As Niobe, the Agent will start to chase you. The large tank of "Dangerous Gas" you run past can be shot. When the Agent passes it, shoot it. It will explode, and kill the Agent. Note: You might want to enable the "Invisible to enemies" and "Unlimited health" codes.
Play as Niobie and you will start in a room where there is an Agent shooting at you. Ignore the "Don't fight, run message. Instead, take out your MPS gun (you can use a pistol). Shoot him and he will evade the bullets. Get him to dodge all the way to the left or right. At that moment, shoot the explosive barrel. It will kill him, and you may pick up his gun.
While playing as Niobe, when Sparks says run, do not fight him (turn on Focus). Run between the two missiles and turn around, then shoot the bio hazard sign. The Agent should fall and lose his gun. Note: Use the shotgun.
After finding tunnel 7R, An agent will chase you. There is a very easy way to kill him. Occasionally there will be a tower lit by red lights. On this there are four boxes labeled "Danger: Explosive!". Lure the Agent near one of those boxes, step back, and while in Focus mode, shoot the box in first person mode. This should quickly kill him, and you can take his Desert Eagle.