The story surrounds a 13-year-old Kakashi Hatake who embarked on a dangerous mission with his team, which included another boy named Obito Uchiha, from the same clan as Sasuke Uchiha, a medical-nin kunoichi named Rin, and their teacher, Minato Namikaze.

This arc answered many questions about Kakashi's past. It was learned how Kakashi received his Sharingan, the identity of Obito, and when Kakashi became a Jonin. It also gave a glimpse of what Minato was like when he was still alive.