Jin-Roh borrows heavily and overtly from the tale of Little Red Riding Hood - the older, darker version that existed even before the Brothers Grimm and certainly before it was Bowdlerized and "cleaned up". The female terrorists who carry bombs for the Sect are known as "Red Riding Hoods," and Kei reads a bloody version of the tale to Fuse throughout the film.
The film itself, in fact, can be read as a modernized version of the old children's tale: Fuse appears to be at heart a wolf in human clothing - as evidenced by the scene where after practicing storming a building (and failing), Fuse is left as the only one among the cadets who is calm. The scene alternates with another scene where Tohbe (still in Panzer armor as the sole enemy during the exercise) is talking with Henmi. One of the topics is about how some people find comfort in reacting to the tough training like animals (here animal can be understood more as wolf than as mindless berserker). Plus, when asked by Kei as to why he joined the Panzer Cops, Fuse can only reply that it was because it was as though "I finally found a place where I belonged."
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The story is set in a parallel Japan, in the 1950s, and focuses on Kazuki Fuse, a member of the elite Kerberos Panzer Cops, a metropolitan antiterror unit equipped with heavy personal armor ("Protect-Gear"), Stahlhelm helmet enhanced with masks containing breathing and night-vision gear, and German-built MG42 machine guns. Trained to behave like a pack of dogs, hence the "Kerberos" term, Fuse confronts his own humanity when he fails to shoot a young female terrorist; the girl detonates a bomb in front of him, not only killing herself but bringing damage in the capital and undermining the unit's efficiency. Fuse strikes up an ill-fated romance with Kei -- a terrorist posing as the sister of the deceased --, who he meets as she mourns her death.