Nagato confirms Yahiko’s death
Yahiko was one of the three abandoned ninjas of war together with Nagato and Konan. He was a brave boy back then with same principle of gaining peace in the ninja world. He served as leader for his two fellows and achieved power to lead a gang. Together with his gang, their mission is to bring peace without use of brutal force.
Being the leader did not bring peace at all, instead led more Pain. Hanzo betrayed them, forcing Nagato to choose which one to save between Konan and Yahiko. It was a losing situation and nothing else Nagato could do but to make the right judgement. So, with Yahiko’s willing, Nagato killed him to save Konan. “I just want to protect them no matter how much pain it causes”, said Nagato.
Having learned the story, we think that Nagato revived Yahiko with his Rinnegan, controlling him all along to have him on their side as long as possible. And maybe it’s one of the reasons behind his current sickly condition.