A young Samurai, Hamato Koji, is roaming the woods in search of the shrine of Shibano Sama that his sensei instructed him to find, in order to start his own ninja clan. He however encounters Shredder and Oroku Sancho's men, who Shredder orders to attack Koji.
The Turtles and Splinter go back in time to help protect Hamato Koji from the Shredder. They arrive just in time to help Koji defend himself against Shredder and Oroko Sancho's men.
They assist Koji in his quest and discover the location of the Shibano Sama shrine. Inside they discover the Nomi Blade, a legendary sword that can cut through anything, and the Tsunami Box, containing a power greater than any tidal wave. Koji attempts to open the box, but is warned by Splinter that it should only be opened when it's power is needed.
No sooner does Kohji have these magical relics in his possession does he begin to dream about the power of his clan, then they find themselves surrounded by Shredder and his samurais.
During their battle the Tsunami Box is accidentally opened, releasing a giant fire-breathing dragon which, after scaring everyone, heads in the direction of nearby villages.