Each year, three brothers Samuel, Jeffrey and Michael Douglas visits their Japanese grandfather, Mori Shintaro whom the boys affectionately refer to as Grandpa, for the summer. Mori is a highly skilled in the fields of Martial arts and Ninjutsu, and for years he has trained the boys in his techniques. After an organized crime ring proves to be too much for the FBI, it's time for the 3 brother NINJAS! To use their martial arts skills, they team up to battle the crime ring and outwit some very persistent kidnappers!

During a championship baseball match, the three brothers hear that their grandfather in Japan is in trouble, and head out to help him, conceding the match. When they arrive in Japan, they must use all their powers to defend him against his ancient enemy, who has returned to exact revenge.

Rocky, Colt and TumTum must battle an evil wealthy toxic waste dumper in order to save a local Indian tribe and their friend Joe. The 3 Ninjas must help find Joe's father and find a secret disk that contains evidence that could stop the toxic landfill that is destroying the Indian community. However the town is owned by the rich man and he controls the police and even the mayor. They must fight a motorcycle gang and renegade cowboys in this non-stop ninja adventure.

Three young boys, Rocky, Colt and Tum Tum together with their neighbor girl, computer whiz Amanda are visiting Mega Mountain amusement park when it is invaded by an army of ninjas led by evil Medusa, who wants to take over the park and hold the owners for ransom. Kids and retired TV star Dave Dragon, who made his farewell appearance at the park at the time the ninjas appeared, have to break Medusa's vicious plans.