When playing as Niobe and are being chased by the Agent, get to one of the pillars with the gas tanks. Wait for the Agent, then shoot it as he runs by. If timed correctly, it will explode and he will die. You will even be able to see his body. You will, however, see him at the ladder at the end of the level.

When you are running from the Agent, run past the flammable gas tank. Wait for the agent, then shoot the tank. This will kill the Agent. When you get to the ladder at the end of the level (if you are fast enough), you will see a police officer turning into an Agent. While he is shaking, shoot him in the head. This will kill him again for a very long time.