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!

In the Rain Country, Jiraiya decides to take care of three young orphans for a while. Yahiko, a spunky young boy, wants Jiraiya to train him, Konan, and Nagato to be shinobi, but it's not until he sees a strange phenomenon in Nagato that he decides to do so. What is the secret behind Nagato's Rinnengan eyes? What will become of these three children?

While the members of Team Hebi head towards Itachi's location, Jiraiya infiltrates the Hidden Rain Village in hopes of gathering information on the Akatsuki leader. Jiraiya captures two Rain ninja and interrogates them about Pain, but what he learns shocks even him.

Having suspicions about the Nine-Tails' attack on the Hidden Leaf Village years ago, Jiraiya tells one of his frogs that the time may come when Naruto will need to access the fox's full power. His interrogations finished, Jiraiya sets out in search for Pain, but winds up encountering Konan instead. Is there a connection between Jiraiya, Konan, and the mysterious Pain? Elsewhere, one of Naruto's shadow clones runs into Team Hebi.

Having no other choice against Pain's powerful and strange summonings, Jiraiya undergoes a powerful transformation to go up against Pain with the help of the Toad Sages. Will this Sage Mode be enough for Jiraiya to take on not only the Pain he's been fighting, but two more as well?

Jiraiya is now confronted by two new Pains who both possess different abilities than the one he was fighting. Just who is Pain and how many Pains are there?

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.