The opening scene shows a young Asian gangster of the Yakuza getting a tattoo from an old man with his friends sitting around in a dark room. The gangster threatens the old man with a gun after the old man says the gangster is perhaps not on the path he was chosen for. Soon after, the gangsters receive a letter with a red seal. What they find inside is black powder, which the old man reveals is a sign of death. He dares not speak the word "ninja", and so shows the gangsters a tattoo on his chest of one. The gangsters make fun of the old tattoo artist, and start repeating the word "ninja" in a mocking tone, until one of their heads is sliced in half.
Panic ensues and an action scene takes place, with lots of gunfire and gore during which the killer is not seen. After everyone but the old man is killed, a ninja steps out of the shadows toward the old tattoo artist, who says, "I knew you existed" just before he is killed, and the bloody title splats onto the screen.
After the title, we see a scene of a Europol forensics researcher named Mika Coretti (Naomie Harris) presenting evidence to her disbelieving boss, Ryan Maslow (Ben Miles), of the existence of Ninja clans. However, she gets him to trust her enough to take a look at the evidence. She tries her hardest to convince him as we are moved to the next scene, in which a young Asian man (Rain) fights and kills a disguised woman assassin in a laundromat.
After the fight we cut to Mika and Ryan discussing the report from a KGB spy named Aleksei Sabatin that suggests nine Ninja clans are responsible for many political assassinations, and Ryan decides to help Mika in her investigation.
After such, we cut to the young Asian in his apartment building, as he chats with an old woman about his moving out. In his apartment, we see that he is a ninja, hiding all of his equipment in secret compartments.
He then has a flashback, showing his introduction to his clan as a young boy. The clan is full of young children, orphaned by the clan itself, and trained from a young age to be assassins. The man who introduces him is Ozunu (Sho Kosugi), the leader of the clan. Ozunu gives the boy the name "Raizo".
The next flashback shows Ozunu teaching the children to master their weaknesses. He cuts his hand with a knife, closes it, and recites something in Japanese. When he opens his hand, both the blood and the wound are gone.
The next flashback shows Raizo after a fight with another child of the clan. Raizo is victorious, and the other child lay bruised and beaten. Ozunu tells Raizo how he should have died, being an orphan, but lives because he fought to survive, and did not fear.
We cut to Raizo exercising, until another flashback, showing him as a boy stepping across wooden boards, avoiding the ones that creak. He eventually steps on a creaking board and is punished by having the bottoms of his feet struck with a stick.
We see him sleeping that night, and a girl who is also in the clan sneaks over to heal his feet.
We flash forward to Adult Raizo sleeping in his bed. He holds a gold watch in his hand.
The next scene is of Mika visiting Mrs. Sabatin to discuss her husband's work as a KGB Spy, and how he changed after the report about the ninja clans was released. We see shots of him having locks installed everywhere on his home, as well as several lights and security systems. Mrs. Sabatin then explains how a stranger came to her and her husband's door one day and spoke with Aleksei shortly and walked away afterwards. The same night, he was killed after a power outage.
After telling the story, Mrs. Sabatin brings Mika a small lockbox. Inside are photographs of evidence and security feeds of the man who came to their door. Mika uses the security feed to see the man's face. It is Raizo.
The next scene is of Adult Raizo training with his weapons.
After, we see a flashback of Raizo as a teenager fighting with another orphan named Takeshi. Raizo loses, and is punished by Ozunu. Ozunu leaves Raizo a test: to die from his wound, or heal himself through meditation. Raizo passes, and we cut to the next scene, where Mika continues her research on Aleksei. As she searches through news clippings, an agent from internal affairs walks in and asks her about her relationship with Maslow and his behavior. The agent suggests that perhaps Maslow might be losing his mental stability due to his work. It is then that Mika realizes that she and Maslow are being watched.
Mika and Maslow meet at a public place and discuss the possibility that the clans are behind their being watched. Both agree to be more covert in their actions.
The next scene we see Mika in her apartment looking through Aleksei's research of the nine clans.
The next scene shows Raizo walking down the street in the city of Berlin.
We cut to a flashback of teen Raizo, gardening with Keiko, the same girl who helped him as a boy. She teaches him that everything has a heart, and they quickly develop a romantic relationship.
Flashing forward, we see adult Raizo training with more weapons. This time he wears a blindfold.
From here, we flash back to Teen Raizo training blindfolded to teach him to better use his senses.
After his successful training, we see a boy punished for some unspecified offense. Ozunu orders Keiko to cut him, but she cannot, and instead is cut across her face by Ozunu, which leaves a scar.
Keiko is then put in a cage for several days as punishment.
Days later, she is let out of the cage, but escapes in the night. Raizo pursues her, and she tries to get him to follow her over the wall and escape. He refuses, and lets her go.
The next scene shows Mika and Maslow meeting in Mika's car at night. Maslow reveals that internal affairs, homeland security, and the CIA are ransacking his office, and that Mika must escape before she is targeted, but that he must go back and negotiate.
Mika drives to her apartment building, and discovers there has been a black out. She investigates her apartment, and discovers a letter with a red seal. A ninja quickly tries to assassinate her but is stopped by Raizo, who then kills the ninja and informs Mika that they won't stop until she is dead.
Raizo helps Mika escape, and we see a flashback of Keiko escaping through the woods.
Keiko is caught, and publicly executed by Takeshi.
We cut back to Raizo and Mika in Mika's car, and Raizo says that the ninja are following their scent. Raizo then has a flashback to his first job as a teenager.
Raizo was sent to assassinate a Kingpin and take his gold watch, and a fight scene ensues. Raizo kills the Kingpin and takes the gold watch. He meets Ozunu on a rooftop and then told by Ozunu to keep the watch as a symbol of Ozunu's ownership of him. Directly after, Ozunu orders Raizo to kill a girl accused of desertion. Raizo instead attacks Ozunu, leaving a scar on his face. Raizo then fights the ninjas and nearly dies, falling off the rooftop into the river below.
Flash forward to Raizo and Mika pulling into a hotel. In their room, Raizo tells Mika to wash off her scent.
Afterwards, Mika informs Maslow about Raizo, and asks him to meet them near a railway.
There is an ambush. Raizo realizes this before it happens, but can't stop the CIA taking him into custody. The CIA locks up Raizo and keeps him under surveillance.
Mika questions Maslow, who privately admits that he is faking his cooperation with the CIA, and gives Mika a translocator just in case. Mika then talks to Raizo, who tells her that he saved her because she has a special heart. He then informs her that the ninja are coming.
Soon after, the power goes out, and the ninjas assault the facility where Raizo is being kept.
After a flood of action scenes, Raizo and Mika escape, driving to another hotel, where Raizo rests, dying.
In the night, the ninja abduct Raizo just before the CIA can show up and protect him.
The ninja take him to the orphanage where he was trained, and prepare to execute him. However, it turns out Mika gave Raizo the translocator, which activates, causing Maslow and the CIA show up just in time to save Raizo, and set him loose. Raizo then kills hundreds of ninjas with the help of the CIA, eventually getting to Takeshi and killing him.
Afterwards, the fight between Ozunu and Raizo commences, and Ozunu kills Mika by stabbing her through the heart after she saves Raizo's life, which causes Raizo to go into a rage and kill Ozunu.
After that, Raizo and Maslow inspect Mika, and discover her heart is on the other side of her chest, and that she will live.
Next, we see Raizo at the mostly burnt down orphanage gardening. He gets a flashback of Keiko asking him to follow her over the wall to escape. He climbs that same wall and stands on top, and we close on him looking at the sunrise between the mountains and smiling.