Nagato continues talking to Naruto and describes his second pain, how he and Konan helped Yahiko used what they learned from Jiraiya to create the Akatsuki to bring peace to Hidden Rain Village. But Hanzo deemed Yahiko's group a threat to his regime and allied with Danzo to kidnap Konan. Hanzo orders Nagato to kill Yahiko if he wants her to live and Yahiko sacrfices himself for Konan's sake, horrifying Nagato and forcing him into the crippled state and state of mind he is in today.