At the stroke of midnight, a shocking incident occurs as Tomoe Enjō violently stabs his parents, driven by a fit of rage. In his panic, he flees their apartment, leaving chaos behind. Shortly thereafter, a homeless burglar discovers the gruesome scene. However, to his astonishment, when he brings the police back to the scene, the family appears alive and well, greeting the officers as if nothing had happened.
As life continues, Shiki substantially impacts Tomoe's world when she intervenes to defend him from bullies at school. Sensing a connection, Tomoe impulsively confesses to Shiki that he is a murderer and seeks her help in hiding. To his surprise, Shiki reacts with a calm understanding, stating that she too shares a similar darkness within. Their bond deepens, leading to a month-long stay where Tomoe seeks solace with Shiki while anxiously waiting for news about his deceased parents.
During this time, Tomoe becomes increasingly aware of a mysterious figure, a man clad in a red hat and coat, seemingly tailing Shiki. Although he advises her of his presence, Shiki brushes off his concerns. Tension escalates between them as Tomoe expresses his love, declaring his willingness to die for her since he feels devoid of worth. However, Shiki's profound response causes Tomoe to rethink his situation, prompting him to leave her sanctuary.
Shocked yet again, Tomoe later encounters his mother alive, leading him back to Shiki. Determined to understand the truth, Shiki agrees to accompany Tomoe back to the Ogawa apartment, an ominous red complex newly completed. Upon entering the elevator, they note its odd spiral ascent. Reaching the fourth floor, Shiki opts not to ring the doorbell and enters Tomoe's home unannounced. Within, they witness Tomoe's abusive family dynamic, including a haunting moment of murder-suicide involving his mother. Shiki explains chillingly that these are not real individuals but rather imitation puppets, trapped in a continuous cycle of reliving their final day.
With each revelation, Shiki guides Tomoe to what she claims is his "real home" across the complex, illustrating that due to the building's faulty elevator configuration, residents unknowingly exist in two separate realities. As they step into this hidden space, they encounter the decayed remains of Tomoe's real parents. However, their intrusion activates the undead puppets of the other residents, who aggressively confront them. While Shiki adeptly dispatches the threats, they encounter Souren Araya, revealing a dark connection to the apartment's curse.
Caught in the middle of arbitrary schemes, Souren divulges that he orchestrates horrific experiments aimed at manipulating the residents' destinies, culminating in an eternal cycle of death. He seeks to compel Shiki to confront her own "Origin", which leads to a brutal confrontation that sees Shiki struggle against Souren's overwhelming power, ultimately succumbing to him.
Meanwhile, Tōko Aozaki receives unsettling intel related to the reported murders, leading to an investigation that draws in Mikiya Kokutou, who has just returned from driving school. As they delve deeper into the bizarre architecture of the apartment complex, they discover a web of deceptions surrounding the residents' identities. The strange design ingrains madness into the minds of the inhabitants, complicating their understanding of their lives.
Tomoe and Mikiya eventually forge an unexpected alliance, despite initial friction regarding their motivations. Their paths diverge momentarily, prompting Mikiya to aid Shiki while Tomoe grapples with his past. This journey invites memories that allow Tomoe to reclaim his identity and sense of belonging.
As they attempt to save Shiki, they are confronted by Cornelius Alba, an ominous figure from Tōko's past. Despite his efforts, Mikiya is knocked unconscious. The tension culminates in a chaotic climax as Tōko, though temporarily incapacitated, regains her resolve. She confronts her past and summons a puppet of herself to counter Cornelius, leading to a fierce battle.
Ultimately, the arcs intertwine as Shiki engages in a final duel with Souren, manifesting an explosion of power that reshapes their paths. The outcome raises questions about the cycle of life and death, the meaning of existence, and the entangled fates of each character. As the dust settles, Mikiya enters Shiki's apartment, utilizing a key given to him by Tomoe, hinting at a future still fraught with potential twists and revelations. As Shiki wittily remarks on the key she lacks, the story leaves a lingering sense of both closure and ongoing mystery.