In the village, Guy is pestering Kakashi to compete in another challenge while Tobi sneaks into the village. He summons the Nine-Tails right inside the village and allows it to wreak havoc. Sensing the tailed beast, the Third Hokage prepares to go into battle; Chōza, Shikaku, and Inoichi prepare to defend their village as well. Minato teleports to the village to defend it, and the fox fires a Tailed Beast Ball towards him. Using his Flying Thunder God: Guiding Thunder technique, Minato warps the Tailed Beast Ball to a safe distance away. He is immediately engaged in combat with Tobi, who attempts to use Kamui to send Minato elsewhere; however, Minato teleports to a safe location just in time. Tobi follows Minato there and praises his Flying Thunder God techniques, while Minato, realising that the masked man in front of him possesses a Sharingan strong enough to control the Nine-Tails while infiltrating the village undetected, suspects Tobi to be none other than Madara Uchiha, albeit immediately dismissing the thought since Madara was thought to be long dead.
Minato begins his assault on Tobi, who produces chains from his wrists, but is unable to land a successful hit due to Tobi's intangibility. Noting that Tobi would have to manifest physically in order to strike back, Minato throws one of his Flying Thunder God Kunai at Tobi's head while rushing towards him at the same time. Right as the kunai goes through Tobi's head, he materialises in order to grab a hold of Minato; however, Minato forms his Rasengan and teleports to the kunai's location behind Tobi, and manages to land a successful hit, marking him as well. Tobi is wounded from the attack, as his left arm begins to peel and fall off. Having branded Tobi, Minato is able to teleport to him right away and places a Contract Seal on him, wresting the Nine-Tails from his control.
In the manga, Minato glared at the Nine-Tails and Tobi, the masked man, after telling Kushina that Naruto was safe. In this episode, it happened when Kushina told him that Tobi's objective was to destroy Konoha.
Minato notices Tobi's Sharingan as the latter uses Kamui; however, it is a normal Sharingan eye and not the Mangekyō Sharingan. This goof also persists in the previous episodes up until the point where Tobi's true identity is revealed, at which point his Mangekyō Sharingan is shown whenever he uses Kamui.