Ninja Assassin follows Raizo (Rain), the world's deadliest assassin. Taken from the streets as a child, he was transformed into a trained killer by the secretive Ozunu Clan. Raizo breaks free from them and vanishes after he witnesses the merciless execution of his friend. Now he waits, preparing to exact his revenge.
Meanwhile, in Berlin, Europol agent Mika Coretti (Naomie Harris) has stumbled upon a money trail linking several political murders to an underground network of assassins from the Far East. Her investigation makes her a target, and the Ozunu Clan sends a team of killers, led by the lethal Takeshi (Rick Yune), to silence her forever.
Raizo saves Mika from her attackers. Now, entangled in a deadly game of cat and mouse through the streets of Europe, Raizo and Mika must trust one another if they hope to survive and finally bring down the elusive Ozunu Clan.