Deep within the Hidden Leaf Village, young ninja Naruto Uzumaki carries sealed inside him the Nine-Tailed Fox Spirit, which once almost destroyed the village. Always an outcast because of his secret, now Naruto battles alongside his teammates Sasuke and Sakura to prove to himself and everyone else that he's the greatest ninja ever. But he's got a long list of challenges to face before he gets there!

It's down and dirty time. Splinter is imprisoned. Leo is dying of poison. Don and Usagi are fighting for their lives and the life of the Daimyo against a horde of assassins.

将施奈德回老家之后，四只原本亲如兄弟的神龟由于没有了敌人，于是不再想以往一样一起战斗，而是各自在喜欢的领域内钻研，以往一起行动的忍者神龟们变成了四个独来独往的“独行侠”！ 这时，纽约市中发生一连窜的怪事。原来实业家马克西米林安•J•威特斯意图征服纽约市，秘密培养了一支远古怪兽组成的军队，加上恶名昭彰的忍者组织Foot Clan，各种黑暗势力又在城市的角落里蠢蠢欲动！ 神龟们又处于备战状态了！他们再次联合起来，准备向黑暗势力出击！