As it said last chapter, Madara is the puppeteer. He can basically drop Nagato like a fly and continue on planning Akatsuki's goals as the mastermind.
I would also like to point out, as much as Pain was leader of the Akatsuki and acting "all God almighty by blowing up villages without any remorse", he's still a human being. More or less, coming to Konoha by attacking and capturing Naruto is a way of showing how Naruto can handle the battlefield by himself when the fight becomes too dangerous, plus showing that Pain wasn't the final villan of the series. I noticed that way back around the 300s when Kyuubi mentioned Madara's name (even though, we haven't heard of Pain's name yet back then). It brought certain theories that someone was behind all of this as the great mastermind which we now realize it was Madara.
yes. And...well...He said all that i really give a damn about.
hell yes.
I beleive Naruto realized the magnitude of the situation, and in doing so, took it all upon himself for, what is seemed like, the sake of the village and its inhabitants.
Genius (Tensai)
Edited by jworks, 27 March 2009 - 11:25 PM.