Arc 3The Red-Eyed Shinobi
Shinji Uchiha subdued the Nine-Tails, confronted Obito, and made plans involving Mei Terumi and Root. The arc left Shinji leading a mission outside Konoha as Jiraiya considered approaching him as a disciple.
- Shinji Uchiha fought Naruto’s Nine-Tails transformation inside the Four Red Yang Formation, drew the beast into the Heavenly Pillar Time realm, and subdued it.
- Shinji confronted Obito at Kage Rock and later ambushed him in the Land of Rain, forcing Obito to seek Akatsuki’s power.
- Shinji offered Mei Terumi help to kill Karatachi Yagura in exchange for Kirigakure’s seven Ninja Blades, while Tsunade refused Hiruzen’s request to become Hokage.
- Shinji visited Gekko Hayate in the hospital and encouraged Uzuki Yugao to join the Konoha Military Police Force.
- Shinji recruited Kakashi, Anko, and Yugao for a mission, while Itachi sent him a warning about Orochimaru and Shisui sent him a note about Root.
- Root ninja asked Shinji to lead them, and he removed their seals and helped sixteen of them leave Konoha to form an independent organization.
- Jiraiya heard the Great Toad Sage’s incomplete prophecy about a gentle boy with red eyes, then asked Tsunade whether Shinji would accept him as a disciple.