The game features four "biomes", or locales of the underworld: Tartarus, Asphodel, Elysium, and the Temple of Styx.
The game is presented in an isometric view with the player in control of Zagreus. The player starts a run-through of the game by trying to fight their way through a number of rooms; the room layouts are pre-determined, but their order and the enemies that appear are randomly determined.
The game has a hack and slash combat system. The player has a primary weapon, a special attack, and a magic "cast" which can be used from long range.
Upon starting a run, one of the Olympians will provide a gift, a choice of three persistent boosts for that run that the player can select from; the gifts are themed based on the Olympian, for example with Zeus providing lightning damage effects.
Subsequently, after clearing a room, the player will be shown the type of reward they may earn if they complete the next room or choice of next rooms, ranging from additional Olympian gifts, restorative items, in-game currency, a store to purchase improvements, or keys that can be used in the meta-game to improve Zagreus' initial attributes for the next run.
Should Zagreus' health points drop to zero, he "dies" and ends up facing his father, removing all gifts granted from the last run.
Between runs, Zagreus can explore the Underworld before setting on a new quest. Here, the player can use the keys to unlock permanent upgrades for Zagreus, order construction of new support features for the Underworld, or obtain new weapons.
They can also have Zagreus interact with the various characters of the Underworld, which provide narrative elements to the game and may also provide quests with additional rewards.
Plot
Zagreus, the son of Hades, seeks to escape his father's realm in the Underworld. He is aided by his adoptive mother Nyx, who gives him a special mirror that empowers him with various abilities via collected Darkness; the Gods of Olympus to whom he has reached out, who provide him with Boons that give him special powers, and his mentor Achilles, who provides him with the Infernal Arms, weapons that possess powerful and hidden aspects of their past, present, and future wielders.
Hades hinders Zagreus' progress by unleashing the Underworld's various residents on him, including the Fury Megaera, Zagreus' ex-lover (and later on her sisters Alecto and Tisiphone); a Lernean Bone Hydra; the legendary Theseus alongside his new partner Asterius, and finally Hades himself.
It's eventually revealed that Zagreus wishes to escape the Underworld to find Persephone, his birth mother whom he never knew, having always been told he was the child of Nyx. Hades refuses to even allow her name to be spoken in his House and it is said that unimaginable punishment should befall anyone who disobeys his order.
Nyx, on the other hand, decides to help Zagreus find the truth about his real mother for himself by putting him in contact with his relatives on Olympus. After finally defeating Hades for the first time, Zagreus finds Persephone in Greece.
After a tearful reunion, Zagreus discovers that since he is bound to the Underworld like his father, he cannot survive long on the surface. Despite this, he promises to keep escaping to spend time with Persephone and learn the truth of her absence.
Over the course of these visits, Persephone explains that she had a loving marriage to Hades (which the latter later states was a result of Zeus having "given" her to Hades as a gift for taking charge of the Underworld, something which Hades thought was incredibly disrespectful and never forgave Zeus for) until Zagreus was stillborn due to the Fates having decreed that Hades would never sire an heir.
Persephone ran away in grief but refused to return to her birthplace on Olympus which she disliked due to the constant bickering and posturing of the Gods. However, Zagreus was eventually brought back to life via Nyx's powers in an extremely lengthy process.
Persephone refuses to return to the Underworld because she fears retribution from the Olympians towards Hades and the Underworld should they discover the truth about her disappearance, especially her mother Demeter who has covered the mortal world in an endless winter in grief for her daughter.
Zagreus eventually convinces her to return by reminding her of the bonds of family and they finally sail down from Greece towards the House of Hades on the River Styx ferried by Charon. Persephone resumes her duties as Queen of the Underworld and Hades, now with a renewed respect for his son, allows Zagreus to continue his escape attempts under the guise of finding security vulnerabilities in the Underworld.
In an epilogue, Persephone comes up with the idea of reconciling with the Olympians by inviting them all to a feast in the House of Hades. There they claim that Hades and Persephone eloped and had Zagreus, but avoided telling them about Persephone's resentment of Olympus and further add a false claim that due to her having eaten Underworld pomegranate seeds, she can only leave the Underworld a few months out of the year.
The Olympians readily accept this explanation though it's implied they all know what really happened and simply wish to move on. Everyone now reconciled, Zagreus' new duties to escape his home continue.