Having become genin, Jiraiya, Tsunade, and Orochimaru are assigned to the future Third Hokage's platoon. Watching Sarutobi's space/time ninjutsu, Jiraiya becomes absorbed into learning it. One day, Jiraiya loses his way and stumbles upon Myouboku Mountain. There he meets the Great Toad Sage who predicted his arrival. See the origins of the Toad Sage Jiraiya!

Jiraiya realizes that the six Pains are all ninja he's met before. Putting various pieces of information together, Jiraiya figures out Pain's true identity, but Pain doesn't intend to allow Jiraiya to leave with that information alive. Elsewhere, the fated meeting between Itachi and Sasuke arrives, and Sasuke foresees Itachi's death.

After failing to bring back Sasuke, the Leaf ninja start heading back to the Hidden Leaf Village. Tsunade, however, sends Katsuyu to inform them that the barrier of Mount Katsunagi of the Tsuchigumo Clan, which holds a powerful forbidden jutsu, is broken. While Kakashi and Team 8 head back to the Leaf Village, Team 7, lead by Yamato, must check out what events are taking place.

After the peformance of the forbidden jutsu, Hotaru is horrified to see the damage the jutsu has done. Shiranami then notices the forbidden jutsu overflowing with chakra and the fact that it would destroy itself along with Hotaru. While Naruto chases the fleeing Shiranami, Utakata tries to save Hotaru using the hidden power within him. Can Utakata save Hotaru?

Shikamaru tries to decipher the dying message Jiraiya left before his death but cannot figure out what it says. Shikamaru asks for Naruto's help, thinking he might know the code. Can the saddened Naruto decipher Jiraiya's dying message?

Naruto thinks back to the time when he encountered the soul of a man named Kisuke. Kisuke didn't recall anything about who he was, but a visit to the Leaf Village's hospital revealed something startling. Meanwhile, higher-ups of the Fire Country met to decide on a new security system for the Leaf Village put together by a ninja named Sabiru. Who exactly were Kisuke and Sabiru, and what connection did the two have?