Kei Amemiya, a 17–18-year-old former operative of the left-wing terrorist group Sect in an alternate postwar Japan, initially evaded suspicion as a courier by leveraging her youthful innocence, earning the codename "Little Red Riding Hood" for transporting explosives. Captured by the Metropolitan Police Public Security Division, she is compelled to infiltrate the Kerberos unit’s ranks under a fabricated identity as the older sister of Nanami Agawa—a deceased Sect courier who died by suicide during a clash with Kerberos member Kazuki Fuse. Public Security weaponizes this false kinship to exploit Fuse’s guilt, positioning Kei as a pawn to entrap him.

Her mission blurs when a chance meeting at Nanami’s grave sparks an unexpected bond with Fuse. What begins as calculated manipulation gradually deepens into authentic emotional ties, conflicting with her coerced role in the conspiracy. As Public Security’s plot unfolds, Kei becomes bait in a staged museum ambush designed to frame Fuse and dismantle Kerberos. Fuse rescues her, and their flight leads them into the sewers, where Kerberos’s clandestine Jin-Roh unit intercepts them. The Jin-Roh operatives expose their knowledge of Kei’s involvement, leveraging her survival to unmask Public Security’s scheme.

Cornered and hunted, Kei faces a final reckoning when Jin-Roh orders Fuse to execute her, ensuring the conspiracy’s erasure. In her last moments, she echoes the "Little Red Riding Hood" tale, acknowledging Fuse’s paradoxical role as both her protector and executioner. Her death becomes a catalyst, cementing the cycle of manipulation and tragedy woven by institutional rivalries, loyalty, and the personal costs of subterfuge.