Yahiko, Konan, and Nagato from when they were kids
Konan, Nagato, and Yahiko are Jiraiya’s students from the Amegakure (Hidden Village of Rain). Jiraiya voluntarily took them as students and looked after them even though he was still at enemy’s territory. Jiraiya was also the one who taught Konan, Nagato, and Yahiko how to mold chakra and how to use ninjutsu’s. Jiraiya then left them after he was confident they were capable enough to take care of themselves. The three then became ones of Hidden Village of Rain’s most powerful ninjas. They formed an organization to work toward peace. Things took a horrible turn and Yahiko died in a surprise ambush led by Hanzou (Amegakure) and Danzou (Konohagakure).
The Meaning Behind Akatsuki Symbol
After that, Nagato took over as the leader of the organization. The organization that years after became what we know now as ‘Akatsuki’. In Naruto manga chapter 510, when Uchiha Madara confronted Konan to take Nagato’s Rinnegan, Konan claimed that Yahiko was the very person who founded Akatsuki before Uchiha Madara took over the organization. The red cloud symbol of Akatsuki was initially the symbol of war’s rain of blood that fell on the Hidden Village of Rain. This was the reason why Konan still wore the Akatsuki uniform even after quitting Akatsuki.
Nagato led Akatsuki as the “front leader” while being ordered around by the “real” leader, which is Uchiha Madara, until he met Naruto. Nagato fought Naruto when he came to Konoha in search of Kyubi/Naruto. Naruto defeated the Six Pains and went to see Nagato face to face. His determination convinced Nagato to switch sides and he ended up dying after resurrecting all the people in Konoha that he killed, betraying Uchiha Madara.
In Naruto manga chapter 510, it was also revealed that Nagato was actually a descendant of Uzumaki clan, the same clan as Naruto’s mother. Before his death, Nagato used his Sage of Six Paths power to turn his red hair to white, giving signal that he’s “leaving”, initially a mean that the three of them and Jiraiya used in the past to give one another signal if they’re home or not, meant to distinguish their comrade from disguised enemy or to tell if their comrade has been kidnapped by enemy.
Konan died in the hand of Uchiha Madara in Naruto manga chapter 510. After turning her back on Akatsuki, Uchiha Madara came after her to kill her for betraying him and for leaving Akatsuki. Konan confronted Madara with her plan to kill him, which she did not succeed, though she managed to inflict injury on him. Her ultimate paper clone forbidden jutsu failed against Madara’s izanagi jutsu. Madara took the Rinnegan eye from Nagato after killing Konan.