However, at some point before the events of the first movie, things were set in motion, which resulted in Agent Smith becoming more than the sum of his programming, and his motivations changed ...

Agent Smith is the best bad guy in The Matrix and ... he eventually splits from his fellow Agents and goes rogue, seemingly ...

Others noted that Agent Smith should have just been in the game when it was released. Fans waited over a year for the game to be re-released but then only came with two more characters.