In 1991, after taking down the Katana crime organization, LAPD Detective Joe Marshall plans to settle down with his girlfriend Jennifer when she is suddenly murdered by a young boy at a park.
Twenty-five years later, Katana boss Fuj Fujiyama has successfully rebuilt his syndicate into a powerful multi-national organization, but is caught up in the midst of a gang war with the Shinjuku and Ginza clans. He informs his Vice President Doggé Sakamoto and subordinates that the war has awakened a long-missing Joe, and they must defeat him in order to secure the future of the clan.
Following the murder of a senator at the hands of Katana agent Hera and the Katana’s massacre of the Shinjuku at a night club, Joe’s old partner Detective Frank Washington is led to a secret compound 400 miles away from Los Angeles and reunited with Joe, who has lived in self-imposed exile since Jennifer’s death. After dispatching a group of ninjas at the compound, Joe reluctantly agrees to again team up with Frank after being told that the case of his wife’s murder will be reopened for his vengeance.
During a surveillance mission, Joe enters a nightclub, where he is suddenly greeted by a blonde Milena before a shootout between the Katana and the Ginza forces. Soon after, Frank warns Joe that Milena is not who she says she is. The next day, Frank is suspended due to his failure to stop the war while Joe is informed that the case is now under the jurisdiction of FBI Agent Carter, who is actually the Ginza’s new leader.
Joe and Frank decide to work outside the law to take down all the clans at the secret hideout known as “The Complex”. Joe storms through The Complex, encountering the Ginza clan before Carter is shot by Mola Ram, leader of the Yick Lung clan. Joe kills Fujiyama and his henchwomen, then defeats Doggé in a sword fight. Linton Kitano, the new leader of the Shinjuku clan, battles Joe and is swiftly taken down, but confesses to Joe that he was the one who murdered Jennifer 25 years before.
Linton prepares to commit seppuku, but Milena intervenes, revealing that she is his sister and they used Joe to infiltrate the Katana and help the Shinjuku become the only clan in the country. A disillusioned Joe leaves The Complex and parts ways with Frank and Detective Higgins before Lauren Kimura, a former Katana henchwoman, proposes to join forces with him.
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