In an alternate version of Egypt, the world is flat and the Egyptian gods live among humans, they differ from humans by their greater height, golden blood, and ability to transform into their divine forms.

Bek, a young thief with little faith in the gods, and his love Zaya, who has more faith in the gods than him, are attending the coronation of Horus. During the ceremony, Osiris is killed by his extremely jealous brother Set, who seizes the throne and declares a new regime where the dead will have to pay with riches to pass into the afterlife. Horus is stripped of his eyes, the source of his power, and almost killed. His love, Hathor pleads with Set in surrender to spare him and he is instead exiled.

A year later, Bek has been working as a slave building monuments while Zaya is now under the ownership of Set's chief architect Urshu. Believing that Horus is the only one who can defeat Set, she gives Bek the floor plans to his treasure vault and also manages to get a glimpse of the plans for his pyramid. Bek is able to steal back one of Horus' eyes by sneaking into the treasure vault. However, Urshu finds out about their theft and kills Zaya as the couple flee. Bek takes her body to the blind Horus and makes a bargain: Horus agrees to bring Zaya back from the dead for his eye and Bek's knowledge about Set's pyramid.

The two fly to the divine vessel of Horus' grandfather Ra. Horus is unable to convince his grandfather to regrant him his power so he can defeat Set himself, as Ra is both neutral about their conflict and daily at war with the enormous shadow beast Apophis that threatens to devour the world. Ra does however allow Horus to obtain a vial of the divine waters that surround his vessel, which can extinguish the desert thirst and weaken Set gravely. Ra tells Horus that his weakness is the result of him not fulfilling his destiny, which Horus believes means avenging his parents' deaths.

Elsewhere, Set asks Hathor to take him to the underworld which he next desires to conquer, but she refuses and manages to escape. After surviving an attack by Set's Egyptian Minotaurs led by Mnevis and an attack by some of Set's minions and their giant cobras, Hathor finds and saves Bek and Horus. Horus at first doesn't trust her as she is a mistress of Set, who had blinded him, while she tries to convince him that Set is her enemy as well. When they tell her of their plan regarding Set's pyramid, she warns them of a guardian sphinx who will kill anyone not wise enough to solve a riddle. The group then heads to the library of Thoth, God of Wisdom, so they can recruit him to solve the riddle.

Arriving at Set's pyramid, they overcome its traps including the sphinx, to reach the source of Set's power. But before they can pour the divine water, Set traps them and reveals to Bek that Horus cannot bring Zaya back from the dead. Set destroys their flask of divine water and kills Thoth by taking his brain. Horus is able to save Hathor and Bek. Horus admits to caring more about his revenge than the mortals. Hathor sacrifices her own safety for Zaya's payment into the afterlife by giving Bek her bracelet and calls Anubis to take him to Zaya, letting herself be dragged to the underworld.

Having combined Thoth's brain, Osiris's heart, Horus's eye, and wings from Nephthys with himself, Set travels to Ra, appealing to his father for approval and questioning his favoritism for Osiris and denying him the throne and children. Ra claims that all of Set's prior mistreatments were tests preparing Set for his true role: the honor and burden of taking Ra's place as the defender of the world aboard his solar barge, fighting against the demon Apophis. Set is dismayed to hear his destiny is to be alone above the planet until he dies and refuses the offer. He wants to destroy the afterlife so that he can be immortal. Ra tries to fight Set by blasting him with his spear, though Set survives. He stabs Ra to his surprise, takes his spear of power, and casts him off the boat freeing Apophis to consume both the mortal and underworld realms.

Bek finds Zaya, who refuses Hathor's gift as she doesn't want an afterlife without Bek, but then Apophis attacks and the gate to the afterlife is closed. Bek returns to the mortal world, where Horus is amazed that Bek still wants to help take down Set. Bek tells him it was Zaya who told him to, as she still has faith in Horus.

Horus climbs up the outer wall of an obelisk Set is standing on and attempts to battle him, but is heavily outmatched. Whilst Bek fights Urshu who is thrown off to his death, Bek ascends on the inside and joins the battle, removing Horus's stolen eye from Set's armor, being wounded in the process. As Bek slides toward the edge of the obelisk, he throws the eye toward Horus, who must choose to catch it or save Bek instead. Horus reaches for Bek and apologizes for all he has put him through. As they plummet toward the ground, Horus finds that he now has the power to transform into his divine form and he catches Bek and flies him to safety. Horus realizes that it wasn't the recovery of his eye nor revenge that was his destiny, it was the protection of his people that he needed to fight for. Now, Horus has the strength for battling Set, and he gains the obelisk and kills him. After the battle and Set's death, he then finds Ra wounded and floating in space, and returns his spear to him, allowing Ra to once again repel Apophis and for Anubis to reopen the gates.

As Horus returns to Bek, a child holds out his other eye which she has found, while people cheer him. But Horus's joy turns to sadness as he arrives to find Bek dying from the wounds he sustained whilst fighting Set. Horus carries him to Osiris's tomb and lays him beside Zaya. Ra arrives and offers to bestow any power on him to repay Horus for his life and Egypt's survival. All Horus wants is bringing Bek and Zaya back to life. The other gods are also revived and have their attributes restored (except for Osiris and Isis, who died a full year before and have already passed into the Afterlife). Horus is crowned king by Thoth and declares the afterlife will be for those who do good in the world. Bek is made chief advisor, and he gives Horus back Hathor's bracelet letting him leave to rescue her from the underworld.

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