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.

It's the 17th century, and Native American Squanto roams free in the New World until he's captured by visiting sailors who take him back to England. Monk Brother Daniel teaches him social customs, but other Englishmen aren't as kind. Squanto becomes the unwilling star of performances that highlight his fighting skills, but he eventually engineers a return trip to America. He finds that his home has changed forever, and he must chart a new path for his people.