As a result of having the Nine Tails sealed inside of him, Naruto is feared and hated by the villagers. He trains all alone in the woods, but one day, a certain man appears and strikes up a conversation with Naruto. Elsewhere, in the Leaf Village, a celebration is held to mark Hinata's third birthday, where she meets Neji for the first time.

Sasuke begins his own investigation into the incidents. He overcomes many dangers on his path to the truth. The Exploding Humans, the Ketsuryugan, the Chinoike Clan, and the Uchiha Clan—just how are they connected? Where does his journey lead? The mystery is about to be solved...