After the cutscene, in which the Proto stalks Kurtis via the ductwork, you end up trapped with it in this large, open room.
You'll need to subdue the Proto-Nephilim (9) four times in order actually kill it. So, as soon as you regain control after the cutscene, equip the Chirugai and activate the psychic shield (Duck). Kurtis may take a little damage while you're doing this, but once the shield is active, it helps protect him from the Proto's attacks.
Now quickly throw the Chirugai (Action) or slash with the blade at close range (Jump).
When the shield dissipates (Kurtis stops glowing)...
...re-activate it by pressing Duck again, and continue fighting.
The goal is to do as much damage as possible, as quickly as possible. So don't be afraid to move in close, as long as Kurtis is shielded.
When its health bar is reduced by about half, Kurtis will no longer target the Proto.
It will then scamper off into the air ducts, giving you a few moments to regroup.
During the lull, while the Proto makes its way through the ducts, you can pick up the large health pack (8) in the near left corner of the room and/or unlimited Boran ammo (9) in the far left corner. (This pickup respawns but only if you run out of ammo. It gives you 2 more Boran clips each time you pick it up.) You will be able to get these pickups after the fight, so leave them for now unless you're desperate.
Watch the ducts on the far wall, and when the Proto emerges, re-activate the psychic shield...
...and continue throwing the Chirugai.
After two or three more hits, the Proto will retreat into the ducts again.
Repeat the process twice more: Activate the shield as the Proto climbs down to the floor...
...then throw the Chirugai to chip away at its health...
...until it runs back into the ducts.
When it descends for the last time, it should be almost finished.
Hit it once or twice more, and Kurtis will say, "Time to die, Monkey!"
A moment later, a cutscene kicks in. Kurtis stabs the Proto-Nephilim with his Periapt Shard. The beast gets a brief second wind then falls dead. The "Great Flood" achievement/trophy unlocks here.
After the cutscene, Kurtis deadpans, "That's my demon quota for today. Time to get the power on again." If you managed to defeat the Proto without healing or using the Boran X, the "You're Just a Monkey" achievement/trophy unlocks here.
Pick up the large health pack (9)...
...and Boran ammo (10) if you didn't get them during the fight. Approach the machine with all the hoses and dials. Pull the switch to turn on the power and trigger the final cutscene.
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