According to Madara, Nagato is a descendant of the Uzumaki clan. During the Second Shinobi World War , Nagato lived with his parents in a village near Amegakure. One day two Konoha shinobi broke into their home looking for food,
unaware that the place was still inhabited.
Nagato's parents, believing they were going to
be killed, attacked the two so that Nagato could
escape. Having mistaken them to be enemy ninja,
the Konoha ninja killed his parents. In his grief, Nagato awakened his Rinnegan and killed the assailants. He would come to consider this incident the first great pain of his life.
His family gone, Nagato wandered the country,
going from house to house asking for food. In
time he met a dog named Chibi and, later, Konan and Yahiko, who began travelling with him in his search for food. One day, Chibi was killed in the
crossfire from Hanzō's fight with the soon-to-be Sannin. Nagato mourned his death and promised himself that he would change the world. When
the war ended, the three orphans ran into the
Sannin. Rather than return to Konoha with his
team-mates, Jiraiya decided to teach the three how to look after themselves.
Soon after Jiraiya
began living with
Nagato and Yahiko
were attacked by
an Iwagakure ninja. Nagato
Rinnegan to defend Yahiko, killing the ninja.
When Jiraiya found out about this, he decided to train them in ninjutsu. Nagato was very emotional about killing the ninja, and asked
Jiraiya for help so he could protect Konan and
Yahiko. Jiraiya's response was for Nagato to
grow up and to use his eyes to find the peace
that they both desired for the world. Three years
later the orphans had become competent ninja, so Jiraiya returned to Konoha.
Over the years, news of the three's exploits
would reach Jiraiya which often consisted of the
death of someone who opposed them;
eventually he received word that they had all died. In truth, Nagato, Konan, and Yahiko began a quest to find peace. They became full-
fledged Amegakure ninja and gathered followers
who shared their philosophies of an end to war.
Hanzō, the leader of Amegakure, viewed the group as a threat to his rule and schemed with
Konoha's Root to eliminate them. Claiming to want to discuss peace, Hanzō lured Nagato, Yahiko, and Konan to an ambush. There he forced
Nagato to choose between killing Yahiko or
Konan. Not wanting to force Nagato to make the
choice, Yahiko impaled himself with a kunai that
was placed in Nagato's hand. With Yahiko's
dying breath, he told Nagato to survive, because he believed in Jiraiya's words that Nagato would
become the world's saviour. This would become
the second great pain of Nagato's life.
Devastated, Nagato retrieved Konan and Yahiko's
body and launched an attack against Hanzō's men. With the Summoning: Demonic Statue of the Outer Path he was able to kill all but Hanzō. However, the technique left Nagato emaciated,
with numerous chakra rods embedded in his
back. He severed his loyalties with Amegakure
by scratching through the symbol of his
Amegakure forehead protector, resolving to
teach the village and the world his pain. Yahiko's body would later be incorporated into the Six Paths of Pain as the Deva Path.
Upon adopting the alias "Pain", Nagato led the
rebelling forces in the Amegakure civil war, and
took control of the village by assassinating Hanzō while using his Six Paths of Pain. He then
solidified his leadership by systematically killing
anyone who had ties to the former leader. At
some point he assisted Madara Uchiha in the creation of Akatsuki , using Amegakure as his base of operations.
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