These guys are both sentient programs. This battle took place where it always does with matrix battles, a construct of my old high school's parking lot.
I did this battle before Reloaded but I waited until now to do it so I could use info from the sequel. The Agent's gun and superfast punches are
useless against The Doctor due to his intangible form. The Doctor's intangible attacks on his oponent's organs would work on the Agent if he wasn't so fast. My reason for saying so is that if Trinity
could kill an Agent, or at least the human host, with a shot to the head than a punctured heart should do the same.
Agent Smith has the ability to transfer himself from person to person, but according to my rules thereare no other people for him to go to, thereofore the previous fact mentioned means that he will be killed.
I originally thought that Agent Smith would eventually hit the mobile emitter, which means I got lazy and couldn't think of something. But after seeing
Reloaded I am sure that Agent Smith would win. He has the ability to copy himself by touching others. This is something outside the
rules of the Martrix which means it has to do with manipulating code. This means that the Doctor's intangible form won't save him from Agent Smith's copying ability.
Once he is copied the Doctor no longer exists and only Agent Smith is left: TKO.