After completing the Armored Warfare Facility, head up and right to exit. Move down to encounter an explosive device. Charge up beforehand and use Keratosis to withstand the blast. Flip the switch to deactivate the device, then proceed through the pipe to enter the Bunker.
Navigating the Bunker
Take the only available path downward to a large room with various routes, most of which are blocked. Drop biomass in the pool in the bottom-right corner of the pyramid to become smaller, then squeeze through the pyramid doorway and head right. Use invisibility to bypass the laser, then continue right, going above the elevator shaft and down to your left. Defeat the enemy in the room, then shoot the elevator switch below with your cobweb to raise the elevator, allowing you to navigate to the next room. Take out the human inside.
Continue past the nuclear reactor and head down through the right shaft. After a few turns, reach a room with metal squares and an enemy. Use Parasitism to control the soldier, shoot through the glass doors, and drop down. Flip the switch to open the next gate, and shoot through the glass doors in the previous room.
Regain control of your monster form, head back up, and use cobwebs to lift the elevator. Move up, then go left and under the elevator through a small pipe. Head down, save, and deposit biomass in the next room.
Proceed right through the room with the previously controlled soldier. In the next room, defeat the enemies, head to the top-right, and flip the switch to unlock the nuclear reactor core. Grab it, return up the elevator to the reactor room, and place the core in the reactor, which opens additional gates in the level.
Exploring the Pyramid and Bunker-Jungle
Return to the pyramid room, go left and recharge using the power box. Swim left, avoiding explosives with Keratosis, then head down the pipe to the room below. Clear two enemies, move left to clear another, then continue through the left pipe to eliminate enemies in the next room. Head up, deposit biomass, and proceed right.
Swim down into the water, taking the left pipe while avoiding explosives. Pull the lever, follow the pipe down, recharge energy, and deposit biomass to become smaller. Use cobwebs to activate the lever again. Return to the hive and save.
Head right from the hive into the Bunker-Jungle. Use Keratosis to survive any bombs, then return to the pyramid room. Move up and to the left, depositing biomass if needed. Navigate to the ruins area and clear all enemies. Use webs to defeat drones, then exit top-right. Save, spread biomass, and remove the metal cork to continue.
Exit right and go back to the pyramid room, taking the top-right entrance to the Bunker-Excavation Site. Clear enemies in the room and squeeze through the central doorway to access another ruins area. Defeat all humans to grow back to maximum size, then remove the cork on the side of the wall. Backtrack, deposit biomass, and use cobwebs to open both gates below.
Reaching the Bunker-Pier and Final Exit
From the pyramid room, exit bottom-right to the Bunker-Pier. Take the top walkway, using Parasitism to control soldiers and clear enemies. Swim down through pipes, then continue left. In the next room, use two switches to activate explosives that take out nearby enemies. Deactivate the switches, continue left, and reach the final biomass deposit.
Clear a room full of enemies and drones to unlock the path. Move up and into the main Bunker area.
Finally, squeeze through the central bunker doorway to escape.