no one kills nagato
he dies cz he uses 2 much chakra or something when he uses his ninjutsu that brings the dead back to life.
ps: there is no human, animal or a plant that can bring anything or anyone to life!
this is a stupid ending.
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Nagato in naruto is pein.Nagato became pein in the 2nd great ninja war.Jiraiya took him,yahiko,and konan as his students.Now nagato is the akatsuki member known as pein.Pein is not the lleader of the akatsuki though.
Yahiko killed himself of the kunai of Nagato, when Hanzo the Salamander ordered Nagato to kill Yahiko or he would kill Konan who he had captured because he believed they were getting to powerful and will threaten his ruling. Nagato went on to use Yahiko's body for the Deva Path of his Six Paths of Pain, whom Naruto was able to defeat when he returned to the Leaf-Village when it was under-attack by Nagato and his Pains. Later Konan takes his body along with Nagatos back to the Village Hidden in Rain where she became the new leader.
Shizune is alive because after Naruto convinced Nagato to stop attacking or whatever, Nagato used one of the last powers of the Sage of Six Paths to bring everyone back!
Hatake Kakashi does die fighting pain. But after Naruto defeats all of the bodies of Nagato (who is the actual person controlling the six other bodies) and Naruto goes to talk to Nagato. After they talk and Naruto hears Konan, Nagato, and Yahiko's story, he gives Nagato his answer to finding peace. Nagato is changed and uses his last bit of energy to bring back to life everyone that was killed in the attack on Konoha. That includes Kakashi! So Kakashi is brought back to life. it is in naruto shipudden episode 159!!!
He didn't follow him, but rather Madara/Tobi says he controlled Nagato to see the scroll that the six paths sage created (Read chapter 467) and says that the sharingan, mangekyo sharingan and rinnegan are needed to fully understand the whole tablet.