Kratos recovers Pandora's Box from Ares, opens it, and uses its power to become godlike. Despite Ares' best efforts to destroy Kratos physically and mentally, including stripping him of the Blades of Chaos and all magic, he survives and kills Ares with the Blade of the Gods. Athens is saved, and although Athena tells Kratos his sins are forgiven, the gods cannot rid him of his nightmares. Forsaken by the gods, he tries to commit suicide by casting himself into the Aegean Sea, but Athena intervenes and transports him to Mount Olympus. As a reward for his services to the gods, she provides Kratos with a new set of blades and the seat as the new God of War.

Kratos enters the Desert of Lost Souls, and Athena tells him Pandora's Box is hidden in a temple chained to the back of the Titan Cronos—a punishment by Zeus for Cronos' role in the Great War. Kratos summons Cronos, climbs for three days before reaching the Temple entrance, overcomes an array of deadly traps and an army of monsters, and eventually finds the Box. But Ares, aware of his former servant's success, kills Kratos as the latter is leaving the Temple. While harpies take the Box to Ares, Kratos falls into the Underworld. He battles his way through the fiery realm, and with help from the mysterious gravedigger, who tells him Athena is not the only god watching over him, he escapes and returns to Athens.