While 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 can even see his body. You will, however, see him at the ladder toward the end of the level.
While 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. Shoot him in the head while he is shaking. This will kill him again for a very long time.