Technically Agent Smith was defeated in the first film, and he was supposed to die according to the Matrix program. But it seems he became aware this time of his programming and altered it. Which is why he is no longer an agent. Like stated in other threads he probably wants to get rid of the Matrix for good. The only way to do that is to defeat Neo since he is the only one that has the power(choice) to create another Zion once the current Zion is destroyed. At least according to the Architect. I have a feeling Smith and Neo will fight inside and outside of "the Matrix" at some point.
To answer whomever asked how Morpheus escaped once the keymaker got through the door to the mainframe entrance. The keymaker told him which this door will take you home, then told Neo you know which door to take. Also I was wrong, I got confused when they had another black actress at the power plant. I thought she was Naobi, but then when I watched it again I heard Link say she made it back okay.
