This story takes place a few months after the first. Neo now knows that he is ''the one'' meaning that he can change things within the matrix and fight agents that are hunting him down. Agent Smith returns to take on Neo after being ''released'' from the matrix.
The main threat in the film is the ever approching machines intent on destroying Zion, the last refuge of humans detached from the matrix. With the help of his crew (morpheous, trinity, link) he must enter the matrix and try to stop the machines from destroying Zion by entering the most deepest areas of the matrix.
