozymandias' sister, who had become attracted to the mysterious slave, but Nur is ultimately rejected by Nephri for his inhuman appearance, and she turns to her brother for protection in her panic. Heartbroken by this final rejection, En Sabah Nur's prodigious mutant abilities fully emerge in his enraged state, and he renames himself Apocalypse. Rama-Tut flees the former slave's rampage, while Nur uses his advanced technology to enslave and transform his former tormentor, Ozymandias, into a blind seer made of living stone, who would forever chronicle Apocalypse's future destinies. the Doctor had followed Apocalypse and persuaded him to stop. Fifty years later, Nur revisits Nephri, now an elderly Egyptian Queen on her deathbed, and mocks the loss of her beauty and vitality, in contrast to his own unchanged appearance, despite the passage of time. During this time Nur joined forces with the original Moon Knight and Imhotep to form the first incarnation of S.H.I.E.L.D. and successfully fended off a Brood invasion with the help of the Vortex Guardians.
Apocalypse travelled the world in his new form, wondering at the marvels he saw. He encountered the Doctor in Rome, though neither recognized each other. Selene also arrived in order to initiate her plan to mutate the ancient philosophers and scientists to create a world order of Externals. Apocalypse and the Doctor banded together a small band of mutants, one of which would grow to be Gideon. The battle that ensued came to the attention of the Shi'ar Imperial Guard who arrived and helped Selene. Rome was obliterated and Selene escaped with Gideon, and left an astonished Nur with the complexity of his origins. He later shed all good from himself and established his place as one of the greatest and most powerful villains ever. He has currently created his own planet in the year 7049 A.D.