On some levels you have grenades or grenade launchers. Three launched at far range or one at close range will kill them. If they do not die, pull out a gun. When the auto aim is red, it indicates near death; you can easily take them in hand to hand combat. Occasionally sparking objects are nearby. Knock them into it and will die.
During the level where the Agents chase you up the stairs and onto the rooftops, you can kill them. Before entering the levels, make sure you have the "Unlimited ammunition", "Unlimited health", and "All weapons" codes enabled. At the start of the level, cycle through your weapons and select the grenade launcher. As soon as an Agent runs after you, shoot him three times with the grenade launcher. Wait until the smoke clears and they will be dead.
This trick works best if you are Ghost. In any level that has an Agent and you are or can get to a roof, go up to the Agent. He might kick or punch you back; watch the ledges. Hit him once or twice so that the camera pans to the side. Walk up to him, punch him, then do a Focus Kick (without pressing a direction). The agent will fly back. While he is on the ground press PUNCH, PUNCH, FOCUS + BACK + PUNCH. This will do an uppercut, sending him flying. Once he is in the air, press KICK and Ghost will do a flying kick, sending the Agent soaring across the room. If you are on a roof, do this to send him flying over the edge, where he dies on impact.
Activate the "Unlimited ammunition" code and obtain the GP gun (which takes the oxygen out the air). It can kill an Agent.
The first time you face an Agent, run. Towards the end of the pursuit, the Agent drops directly in front of you. Note that there is is a gap in the building between you and him. Focus and make the jump. After that, while he still getting up from the fall, run behind him with your back close to the wall and do a kick off the wall. He will fly into the gap, and get killed.
When fighting Agents, kick repeatedly at them while they are near a wall. They will soon be laying in the wall.
In levels with several Agents, use Invisibility and hit one. It may make him fight his partner.
On the level with the Gp-25 Launcher, go up to an Agent and shoot him. He will try dodging it, but the smoke kills him. Note: You must be Niobe to see an Agent in this level.
You can kill Agents in either of two ways, using a grenade launcher/thrown grenades, or by hand to hand combat. However, to kill them in hand to hand combat, you need to be on a level with rooftops or windows. This strategy works best with Ghost, as his punch combo involves sending an Agent in air, and you can follow up with a jump kick. In order to get close enough to the Agent to send him in his downward plummet, you need to enable the "Unlimited Focus" and "Unlimited Health" codes. The "Swordfight" code also works well for taking on multiple Agents, but is not necessary. First, shoot at the Agent so that he starts dodging the bullets. After that, use your Focus, get into him, and use the back punch combo that uses the two uppercuts. Next, kick at him and repeat until the Agent has fallen to his demise. Throwing works as well, if do are not using the sword
An easy way to kill Agents is to blow them apart with explosive weapons. Enabling the 7F4DF451 code is recommended. Three to four grenades may be needed.
To kill any Agent you encounter, activate the 0034AFFF code. Take out your grenade launcher and blow him up about four times. Note: The explosions will kill you if you do not have infinite health active.
In the final level at the Nuclear Power Plant, you must escape from several Agents. In the Transformer Field-level, you should have acquired a Chloride-gun (gas-grenade launcher weapon). When you use it against Agents, they will choke and die.