Online
The Agents lived on in the film's continuation, the MMORPG The Matrix Online. In line with the brokered truce created by Neo at the end of The Matrix Revolutions, Agents were no longer assigned to kill redpills on sight. Instead, they guard various areas of the Matrix that are still restricted to the awakened. The Agents revert to their original programming with the collapse of the Truce.
Read more about this topic: Agent (The Matrix)