The Matrix is a giant virtual reality simulation where the machines that currently rule the world are storing what’s left of the human race. There is a small resistance force of humans outside the Matrix who, because they are aware of the simulation’s nature, can hack the system to a limited degree giving them low level superhuman powers, awesome guns, and so on. They have a prophecy about a Chosen One — Neo — a man who has the extraordinary power to perceive and directly manipulate the computer code that makes up the Matrix. This ability will let him change the Matrix in ways the resistance fighters can barely imagine, but only if he has the chance to discover and develop them.
The Agents are programs that run in the Matrix to stop people from realizing they live in a simulation. They’re the machines’ front line of soldiers inside the Matrix against the resistance and, because they’re programs made for that purpose, have abilities “written in” far above even the resistance fighters. The resistance’s strategy for the Agents is literally to just run away. The Agents are also aware that Neo might be that Chosen One and take extraordinary measures first to capture him, and after he escapes and starts learning about his powers to kill him.
More here.