You must collect three cogs to repair the elevator to the boss fight:
1. Use the Anywhere But Here! Gobblegum at any point after you mesmerized the poster, and you will be teleported into an Egg Hatching Room, and a cog will be on the floor to collect. You can then drop down to one of the laboratories to leave.
2. Electrify your shield the same way you did when upgrading the KT-4, and approach the zipline at the laboratory. Pay attention to a small dock below the zipline. On that dock is the cog, and you must take the zipline, and drop at the precise time onto the dock. In Solo, you should electrify the panel, then take the zipline, and knife while you are over the dock. In Co-Op, one player should take the zipline, and the other should electrify the panel while the other is over the dock. Be very careful here as you can drop into the water and die. You can do this from either side of the zipline. Once you are on the dock, collect the cog.
3. Plant seeds anywhere on the map, and water them with Blue Water, then shoot them with the KT-4/Masamune. Do this three times, and there is a chance that it will grow into a plant you can open and reveal an AA Shell. Pick up the AA Shell, and approach an AA gun to the right as you enter the bunker, where the KN-44 wallbuy is. Over time, a cargo plane will repeatedly fly over the map and in the path of the AA Gun. Simply interact with the AA Gun to place the shell inside, and then wait for the plane to be directly in its line of sight. Once it is, interact with the gun to fire and destroy the plane. If you destroy it, a cog will fly to one of three locations on the map and will be smoking. It can be on the right path to the Blue Water, near the bunker entrance, or near the Green Water.
With all three cogs collected, go to the entrance to the bunker, and upon entering and to the left is an elevator close off. Use the Skull of Nan Sapwe to mesmerize the wall to the left of the elevator, to reveal an area where you can place the cogs into the machine.