Set halfway through Kratos' 10 years of service to the Gods,[6] Chains of Olympus begins with the gods sending Kratos to the city of Attica to help defend the city from the invading Persian army. Kratos confronts the Persian King inside the city and kills him. Later, he witnesses the sun fall from the sky, plunging the world in darkness. Following the dim remaining light on the horizon, Kratos fights his way through the city of Marathon, along the way encountering the black fog of Morpheus, which now covers the land in darkness.
Eventually Kratos makes his way to the Temple of Helios. There, he encounters a statue of Athena, who tells him that Helios has disappeared and needs to be saved. Morpheus has used this to his advantage to cause the gods to fall into a deep slumber. Kratos fights his way through the Temple of Helios and is sent to the caves within the temple of Olympus by Eos. Meeting her in the caves, Eos tells Kratos that she will guarantee the gods' promise of relieving him from his nightmares if he will help her save Helios from Atlas, who has abducted him. Kratos does not believe her, however, he reluctantly agrees to help. Kratos retrieves the primordial fire needed to awaken the fire steeds from the cave and returns to the temple.
The horses lead Kratos into the underworld before retreating. There, he meets Charon at the River Styx. Charon tells him to leave, and that it is not yet his time. With Kratos refusing to leave, they battle, ending with Charon knocking Kratos unconscious and dropping him into Tartarus. There, Kratos witnesses the breaking of the chains binding Atlas. Kratos eventually fights and climbs his way out of Tartarus, this time killing Charon. Kratos takes the ferry and follows the light of Helios down the River Styx, eventually coming upon the Temple of Persephone, Queen of the Underworld.
Inside the temple, Persephone tells Kratos that his daughter, Calliope, is in the fields of Elysium and that the only way to see her again is for Kratos to let go of his past evils, giving up the powers given to him by the gods; however, Persephone warns him that the world will suffer for his choice. After transferring his power and weapons into the Forsaken Tree, Kratos regains his humanity. He once again becomes a normal man, and is reunited with Calliope. However, Persephone appears, taunting Kratos' choice. She then reveals to him her true plans: Bitter at being betrayed by Zeus, tricked by Hades and abandoned by the gods, Persephone was the one who had freed Atlas. While Kratos was disarming himself, Atlas was carrying out Persephone's plan to destroy the pillar that holds the world, and with it, Olympus, killing everyone. Kratos realizes now that if he stays with Calliope, it would mean the end of the world. He sacrifices seeing his daughter again in order to regain his power by killing all the souls in Elysium. He once more becomes the Ghost of Sparta, regaining his pale complexion.
Kratos pursues Persephone, catching her at the pillar. There, Kratos and Persephone engage in battle. After being attacked by Atlas, Kratos chains him to the roof of the underworld before returning to battle Persephone and eventually killing her with Zeus' Gauntlet. Dying, the goddess taunts Kratos as her body explodes, severing the pillar in the shockwave with Atlas now the only thing holding the world up. Though the Titan gloats to Kratos about the gods' true plans for him, Kratos believes his path is clear: he will serve them only so they will keep their promise to free him from his nightmares. Atlas ends by foretelling that they will meet again.
Keeping his own promise to the gods, Kratos returns Helios to the sky. But he is left with the knowledge that his sins have consumed him, and he will never be pure enough to see his daughter again. Weak from battle, Kratos loses consciousness and falls from the sun chariot, but is suddenly stopped before striking the ground. Athena and Helios approach him and, as they praise him for his work, remove the Sun Shield and the Gauntlet of Zeus. As they depart through the gate to Olympus, Helios suggests helping further. Athena disagrees, as the pair retreat through the gateway to Olympus.