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Somewhere in an underground lair, Orochimaru's experiment is brought to life by a struck of lightning. However, Orochimaru's plan backfires as the experiment attacks him and begins to destroy the building, forcing him and Kabuto to evacuate. The next day, Itachi and Kisame find the broken experiment in the destroyed building and brings it back to their leader, Pain. In a secret Akatsuki hideout, Pain uses the King of Hell to repair it, as well as add new modifications to it. The Akatsuki leader then instructs Itachi to capture the Nine-Tails with the newly repaired experiment, now hooded by a cloak, joining him in his mission. Itachi soon arrives near Konohagakure and orders it to capture Naruto. It begins its search for Naruto, attacking several villagers and defeats Team Guy in the process. Naruto himself shows up to stop it so that he can get back to training. Naruto attacks the experiment with his multitude of clones, but it easily repels the assault. Naruto manages to land a hit on its cloak, tearing it apart, and is revealed to be a mechanical replica of himself known as Mecha-Naruto. Mecha-Naruto begins siphoning Naruto's Nine Tails chakra, causing him to lose his strength. Kakashi and Yamato arrive with Kakashi distracting Mecha-Naruto with his Lightning Cutter, giving Yamato the opportunity to save Naruto. The trio manage to escape using a secret tunnel and Mecha-Naruto begins to destroy the village in an effort to find Naruto. In the Hokage's office, Tsunade devises a plan to lure Mecha-Naruto away from the village: Naruto rides away from the village in a palanquin with Yamato while Chōji, Kiba, Neji and Shikamaru act as bearers and Kakashi as backup. The plan is put into action and Mecha-Naruto starts pursuing the palanquin. Shino, not wanting to be left behind like last time, arrives to distract Mecha-Naruto, but is defeated. The group decides to escape into the forest, with Shikamaru switching places with Kakashi so that he can try to defeat Mecha-Naruto. However, Shikamaru is defeated after being smashed into the ground by Mecha-Naruto. Tsunade then orders Shizune to request assistance from Sunagakure.

Shikamaru is overwhelmed by Mecha-Naruto and continues to follow the group while firing missiles in the process. Chōji uses his Human Bullet Tank in an attempt to distract Mecha-Naruto but ultimately fails. Kiba and Akamaru transform into a double-headed wolf and attack using the Fang Passing Fang but is easily countered by the mecha. The palanquin carrying Naruto falls over since there was no one holding it. Neji is next to join the fray, using his Eight Trigrams Palms Revolving Heaven. Mecha-Naruto tries blasting the rotating shield with lasers, but to no effect. After dominating Neji's technique with high speed, Mecha-Naruto breaks through and eliminates him and Yamato. Kakashi uses his Sharingan in a failed attempt to defeat the mecha. Just as Naruto is cornered by his mechanised replica, Gaara arrives in time to save him. As he is about to crush Mecha-Naruto's arm, Deidara appears and taunts the young man, forcing the Kazekage to chase after him. Naruto and Mecha-Naruto are summoned into a snake's stomach by Orochimaru who reprogrammed Mecha-Naruto to obey him. Jiraiya then appears and summons Gamabunta thus freeing them from the snake's stomach. Mecha-Naruto easily overwhelms Naruto who was nearly drained of the Nine-Tails' chakra. Mecha-Naruto changes its programmings – courtesy of Itachi – and returns the Nine-Tails' chakra back to Naruto. As Mecha-Naruto bisects Orochimaru in half to protect Naruto, he activates a switch, causing Mecha-Kurama to appear and causes mayhem at Konohagakure. Mecha-Naruto encases itself onto Naruto and battle Mecha-Kurama but their attacks have no effect whatsoever. Mecha-Naruto ultimately sacrifices itself to destroy Mecha Nine-Tails. While the villagers celebrate Naruto's victory, they are comically drowned by Gaara's Quicksand Waterfall Flow.