Fourth Hokage

For his performance during the War, Minato was chosen over Orochimaru to become Fourth Hokage. He taught the Flying Thunder God Technique to the Hokage Guard Platoon to better aid them in their duties of serving the Hokage at any given time. In the anime, he also tried to help Kakashi, now an Anbu, emerge from the darkness he'd fallen into after Obito and Rin's deaths. During the gradual transfer of responsibilities from the Third Hokage to him, the Third advised Minato to restore Kakashi's value of life by tasking him with protecting Kushina during her pregnancy.

As a jinchūriki, the strain of childbirth would weaken the seal keeping the Nine-Tails sealed into Kushina. For that reason special precautions had to be taken: the child would secretly be delivered in a remote location outside of the village, with barriers around the area and several Anbu guards as extra protection. Minato was not greatly worried about the birth, and in fact gave Kakashi the day off in gratitude for his good work. He and Kushina had already decided on a name for their son, "Naruto", after the main character of Jiraiya's first book, hoping that their Naruto would be just as determined as the character (and thus its author). Jiraiya tried to convince them to make a different choice since that would make him Naruto's godfather, but they insisted that this was a good thing.

Naruto was born on the night of October 10. Only moments after the birth Minato began making preparations to restore the Nine-Tails' weakened seal, but he was interrupted by the arrival of a masked man, otherwise known as Tobi. Tobi killed the Anbu guards and midwives and took the newborn Naruto hostage, threatening to kill him if Minato didn't back away from Kushina. Minato immediately took Naruto back from him, yet discovered explosive tags had been planted on Naruto. Minato was forced to teleport away to keep Naruto from harm, allowing Tobi to escape with Kushina. He found a safe place for Naruto and teleported to Kushina in time to save her from being killed by the Nine-Tails, extracted from her body by Tobi. He reunited mother and son before heading out to protect the village.

Minato returned to the village in the early stages of the Nine-Tails' attack on Konoha, arriving in time to teleport away a Tailed Beast Ball before it destroyed the Hokage Rock. He attempted to reach the Third Hokage so that he could inform him of what happened, but was interrupted by Tobi, who tried to warp him away. Minato reacted in time to escape, but Tobi pursued him. Because Tobi was controlling the Nine-Tails' actions, defeating him was of prime importance in order to save Konoha. Minato initially struggled to successfully strike him but, after several failed attacks, he finally hit him with a Rasengan and branded him with a Flying Thunder God seal, allowing him to teleport to Tobi whenever he wanted. He then used a Contract Seal on Tobi to release the Nine-Tails from his control, forcing him to flee.

No longer being controlled, the Nine-Tails began retreating from the village, though it continued to attack the Konoha ninja that pursued it. As it prepared another Tailed Beast Ball, Minato once again arrived in time to stop it, this time by dropping Gamabunta on top of it. He had Gamabunta keep it restrained while he gathered the chakra needed to transport the Nine-Tails to Naruto and Kushina's location, the farthest from the village he could get. Kushina restrained it and erected a barrier so that it couldn't escape while they decided what to do. Already dying from the Nine-Tails' removal, Kushina offered to have it sealed back into her so it would die with her. Minato rejected this, believing the Nine-Tails' power would be needed in the future if and when Tobi struck again. Remembering Jiraiya's words about the "Child of the Prophecy", Minato decided to believe that Naruto was that child and that he would someday save the world. To prepare Naruto for this, Minato would make Naruto the Nine-Tails' new jinchūriki so he could make use of its strength

Because the Nine-Tails' chakra was too immense to seal into an infant, Minato used the Dead Demon Consuming Seal to cut its chakra in half, sealing the Yin half in himself. Realising what they were planning, the Nine-Tails tried to kill Naruto, but Minato and Kushina used themselves as shields. With his last ounce of strength, Minato summoned Gerotora, gave him the key to the seal he would use on Naruto, and sent him to Jiraiya. Meanwhile, Kushina told Naruto how much his parents loved him, which Minato seconded. He sealed the Nine-Tails' Yang half into Naruto, weaving Kushina's chakra into the seal so that she could someday assist Naruto with learning to control the Nine-Tails and its chakra.[27] He mingled in some of his own chakra, too, programming it to activate if ever the seal was about to break so that he could restore it.[28] Seeing the Third Hokage nearby, Minato communicated to him a final request for the villagers of Konoha: to think of Naruto as a hero and not the container of the monster that caused so much death and destruction.[29] With that, his soul was consumed by the Shinigami, ending Minato's life.