Shredder uses a time machine to travel back to Ancient Japan in the year 1583. He plans to defeat Hamato Koji, the man who founded the Foot Clan, and Splinter's great ancestor, for if Hamato Koji is defeated, then Master Splinter would never have been born and the Turtles would forever remain ordinary turtles.

In an attempt to finally defeat the Turtles once and for all, Shredder assembles Leatherhead, Tempestra, Scumbug, Chrome Dome, Antrax, The Rat King and Slash to form a team that proves too much for the TMNT.