City Hunter, the globally adored hero, becomes embroiled in an adventure that takes him deep into the political intrigue of a Third World country and into the pain and anguish of one man's tortured past. James McGuire's life is so dangerous he has to hire bodyguards for his Secret Service agents. It doesn't help that his chief agent is actually his long-lost daughter. Luckily for him, City Hunter and Kaori are behind on the rent and need the work. But a dark secret from McGuire's past threatens to destroy him and his lonely daughter Anna. Will he live to rescue his country? Will his resentful daughter learn to love him again? Will City Hunter finally get some action?
The story is set in 2027, one year after the end of the fourth non-nuclear war. New Port City is still reeling from the war's aftermath when it suffers a bombing caused by a self-propelled mine. Then, a military member implicated in arms-dealing bribes is gunned down. During the investigation, Public Security Section's Daisuke Aramaki encounters Motoko Kusanagi, the cyborg, wizard-level hacker assigned to the military's 501st Secret Unit. Batou, a man with the "eye that does not sleep," suspects that Kusanagi is the one behind the bombing. The Niihama Prefectural Police detective Togusa is pursuing his own dual cases of the shooting death and a prostitute's murder. Motoko herself is being watched by the 501st Secret Unit's head Kurutsu and cyborg agents.