Raizo (Rain) is raised by the Ozunu Clan to become the most lethal Ninja assassin in the world. As a child, Raizo being an orphan is taking by Lord Ozuno(Sho Kousugi)and is enrolled in severe brutal training. The only generosity he ever receives is from a kunoichi named Kiriko (Kylie Goldstein), with whom he develops a romantic bond. However, as time goes on, Kiriko becomes disenchanted with the Clan's routine, and wishes to abandon it for freedom. One rainy night, Kiriko decides to make her escape and encourages Raizo to join her; but he decides to stay. Branded as a traitor, Kiriko is caught and later executed in front of Raizo by her elder ninja brother Takeshi (Rick Yune). As a result of Kiriko's death, Raizo begins to harbor resentment and doubt towards the Clan.
After completing his first assassination, Raizo meets the rest of his Clan atop a city skyscraper in Berlin. There he is instructed by Lord Ozunu to execute another kunoichi traitor like Kiriko. He rebels against Lord Ozunu, and engages in combat against his fellow ninja kin. Barely surviving, he falls over the edge of the skyscraper and into a nearby pool. Raizo recovers and begins to intervene and foil subsequent Ozunu assassination attempts. Meanwhile, Europol agent Mika Coretti (Naomie Harris) has been investigating money-linked political murders, and finds out that they are possibly connected to the Clan. She defies her superior, Ryan Maslow (Ben Miles), and retrieves secret agency files to find out more about the investigation.
Mika meets Raizo and convinces him to see Maslow for protection as well as to provide evidence against the Clan. But Raizo is later set-up by Maslow, and abducted by agents from Europol for interrogation. Although feeling betrayed, Maslow secretly assures Mika that he is still on her side and gives her a tracking device for emergencies. The Ozunu ninjas infiltrate the Europol headquarters in an attempt to kill Raizo and everybody inside .Mika frees Raizo and they both manage to escape, but Raizo suffers near mortal wounds mika then takes him to a hotel after the battle aginst the ninjas. Resting in a motel, Mika implants the tracking device into Raizo, as the ninjas remain in pursuit of him. Unable to fend against the Clan, she hides outside the motel until special forces arrive to help her. By the time they arrive though, the ninjas have already kidnapped Raizo, bringing him before Lord Ozunu for prosecution.
Europol special forces and tactical teams led by Maslow storm the secluded Ozunu retreat nestled in the mountains by following the signal of the tracking device that is inside Raizo. Raizo and Lord Ozunu confront each other in a sword duel. Mika interfere to help, but is stabbed by Lord Ozunu. Enraged, Raizo uses a 'shadow blending' technique for the first time to distract and kill Lord Ozunu. Mika, seemingly fatally wounded, is in fact saved by a quirk of birth–her heart is actually on the opposite side of her chest. Raizo later symbolically climbs the same wall Kiriko did while trying to escape in the past, and looks out at the surrounding countryside. He then recognizes his freedom for the first time.