In the turbulent backdrop of 1950s Tokyo, where the streets of Akasaka are ablaze with unrest, the Sect's secret operatives, including Nanami Agawa, a young courier likened to Little Red Riding Hood, labor intensely to stoke the flames of chaos. Amid the turmoil, the Self-Police struggle to regain control, suffering heavy losses as several of their officers fall prey to a strategically placed satchel charge set by the Sect. To counter this escalating violence, the Capital Police dispatch their elite Special Armed Garrison Kerberos unit, which quickly annihilates the Sect's members and destroys their stockpile of explosives.
Among them, Kazuki Fuse, a member of Kerberos, finds himself grappling with a moral dilemma when he encounters Nanami as she attempts to flee. Caught between his duty and his conscience, he hesitates when ordered by his superior to execute her. In a dramatic turn of events, rather than yielding, Nanami detonates a devastating satchel charge, taking her own life and plunging the area into darkness. This catastrophic act allows the rioters above to seize control, leaving a blemish on Kerberos' reputation and imposing a heavy burden on Fuse, who faces disciplinary actions for his inaction and is subjected to retraining under the stern supervision of drill instructor Hachiroh Tohbe.
Burdened with guilt, Fuse pays a visit to Nanami's grave, where he encounters Kei Amemiya, an enigmatic young woman claiming to be her sister. Despite their shared sorrow, they forge a strong connection that transcends the tragedy of their meeting. However, it soon comes to light that Kei is not who she pretends to be; she is a former Little Red Riding Hood courier who has been manipulated into serving the interests of Public Security. This clandestine organization aims to dismantle Kerberos, pivoting their counterterrorism strategies from brute force to strategic intelligence gathering.
Public Security seeks to ensnare Fuse by using Kei as bait in a trap laid at a museum, designed to tarnish Kerberos' reputation and advance their agenda. Defying the odds, Fuse infiltrates the museum, dispatches Public Security’s agents, and escapes with Kei, outmaneuvering both the Self-Police and Public Security’s schemes. As Kei sheds her facade, she proposes they flee together, but Fuse remains committed to his duties. Throughout this tumultuous journey, Fuse and Kei's bond strengthens, blossoming into a profound love that is tested by the chaos surrounding them.
As the clash subsides, Fuse and Kei delve into a labyrinthine sewer system, seeking refuge from the relentless gunfire. Here, they encounter a secretive group known as Jin-Roh, an elite counterintelligence unit dedicated to protecting Kerberos from Public Security’s threats. Led by the steadfast Tohbe and the shrewd Hajime Handa, Jin-Roh offers Fuse a lifeline, arming him with an MG 42 and Protect Gear, while enlightening him about Kei's involvement and her significance as a living witness to Public Security's nefarious plans. As they escape with Kei, they leave behind a web of secrets and ominous foretellings.
Public Security's special forces, commanded by Hemni, track down Fuse and Kei to the sewer hideout using a concealed device in Kei's bag. However, instead of confronting their intended targets, they face a hail of gunfire from a prepared Fuse, who systematically takes out the Public Security agents and engages in a fierce duel with a severely injured Hemni.
Reunited with Jin-Roh in a desolate junkyard littered with remnants of urban decay, Fuse confronts a harrowing choice. Tasked with eliminating Kei to safeguard her from being captured by Public Security, he is torn apart by the moral complexities of the situation. Sensing her fate, Kei embraces Fuse and recites the haunting tale of Little Red Riding Hood, detailing the wolf's ghastly disguise. Terrified by the weight of his duty, Fuse's internal struggle intensifies, culminating in a devastating choice to end Kei’s life. Nearby, Tohbe gravely draws a parallel between Kei’s fate and the story of Red Riding Hood, emphasizing the grim reality of the wolf’s victory as the dark truths surrounding Kerberos unfold before them.
