They are the world's top spies, or at least they like to think so. Every territory has one. Though they are seemingly invincible, they all have a secret weakness. Later, you will be able to uncover these fatal flaws through optional objectives. Until then, you will only be able to distract or weaken them until their mission is over.
Be especially wary of fighting Super Agents, as they are the only ones capable of killing your Henchmen. Every time your Henchman is knocked out by a Super Agent, they lose a life. If all three lives are lost, the Henchman is killed and gone for good.