Ninja Assassin follows Raizo, one of the deadliest assassins in the world. Taken from the streets as a child, he was transformed into a trained killer by the Ozunu Clan, a secret society whose very existence is considered a myth. But haunted by the merciless execution of his friend by the Clan, Raizo breaks free from them and vanishes. Now he waits, preparing to exact his revenge.

During the Ming Dynasty, as Japanese pirates wreak havoc along the Chinese coast, laying waste to entire towns, a band of ninjas start appearing and target the Chinese military commander, General Chi. The Master of the Three Arts (who possesses a book illustrating various ninja techniques) is the only one who can combat this new enemy, so he pledges that his students will join Chi's army in their fight to wipe out the killers.

A businessman and his sister-in-law are targeted for assassination by a band of evil ninjas and their vicious leader (Yasuaki Kurata). The ninjas are committing bizarre murders all over the city, and the police can't seem to pick up their trail -- so they call in ninja hunter and Kendo master Mr. Chow (Kuan Tai Chen). To take down the silent killers, Mr. Chow will have to fight against incredible odds in this campy ninja classic.

The heirs to a major corporation are being brutally killed off one by one, and John Lee, the company's chairman, suspects that a mafia takeover is behind it. But, before he can uncover any evidence, he too is savagely murdered. Carol, his daughter and a friend, Brian Roberts, continue the investigation where he left off while police Captain Roberts follow up on a few suspicions of his own. The actions become explosive and deadly when they are attacked by ruthless, ninja assassins who try to prevent them from finding out who the maniacal, cold blooded killer is inside the company.