The gods of Heliopolis came into existence over several generations, even as the Olympian gods derived from the older generation of Titans. Before there were any other gods there was Nun, the essence of chaos or the Primordian Ocean of Nothingness. Nun was said to sire Atum, the first physically manifested god among the Heliopolitans (and possibly other pantheons as well). Atum later took the aspect and identity of Ra, the primordial god of the sun and first god to develop a cult of worshipers among the Egyptians. Ra was said to sire the next generation of gods, Shu and Tefnut, without a female mate. Shu took Ra's place when Ra became too weary and old to rule, and became the god of air. His twin sister Tefnut ruled at his side as goddess of the rain. Shu and Tefnut began the fourth generation of gods, Geb and Nut. Geb was a god of the earth, having a natural affinity for mountains and other parts of the earth's crust. Nut was a goddess of the sky, specifically the starry heavens. Geb and Nut succeeded their parents when they too became too infirm to rule, and began the next more numerous generations of gods, eldest among which was Osiris.

Osiris's siblings included Isis, whom he took as a wife, Seth, and Nephthys. Osiris became the head of the pantheon when Geb stepped down, and is credited with the spread of civilization throughout Egypt and beyond. Osiris was the last ruler of Egypt before historical times and the human pharaohs came to rule. Osiris became the benevolent god of the dead, preparing the afterlife for his loyal worshippers. Osiris's wife Isis was believed to teach humanity, the arts of medicine and the principles of domestication. She was also a powerful sorceress who was able to bring Osiris back to life after he had been murdered and dismembered by his jealous younger brother Seth. Seth was the god of evil and destruction, who sought to rule Heliopolis himself, and murdered Osiris in order to do so. His wife Mephthys, daughter of Geb and sister of Isis, was also a goddess of the dead but was not evil like her husband. Nephthys had no offspring with Seth, but bore Osiris a son, Anubis. Anubis invented funeral rites and mummy wrappings, and although it was Isis's magic that rose Osiris from the dead, her magic would have been useless had Anubis not specially prepared Osiris's body.

Osiris and Isis had a son, Horus the god of the sun. Horus was also instrumental in helping raise his father from the dead after Seth's treachery. Upon resurrection, Osiris dispatched his son Horus to find Seth to make him pay for his treachery. Eventually, Horus encountered Seth and their cataclysmic clash lasted centuries. Seth finally got the upper hand over his nephew and Seth used his power to seal Horus, Isis, and Osiris within a pyramid on Earth. There they remained until the Twentieth Century when Odin, then lord of the gods of Asgard, assumed the guise of Atum-Re, an aspect of the first of the gods, in order to free them. Odin's son Thor aided the Heliopolitans in vanquishing Seth.

While Osiris, Isis, and Horus were imprisoned, the moon god Thoth, who had served as Osiris's grand vizier, became head of the Heliopolitan pantheon. Thoth was believed to be a later son of Nun, the primordian chaos, which would make him a brother to Atum. Still, he came along much later than Atum and appears to be a contemporary of Osiris. After each generation of Heliopolitan gods retired from earthly rule, they traveled to the dimension of the celestial Heliopolis to live out eternity. Beginning with the rule of Thoth, however, all of the gods moved to the otherdimensional realm, to traffic with the earth no more. When Osiris returned, Thoth gave up the throne to his mentor. The gods of Heliopolis have remained in their extradimensional realm since, having little traffic with Earth. Like most races of gods, they are believed to be mere figments of myth by most of humanity.