More blathering follows, contains spoilers.
Jin-Roh is a distorted, mirror image of Japan during the third decade of the Showa emperor's reign (1955-1965), a period of unrest and street riots that the movie's creator Mamoru Oshii remembers with an odd nostalgia as a time when society and the future were fluid. He remarks in the interview that the younger people who worked on Jin-Roh were all born after that period, after the Tokyo Olympics, and don't really understand the period or grasp its nature.
Despite Carl Gustav Horn's essay in the booklet suplpied with the special edition of the DVD, I don't understand the period or the metaphor Oshii is trying to show me in the movie any better. It's clear to me that the "thirties" of Hirohito's reign were turbulent and violent, featuring street battles between the political extremes in Japan, but is Horn correct that the old nationalist Right was using the ruling party to reassert itself through the police war? Is Oshii using the movie to condemn both extremes, sympathize with the Left or the Right, or demonstrate their irrelevancy in the context of a Japan returning to the ranks of the great world powers? It's not entirely clear from the interviews or the essay; the subtitles of Oshii's interview are vague in that regard, and Horn seems to see the events of the movie and the Showa 30s through the distorting lens of post-9/11 American liberalism.
Knowing that Oshii has set his movie in an alternate world where the Germans and not the Americans defeated Japan makes it even harder to understand the movie's message, if in fact it has one at all. Perhaps Jin-Roh is best understood as what it appears to be: a doomed romance set in the middle of a three-sided "dirty war" being fought between the paramilitary Special Unit, the Sect and the Capitol Police, where none of the main characters can be described as "good guys".