There's ways to cheat through it, but I've found that the reliable way to get through is to melee the melee enemies, and save your ammo for quickly killing ranged enemies. Shotguns will ignore the agents' dodges and blocks.
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I'm sorry for this comment lol. I figured out a strategy. Keep the dual shotguns you can find around the corner in the room with all the shelves that has the glock and full auto gun (I forgot the name of it) and use it to get through the 2nd last level easily. Keep a machete, and on the last level, sneakily throw it at the grunt with the goggles. Then crouch over to the door and you're done! Also I saw a comment talking about spawning enemies. Is that true? If so, what's the button to spawn them? Also, good job on this game!