Naruto comes face to face with Nagato and Konan. Naruto, wanting to confront the problem of their hate-filled ninja world, asks to hear Nagato’s side of the story before coming up with an answer. Curious to hear Naruto's answer, Nagato then tells Naruto about how he met Yahiko and Konan, and how he later came to meet the Sannin. Nagato's story starts off when he and his parents hear two ninja in their home who are looking around for food, Nagato and his parents try to get away from them but then get caught after Nagato bumps into a vase which falls and breaks. After they are caught, Nagato's father tries to hold off one of the ninja in order to buy some time for Nagato and his mother to escape.
Then the other ninja approaches Nagato's mother and she tells Nagato to run. After the mother is killed, Nagato's father tells Nagato to run. Then Nagato's father is killed and the ninja find out that the people they just killed were not their enemies. Then Nagato sees the village symbol of Konohagakure on the ninja's metal plate. After witnessing his parents' death Nagato activates his Rinnegan and kills the two Konoha ninja. After he attacked the ninja, he passed out then later woke up to find both shinobi and his parents dead on the floor.
Nagato then leaves his home to find food and along the way finds a dog named Chibi who encourages Nagato to keep moving and later meets up with Konan who gives him food and Yahiko. Yahiko tells Nagato that it is okay to steal food because they are living in hard times, so they have to fend for themselves, so they steal from market stands. The three then search out on a mission to find the three Sannin after witnessing their fight with Hanzō on the battlefield after running into explosive traps where Chibi is then killed. Finding the three Sannin was not an easy journey, because in order to do so, they had to go deeper and deeper into the battle site. When they come to one area of the battle site, they run into another explosion and they are blown into a river even after Nagato tries to stop it with his Rinnegan. They are later washed up into a cave. Konan wakes up Yahiko, and Nagato informs him that they have found the three ninja.