The head-fake is that the first movie's premise is that the matrix is virtual reality, while the Nebudchadnezzer ship and Zion, etc. is the actual reality. Now, in the second, we see that escaping from the Matrix just means that you are not escaping at all. First movie: you have volition, and as Trinity says "the matrix can not tell you who you are". Second movie: Neo has been manipulated into becoming a tool and his will has only served to serve as another way of control, the Oracle is a computer program that manipulates him, etc.