[1] The game is set on the Golden Isle, a large open world consisting of seven distinct regions inspired by Greek mythology.

[2] After eons imprisoned under a mountain by Zeus, Typhon escapes, seeking to break the barrier between the mortal realm and Tartaros and remake the world in his own image.

After recovering several artifacts belonging to legendary Greek heroes and receiving a prophecy, Fenyx rescues a young stranger, who helps her reach the Hall of the Gods.

Determined to save humanity, Fenyx agrees to venture out into the Golden Isle to restore the deposed Olympian gods, along the way befriending a 'fire bird' which she names Phosphor.

Fenyx manages to restore Aphrodite, who became a tree without her passion; Ares, who was transformed into a rooster without his pride; Hephaistos, who became one of his automatons without suffering; and Athena, who was turned into a child without the ability to make clear judgments.

Despite their restoration, the gods are unable to agree on a plan to stop Typhon and subsequently revert to their usual bickering and infighting.

Fenyx scales the mountain at the center of the Golden Isle; at the top, she discovers that Ligyron is allied with Typhon, and has collected all the ingredients necessary to create a poison capable of killing the gods.

However, he interrupts when he hears Fenyx is Hermes' child, as this should not be possible; Prometheus then admits that he had manipulated and fabricated parts of the story.

At that moment, Fenyx arrives with Typhon's poison, confirming the entire story was part of Prometheus' plot to have Zeus killed as revenge for imprisoning him.

Afterward, as a reward for helping defeat Typhon, Zeus agrees to return humanity to normal, restores Phosphor as a new creature, the phoenix, and invites Fenyx to live on the Golden Isle with the gods.

According to Ubisoft, the delay gave additional time for the development team to "ensure that their respective innovations are perfectly implemented so as to deliver optimal experiences for players.

"[8] Quebec studio used the additional time to add Zeus and Prometheus as the game's duo narrators, replacing Greek poet Homer, who was initially intended to fulfill this role.

[11] Jeffrey Yohalem, who wrote for previous Ubisoft titles such as Assassin's Creed II, Far Cry 3, and Child of Light, served as narrative director and lead writer.

The humour—particularly that involving the bickering between the narrators Zeus and Prometheus—was inspired by films such as Robin Hood: Men in Tights, The Princess Bride, and The Naked Gun.

In regards to adapting Greek mythology for modern audiences, Yohalem explained that he did not want to avoid the darker aspects of its gods and heroes (providing the example of Paris' kidnapping of Helen of Troy), and instead wanted to specifically highlight those elements through a modern perspective, as it "[speaks] to our current political climate and who we are as human beings on social media."

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In this story arc, the players plays as Ash, a new hero on an epic journey to reunite the Greek Gods including Poseidon and Hades, and bring them back to the Pantheon.