After the flames of human history are restored, a new set of distortions emerges in the world. These are the four Pseudo-Singularities, remnants of the incineration that refuse to fade away. The first of these is designated as Subspecies Singularity I, a malignant and isolated demon realm that has overwritten the Shinjuku ward of Tokyo in the year 1999.

The protagonist, Ritsuka Fujimaru, the last remaining Master of Chaldea, is dispatched to this new Singularity alongside his dependable Demi-Servant partner, Mash Kyrielight. They arrive to find a decadent, nocturnal cityscape ruled by a dark and oppressive atmosphere. This Shinjuku is a closed-off prison for phantom spirits, where the very laws of reality are warped. Upon arrival, they quickly ally with a unique Servant, the Avenger class Jeanne dArc Alter, whose fiery personality and formidable power become crucial to their mission.

The central conflict of this narrative arc revolves around a massive murder case and a conspiracy to completely sever this Shinjuku from the rest of the world. The primary antagonist is the Archer of Shinjuku, a cunning and manipulative figure who operates from the shadows. To neutralize this threat, Ritsuka and his allies must first deal with the Shinjuku Assassin, a Servant who has taken on the guise of the tyrannical king Artoria Pendragon (Alter). In a key operation, the group infiltrates a party hosted by this false king, leading to a direct confrontation where the Assassins true identity and motives are brought to light.

As the investigation deepens, the story unfolds like a hard-boiled detective thriller. The allies are joined by the gentlemanly criminal mastermind, James Moriarty, the Archer of Shinjuku, whose allegiances remain in question. The narrative pits the forces of Chaldea against a host of summoned phantom spirits, including the infamous Hessian Lobo, the Headless Horseman and the wolf king. The climax involves a desperate battle against an entity known as the Avenger of Shinjuku, culminating in a resolution that sees the temporary departure of Jeanne dArc Alter.

The manga is illustrated by Sasakishonen and serves as a direct adaptation of the mobile game's story, expanding on the action and character interactions within this closed-off world. It concludes with the resolution of the Shinjuku phantom incident, allowing Ritsuka and Mash to return to Chaldea, though the lingering effects of this bizarre case hint at the greater mysteries still to come in the remaining Pseudo-Singularities.