A young boy joins a band of ninja during a peasant uprising, all depicted through an experimental form of filming pages from the original manga set to sound.

The son of an assassinated feudal lord, in the Muromachi period, attempts to avenge his father's death and meets Kagemaru, a renegade ninja helping peasants and farmers rebel against Oda Nobunaga ...

But the calm of Solstice Canyon is shattered by a meticulously planned stealth attack on the Takeo home by a masked band of ninja assassins.

Also with this force is Jubei and his band of ninja commandos. And so an epic battle rages between the Tokugawa forces and the Christian rebels but something sinister force awaits in the background.

And they're doing all that while trying to defeat Master Shredder, an old enemy of Splinter who is training a peculiar band of ninjas while hiding in New York City. When they are in the surface ...