smithText=Written May 2003 By Jason Payne (firstname.lastname@example.org) www.X-matrix.net
Agent Smith the Virus
Agent Smith is the only "human" in this world. He's spreading himself like a virus replicating himself over and over until the Matrix will finally get overloaded and fail. Smith wants to leave the Matrix for good (M1: "I must get out of here, I must get free! And in this mind, is the key," squeezing Morpheus' temples, "my key! Once Zion is destroyed, there is no need for me to be here!").
Smith knows that by killing Neo he can escape the Matrix because Neo is the key to resetting the Matrix, or to shut it off. It was originally killing Neo that allowed Smith to become powerful (his cloning ability) - "because of you I've changed - I'm unplugged" - so killing Neo again will allow him to gain Neo's powers completely, and thus gain the power to shut down the Matrix.
Smith, in his current form, is not meant to be there as far as the machines are concerned - he's a computer virus as he has every characteristic of a virus - he multiplies and spreads and infects (and emulates) other programs like one. He is exactly as he himself described humans (M1: "You move to an area and you multiply and multiply until every natural resource is consumed and the only way you can survive is to spread to another area. There is another organism on this planet that follows the same pattern. Do you know what it is? A virus."
Who put him there? Humans in the real real world, i.e., outside of Zion and the Matrix. They're at war with the machines and trying to destroy them by infecting them with this virus - Agent Smith. This is not without irony however, the irony that Agent Smith represents the human race! And Neo represents the machines! Agent Smith says to Neo just after he's seen the Oracle that he became free when Neo destroyed him in the first Matrix (when Neo entered his body and exploded him from inside out) - Smith has the ability to "inherit" other programs' abilities since he is a virus, and thus he inherited some of Neo's abilities. His infectious ability is profound however. He infected Bane in Zion through the phone line. Then he wanted to infect Neo whilst disguised as Bane... by cutting his hand with the knife when Neo was about to board the ship so that when he stabbed Neo, his blood would have infected Neo with Smith's virus, but cunningly unbeknownst to Neo.