The planet Prysmos suffers a collapse of its high-tech civilization due to a solar re-alignment. Two groups rise to dominance from the devastation to wage war upon each other. One is controlled by honest and law-abiding people and the other by criminals and villains. Following an open challenge thrown down by the great wizard Merklynn, fourteen surviving knights are granted powers of transformation and magical energy. The groups are now divided between the good Spectral Knights and the evil Darkling Lords. The battle for supremacy begins...

纽约市下水道，四只小海龟和一只小老鼠由于接触了含有放射性物质的凝胶而变异为巨大的人化生物。暴躁冲动却富有激情的拉斐尔（乔什·帕斯 Josh Pais饰），幽默风趣的的米开朗基罗（迈克林·西提 Michelan Sisti饰），个性沉稳的多纳泰罗（雷夫·提勒顿 Leif Tilden饰）以及他们的领导者达芬奇（大卫·福尔曼 David Forman饰），这四只功夫高强的忍者龟便肩负起为纽约市除暴安良的神圣使命。他们神勇无比、所向匹敌，在多次行侠仗义后，与城市里的一个神秘组织结怨。神秘组织展开一次突袭，由于寡不敌众，忍者神龟受了重伤，同时，他们的老师也被这个神秘组织抓去。

忍者神龟们发现了变种物质的泄漏之处,但史莱德同时也发现这一秘密,于是他们之间又展开了新一轮的战斗,而忍者神龟们也在战斗中得到了提高!

An archaeological expedition finds the mummified bodies of Genghis Khan and his army somewhere in Mongolia. Unaware that the location is cursed, the explorers wake up the former ruler of the Mongolian empire. He warns the intruders that a large calamity will befall the world in one thousand days. The only ones who can prevent this from happening are three persons who bear wolf-shaped arrow scars. They must join forces and kill the "three emperors" so that the Khan's soul can once again sleep for a thousand years.