The assassination of Tokyo governor Takayama causes a stir of public outrage in Tokyo, Japan. Upon hearing the news of the incident, the FBI asks the CIA's Tokyo office to investigate the killing, believing it to be linked to the Yakuza, a dangerous Japanese mafia. Retired CIA agent Travis Hunter and rookie FBI agent Sean Mac are assigned to work on the case and to track down the perpetrators. The Japanese branch of the CIA starts sniffing around under the auspices of the United States Department of Homeland Security. During work, Mac proves to be more of a distraction, not really knowledgeable about procedures or Japanese customs. Hunter was raised in Japan, and has a strong understanding of the Yakuza and their mysterious, eccentric, and sinister ways.
Hunter and Mac discover a plan by Kuroda, the new boss of a new Yakuza outfit, to build an enormous drug-dealing network with a Chinese Tong outfit leader named Chen. Kuroda is killing everyone who gets in his way, and it is revealed that Kuroda masterminded the governor's assassination. Hunter turns for help to Kojima, the second-in-command of an old school Yakuza outfit run by elderly Oyabun Ishikawa. Hunter has been told that Kojima is the only Yakuza player who is capable of defeating Kuroda. Hunter visits Kojima, who says that now that the new Yakuza are joining forces with the Tongs, they are becoming too powerful. Kojima tells Hunter that he would love nothing more than to permanently get rid of Kuroda.
As Hunter gets closer to Kuroda, he begins to endanger everyone associated with him. First, Kuroda has Ishikawa killed, making Kojima the new leader of Ishikawa's Yakuza outfit. Mac gets out of his depth and is also murdered. When Kuroda has Hunter's fiancée Nayako brutally murdered, Hunter's search for Kuroda becomes devastatingly personal. Teaming up with CIA spook Jewel and tattoo artist Kawamura, whose wife and young child were killed by Kuroda, Hunter sets out to take down Kuroda, who uses a temple as his hideout.
By nightfall, they arrive at the hideout and brutally kill all the members with katanas. Akayo arrives to slaughter some members and teams up with the two men. When Kawamura confronts Kuroda, the latter shoots him although the former survives. Hunter then battles Kuroda and kills him by slashing his chest. They leave the crime scene after that.
The three offer their respect to Nayako during a worship service and a ceremony is held to make a replacement of a leader. Kuroda's hideout is investigated and cleaned up with blue spray as his body as well as the bodies of his henchmen are taken away for autopsy while authorities collect the weapons for criminal investigation. Hunter then walks to the park where he and Nayako used to hang out.