The bunker is an underground locations the author of journals 1, 2, and 3 used as a hideaway. He conducted experiments there and kept the Shape Shifter locked away in a cryogenic stasis until it escaped.
The bunker is the secret hideaway the author used to prepare for the end. The end of what, remains unknown.
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The tree used to enter the bunker is located in the Gravity Falls forest. The bunker can be reached by pulling a branch lever and going down the stairs and are shown in the hole that opens up.
The bunker appears inside first as a small room with weapons, food stock, and Spez Dispensers. After lifting up a poster, There is a small hallway leading to another small room. If you step on the middle tile, the room begins closing in. If you press 4 different symbols, a wall opens and you can then go to an even smaller room with surveillance cameras into a computer. After entering a closet and going through Decontamination, you can enter a new cave, which is vast and doesn't have any known entrances. All it holds is a freezing/shape shifting machine.