In 1979, Dr. Saxon, “The Cobra,” orders a group of thugs to rob the box-office of a Los Angeles, California, sports stadium, during a kickboxing competition. The crooks get the money, but Sean Davidson, a young teenager whose father is competing in the tournament, runs into them outside the locker rooms. Sean’s father and his trainer, Izumo, appear. While Izumo pulls the boy to safety, Andreas, the Cobra’s second in command, shoots and kills the father before escaping. For ten years, Izumo trains Sean in Ninjutsu, the secret fighting techniques of the Ninja, while the Cobra uses the stolen money to corrupt the government of Triana, a small Caribbean island. He also builds a large pharmaceutical company. After concocting the perfect virus, he offers to sell it to the highest bidding bidding terrorist organization. However, Andreas, who is now the head of the Trianan military, voices his skepticism and the Cobra is forced to arrange a demonstration on the lethal powers of the virus against a “superhuman.” Chan Lee, a woman who leads an army of Ninjas working for the Cobra, believes the doctor is trying to produce a cure for a serious disease. She suggests they hold a martial arts competition to find a superhuman. A few weeks later, Sean Davidson runs into Curtis Jackson, a friend of his father’s. As they talk about going to the Triana competition, Dexter, a redheaded American who is also competing, introduces himself. When they arrive in Triana, Chan Lee spots Sean and informs the Cobra she has found the perfect candidate for his demonstration. The next day, Sean wins his first match, and celebrates at an outdoor café with Dexter and Curtis when he sees Izumo being forced into a hearse. Sean leaps into a taxi and follows the hearse to a hotel, where he finds Izumo meditating. Before Sean can talk to his master, two Ninjas attack him while others appear and take Izumo away. Sean fights a running battle as he chases the kidnappers over rooftops, down alleys and onto a dockyard. He defeats four shadow warriors only to watch the Ninjas board a speedboat and escape with Izumo. Sean finds Curtis and Dexter, confesses he is a Ninja and asks for their help getting Izumo back. Meanwhile, Chan Lee reports to the Cobra that Sean fell for the Izumo impersonator, but was too strong for her men to capture. Dr. Holger, the Cobra’s chief scientist, wants to kidnap Sean, but the villain decides to give the Ninjas one more chance to prove themselves. Later, Sean, Dexter and Curtis are searching for Izumo when a group of Ninjas attack them with nun chucks, swords, quarterstaffs, fists and pikes. They chase the three surviving attackers back to the Cobra’s pharmaceutical company. Curtis warns their victory was too easy and they are being set up. Sean goes to the Minister of Interior for help, but the Minister’s female secretary refuses to believe that the biggest employer on the island is involved in a kidnapping. Curtis also gets turned down by the police. Later, Andreas and a roomful of terrorists listen to the Cobra’s plea to give him three more days to arrange his demonstration. When Andreas protests, the Cobra takes him aside and reminds the general that he can destroy Andreas as easily as he made him if he does not behave. The Cobra then meets with Chan Lee and claims that without Sean, funding will stop for his "miracle cure." Meanwhile, Sean and Dexter steal two ultra-light airplanes to fly into the pharmaceutical company, but halfway there, Dexter’s plane malfunctions. As the plane is too fragile to touch down on the rough terrain, Dexter is forced to land on the flatbed of a moving truck Curtis is driving. Sean radios for Dexter and Curtis to wait for him outside as he lands on the laboratory rooftop. Through a skylight, he sees Chan Lee fighting off ten sword wielding Ninjas in a training exercise. Entering the building, Sean is attacked and a taser renders him unconsciousness. When Sean regains consciousness, the Cobra explains his plans to inject him with a disease. Sean is placed in a cell where he is visited by Chan Lee, who explains her doubts about the Cobra and offers to help Sean escape. The next morning, the Minister of Interior’s secretary visits the Cobra and demands a bribe to keep silent about his experiments. When she leaves, Dr. Holger is ordered to kill her. As the secretary drives away from the laboratory, Holger follows, then rams her car, trying to make her crash. However, she forces Holger into a pile of gas barrels that explode on impact. Holger crawls out of his automobile seconds before it is engulfed in flames. The secretary pulls over and removes a mask revealing she is really Chan Lee. She finds Curtis and Dexter, confesses her Ninjas are no longer loyal to her, and asks their help in rescuing Sean. Meanwhile, the Cobra injects Sean with the “disease,” and orders Andreas to dump him into the sea. However, Chan Lee, Curtis and Dexter arrive at the Cobra’s ship and battle their way aboard to find Andreas standing over Sean with a machine gun. Sean comes to and recognizes Andreas as the man who killed his father. He grabs the machine gun and unloads a full clip into the killer. Chan Lee tells Sean they must get the antidote before it is too late, but he refuses to go without freeing Izumo. Chan Lee confesses she imitated Sean’s mentor to lure him into the Cobra’s trap. Later, Chan Lee disguises herself as the Minister’s secretary and enters the lab while the men wait outside. Upon entering a prohibited area, she fights her way to the main laboratory. The Cobra learns of Chan Lee’s duplicity and orders Holger to let loose all the Ninjas. The two men go to the lab and find Chan Lee, still disguised as the secretary, removing the vaccine from a safe. Seeing though her disguise, the Cobra has Holger shoot her to death, then gives Holger the antidote for the virus and orders him to wait in the car. Meanwhile, Sean, Curtis and Dexter use machine guns to shoot their way into the building. As the illness spreads throughout his body, Sean finds it harder to battle the Ninjas. Two archers appear and shoot Dexter before Sean kills them by throwing their arrows back at them. Meanwhile, Curtis takes the medicine from Holger. Holger pulls a pistol and opens fire, however, he misses Curtis, who then snaps his neck. Outside, the Minister of Interior appears with a small army of soldiers who battle with the Cobra’s bodyguards. Inside, Sean discovers Chan Lee’s body and the Cobra emptying his safe, but is overcome by his disease. As the Cobra taunts him, Sean uses the mind powers of Ninjutsu to force the disease from his body. Seeing Sean recover, the Cobra turns out the lights and when they come back on, five red clad Ninjas appear. Sean defeats them, then beats up the Cobra. Curtis arrives with the antidote, but Sean does not need it. As they leave, the Cobra attacks with a knife, but Sean kills him with a kick to the head.