Brothers Samuel, Jeffrey, and Michael Douglas spend the summer at the cabin of their Japanese grandfather, Mori Tanaka, who has trained them in ninja martial arts. To prove their mettle, the Douglas boys ambush their grandfather’s car as he returns home, but he outwits them and jumps into a tree. One day, Grandpa gives each boy a ninja mask and assigns ninja names, just as his father once did for him. Samuel becomes “Rocky,” Jeffrey “Colt,” and Michael “Tum Tum.” The boys ask if their father, Federal Bureau of Investigation (FBI) agent Sam Douglas, will be home when they return the next day, and Grandpa explains that his son-in-law is a busy man in a “troublesome job.” Meanwhile, Sam Douglas and other FBI agents are working undercover, buying munitions from illegal arms dealer Hugo Snyder. When they try to arrest him, Snyder’s team of ninjas intervenes, enabling him to escape. Returning to his base, Snyder tells his minion, Brown, that he needs to enlist Mori Tanaka, a former business partner, to train new and better ninjas. At Mori’s cabin, Jeffrey “Colt” Douglas looks at a photograph of his Japanese grandfather and blonde grandmother, and sees the hand of a third person in the picture. He asks his grandfather who it belongs to, but Mori Tanaka is busy talking on the telephone to his daughter, Jessica Douglas. At dinner, Grandpa quizzes the boys on ninja codes and they repeat what they have learned: A ninja uses whatever is around him to trick his enemies; he is honest and good; his mind, body, and spirit are joined as one; he has discipline and self-control; he loves nature; he never fights a battle he cannot win; he never uses his power on those weaker than himself. And he is never overconfident. A limousine arrives and several ninjas surround Mori Tanaka as Hugo Snyder approaches. When Grandpa and the three boys defeat the ninjas, Snyder offers Mori a “fortune” to teach his fighters. However, he warns Mori that the life and honor of his daughter, Jessica Douglas, may be in danger if her husband, Sam, does not cease his investigation. Out of earshot, Rocky, Colt, and Tum Tum watch as the two adults discuss their father, and hug Grandpa after Snyder leaves. Mori teaches the boys a special technique that can be used only in defense of their lives. He explains there are secret places on the body where a blow can stop the enemy in his tracks and make him forget what happened. The boys practice on a dummy whose eyes light up whenever a fist or foot hits the pressure points. Mori drives the boys home to their parents’ suburban neighborhood, and Rocky’s girl friend, Emily, is there to greet them. Rocky, Colt, and Tum Tum are anxious to tell their father about their new ninja identities, but Sam Douglas is distracted by his job and has to leave with his partner, Agent Kurl. Emily tries to rekindle her relationship with Rocky, but he is shy and awkward. Meanwhile, Hugo Snyder plots to hold the children hostage until he has completed his mission, shipping missiles to Colonel Ferq. Since the FBI has his operation under constant surveillance, he needs free-lance kidnappers. Brown offers his sister’s son, Fester, who has done messenger work for Snyder’s operation in the past. When Brown contacts Fester, the young man is robbing a convenience store with his “surfer-dude” cronies, Marcus and Hammer. Fester and his friends drive to the Douglas home, but are frightened away when they see several federal agents. The next morning, the would-be kidnappers try to snatch the brothers as they ride their bicycles to school, but Fester bumps his van into a police car. Meanwhile, two local bullies steal Emily’s bicycle. At the school playground, Rocky and Colt challenge the thieves to a basketball game to win back the bike, and defeat them handily with ninja teamwork. When Fester telephones Brown to report that he still has not nabbed the boys, Hugo Snyder orders him to complete his mission before midnight. Later, Mori Tanaka follows Hugo Snyder and his ninjas to a ship at the harbor and takes photographs. That evening, a babysitter arrives at the Douglas house and Jessica Douglas goes to dinner with her husband. Colt finds a photograph in his father’s file folder that matches the image of his grandparents at Grandpa’s cabin, but the third person is fully visible. Colt recognizes him as the man who came to Grandpa’s cabin, Hugo Snyder. The brothers cannot believe their grandfather is in business with a criminal, but fear that if they tell their father, he will no longer let them visit Grandpa. Later, Fester, Hammer, and Marcus rob a pizza man, deliver the food to the Douglas house, and lock the babysitter in the closet. Rocky, Colt, and Tum Tum fend them off with booby traps, oil, jellybeans, hot sauce, liquid laxative, and other household items, in addition to a few ninja kicks. Fester lures next-door neighbor Emily to the house and grabs her, but the laxative sends two of the would-be kidnappers running for the bathroom, and the ninja brothers knock the third unconscious. However, Rushmore, Snyder's large Asian henchman, arrives with a band of ninjas and takes the boys prisoner. When Sam and Jessica arrive home, Emily gives them a note from the kidnappers, which reads: “Lay off Snyder.” At that moment, Grandpa Mori arrives in ninja gear, saying the bad guys have a ship in the harbor. Sam already knows, as his agents followed Mori during his investigation of Snyder. Rocky, Colt, and Tum Tum are taken to a cargo ship, where a hundred ninjas are training. Brown reveals that their grandfather was Snyder’s ninja teacher. Outside the ship, Mori disarms sentries and climbs aboard on mooring ropes. The brothers lure a guard into their room, knock him unconscious, and run through the corridors, fighting Snyder’s ninjas. Grandpa joins the battle, and Brown renders himself unconscious by running into a pipe. The boys meet their match when the huge Asian henchman, Rushmore, challenges them. Grandpa appears on a catwalk above and tells them to remember the dummy training. The boys kick Rushmore in the secret places and he becomes disoriented. As ninjas attack, Grandpa dives into the action and challenges Hugo Snyder to a personal battle. Tum Tum gives his grandfather jellybeans for luck. Mori Tanaka and Hugo Snyder fight to the death with swords. Snyder blinds Mori with a pepper bomb, but the old Japanese ninja jams jellybeans in Snyder’s mouth and knocks him down. As Snyder grabs a gun, FBI agents, led by Sam Douglas, rush in for an arrest. Afterward, Sam assures his sons that they can still spend their summers with Grandpa. The Douglas family, including Grandpa, goes out for pizza.