When the Metaverse makes an unexpected return in the form of Jails ruled by Shadow-selves known as Monarchs, the Phantom Thieves of Hearts are called back into action once more to reclaim the Desires stolen by these Monarchs from people all across Japan alongside their new allies, such as a mysterious and highly advanced AI known as Sophia and PubSec Inspector Zenkichi Hasegawa.

Ren Amamiya aka the Joker, and his girlfriend, Sumire Yoshizawa aka Violet, have found themselves called upon by Igor and his master Philemon, and are tasked with a new mission: travel back in time to the year 2009 and work to defy fate by ensuring the survival of the Twin Messiahs, while also trying to find another way to prevent the world's destruction at the hands of Nyx.

Waking up on a train without a single memory to his name, a young man named Sakuya Shiomi finds himself entangled in a supernatural murder-kidnapping mystery involving a Shadow World on the backside of the TV that's plauging the town of Inaba, and may also hold the keys to reclaiming his true identity, and reuniting with the girl he loved more than life itself. P3 Hero in P4G.

Shortly after finding himself in the Netherworld, merging with the Proto-Fiend Aogami, and becoming a Nahobino, Naobi Hino meets a creature known as the Demi-Fiend, Agreeing to combine forces while in the Netherworld, the Demi-Fiend and Naobi soon find themselves getting roped into working with the angels of Bethel, and the situation only escalates from there.

Despite the best efforts of the Nahobino, humanity once again finds itself caught in the middle in the war between the servants of Order, led by the new God of Law, the Nahobino himself and his bride, the Goddess Isonokami, and the agents of Chaos, now led by the new Lord of Chaos, the creature known as the Demi-Fiend. Naturally, all Hell breaks loose before long.