Raizo (Rain) is raised by the Ozunu Clan to become one of the most lethal Special Ops ninja assassins in the world. As a child, Raizo experiences severe training under the guidance of his "father", Lord Ozunu (Sho Kosugi): he is whipped and/or cut whenever he fails and is encouraged to hurt his ninja kin for their training failures. The only kindness he ever receives is from a kunoichi (female ninja), Kiriko (Anna Sawai).
As they grow older, Kiriko and Raizo develop a romantic bond, however Kiriko's desire to leave the Ozunu Clan for freedom is greater.
One stormy night, Kiriko decides to escape from the clan. She encourages Raizo to join her, but he decides to stay. They kiss and she then climbs over the wall to freedom; only to be caught and brought back by her ninja kin. Branded as a traitor, Kiriko is executed (a katana through her heart) 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 is instructed by Lord Ozunu to execute an escaped kunoichi like Kiriko. He rebels against his master by slashing his face with a kyoketsu shoge and fights against his ninja kin. Barely surviving, he escapes by falling into a nearby river. Raizo recovers and begins to intervene in Ozunu hits by foiling their attempts.
While staying in Berlin and waiting for Ozunu's next move, Raizo rents a small apartment where he secretly continues to refine his training until it is time to act.
Meanwhile, Europol agent Mika Coretti (Naomie Harris) has been investigating money linked to political murders and finds that it is potentially linked to the Ozunu Clan. She defies her superior, Ryan Maslow (Ben Miles), and retrieves secret agency files to find out more. The clan, finding out about the investigation, attempts to assassinate her but she is rescued by Raizo.
Mika convinces Raizo to meet with Maslow for protection and to provide evidence against the ninja clan, but Raizo is intercepted by a task force for interrogation. Mika feels betrayed that Maslow would trick her that way, but Maslow secretly assures Mika that he is still on her side and gives her a tracking device for emergencies. While Mika warns Maslow of the dangers of keeping Raizo, the Ozunu ninja infiltrate their secret base and slaughter all the officers.
Mika frees Raizo and he lures the ninja away as Mika tries to escape. Raizo kills and fends off as many ninja as he can while Takeshi continues to trail him. He and Mika manage to escape but Raizo suffers mortal wounds around his stomach. Resting in a private area, Mika implants the tracking device into Raizo. Unable to fend against the clan, she hides outside the hotel until special forces arrive to help her. By that time, the ninja have recovered Raizo and taken him back to their base, bringing him before Lord Ozunu for prosecution.
While hidden inside a steel locker Raizo uses his healing techniques to heal all major injuries before being reunited with his "father." Lord Ozunu decides to have Raizo executed as an example but is infuriated by Raizo's defiance to the end; Ozunu strikes against Raizo's internal organs, causing him to spit out the tracking device.
Europol Special Forces Counter-Terrorism tactical teams lead by Maslow storm the hidden Ozunu base and kill most of the ninja in the court yard. Takeshi and Raizo face each other in the burning Ozunu training hall. Raizo slays Takeshi and confronts Lord Ozunu in a sword duel. While Ozuno initially has the upper hand, Mika, fearing for Raizo's life, distracts and shoots Ozunu with her pistol.
Before Raizo can recover, Lord Ozunu stabs Mika in the heart. Emotionally ravaged, Raizo uses the 'shadow blending' technique for the first time and finishes off Ozunu. Mika, seemingly fatally wounded, is in fact saved by a quirk of birth: her heart is on the opposite side of her chest. Mika and Europol leave the destroyed Ozunu compound while Raizo stays behind. Symbolically, he climbs the same wall Kiriko did all those years ago and looks out at the surrounding countryside. Recognizing his freedom for the first time in years, Raizo smiles, ending the film.