The battle for the Sanbi comes to an end as neither the Konoha ninja nor Orochimaru are successful at obtaining it. Tsunade classifies the mission of catching the Sanbi as a failure, for it is too dangerous to accomplish. As Naruto and the others prepare to return home, Yukimaru goes missing. Unbeknownst to everyone, Akatsuki lies in wait, and they have their own plans for the Sanbi.

Over ten years ago, the Five Great Nations’ were in the midst of the Third Great Ninja War. Future Fourth Hokage Minato Namikaze assigns young Kakashi, Obito of the Uchiha clan, and Rin, on a mission to Kannabi Bridge...

While talking with his students, Shino talks about how he and his team got together and became more close as friends and teammates. The story switches to Shino's flashback during the first part of Naruto. They are on a mission assigned by Kurenai in which a Jonin assassin from a neighboring village. Shino gets defeated because of weak taijutsu and descends into depression. He even reveals he was going to abandon the team that helped him because he didn't think he was useful to them. But after his friends get in trouble with the rouge Shino comes back and defeats the rouge.

Taking place in the aftermath of the Kage Summit, Team Kakashi is sent out on a mission by Tsunade to a location known as "The Hole" to investigate an incident where its people were killed.