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The story initially starts by dealing with terrorism in an alternate-universe 1990s era, where Japan is the largest economy in the world. The communist radical group, the Red May, are trying to bring down Japan's economy and take over the government.
In response, a government agency, the Special Security Force, is formed with the ability to act outside the law. However, when the Red May suddenly find themselves being wiped out, the force discovers that something else is hunting the terrorists.