The Agents are the main antagonists of The Matrix franchise. They are an elite team of computer programs engineered by the Architect. In story terms, they are the embodiment of faceless, uncaring, relentless authority.
History
The Agents' purpose is to defend the titular reality from Redpills, whom might reveal it as a false reality.
They also terminate the Exiles, which are programs who don't have a purpose. They work in teams of three: one who acts as the leader and the other two are the subordinates.
Unlike the other programs, the Agents don't have physical form. Instead, they possess Bluepills, humans that are directly connected to the Matrix. Killing them would be impossible since they could just transfer into another host once that body is killed.
It is unknown what happened to the Agents when the Machines and humans formed a peace between each other following Neo's sacrifice to stop Smith from spreading a virus that would destroy both mankind and machines.
Appearance
Agents manifest as prototypical examples of federal agents of the United States government. Almost all share a standard appearance: middle-aged white males wearing dark grey suits and black tie with a tie clip, sunglasses, and an earpiece. In the tie-in media, a few agents have deviated from this norm.
Powers and Abilities
Within the artificial reality of the Matrix universe, Agents possess what would be considered superhuman abilities in the real world. They are capable of dodging bullets, leaping across rooftops and punching through walls or other solid objects. They are armed with large and awkward Desert Eagle pistols, though, being computer programs in a virtual environment, the Agents can wield them effortlessly. Agents can possess ordinary human programs ("Bluepills" i.e. civilians) at will. Their earpiece allows instant communication with other agents anywhere. In addition to their more spectacular combat skills, Agents can create various minor reality-bending phenomenon, such as when they temporarily erased Neo's mouth as an act of intimidation.
Later in the series, "Special Agents" are introduced, who are even stronger and more formidable than the original agents. In addition to appearing physically larger, their names contain two syllables rather than one (i.e Johnson, Thompson, etc.).
Behavior
Most agents lack anything like a personality or inner life, and are focused on nothing other than their mission of protecting the Matrix. The notable exception is series antagonist Agent Smith, who profoundly despises humanity, which he finds physically revolting. He is also the only agent to possess free will and a capacity for self-reflection and contemplation.