Tokyo Xanadu is an action role-playing game with party-based real-time combat that features dungeon exploration, similar to the Persona series by Atlus, as well as Falcom's own Ys and Trails franchises.

One night, while returning from work, Kou notices his classmate Asuka Hiiragi involved with some dangerous individuals.

Concerned for her safety, Kou follows them into a back alley, only to be sucked into a vortex that transports him to a nightmarish realm known as Eclipse.

During a weekend vacation, they learn that Eclipse started spreading after the Great War II and caused the devastating earthquake known as the Tokyo Twilight Disaster.

They recruit Rion Kugayama, a member of a famous idol group, and their English teacher, Gorou Saeki, who is part of the Japan-Self Defense Force.

During this event, they discover that Jun Kohinata, Kou's classmate and friend, is a Seal Knight belonging to the church and tasked with fighting Eclipse.

Shiori explains that she died during the disaster but was brought back to life by the mythical Greed called the Twilight Apostle.

Influenced by the Apostle, Shiori aimed to engulf the world in Eclipse to change the fact of her death, but the X.R.C members defeat her, and she passes away after bidding a tearful farewell to her friends.

The side stories involve all X.R.C members (minus Kou), Jun Kohinata, and Gorou Saeki investigating a peculiar form of Eclipse.

In the After Story, the X.R.C members, along with Kou's old friend Ryouta Ibuki, are trapped in an Eclipse identical to Morimiya by a child wearing a fox mask, who is revealed to be a younger version of Kou—the Twilight Apostle.

The X.R.C members and their allies vow to prepare themselves for future battles, and the story concludes with the start of the autumn festival and everyone enjoying themselves.