The bunker in The Witness is located behind the jungle and the mountain, just on the coast. The entrance is blocked by a sliding door with a puzzle on the front. It follows the same rule as a number of the puzzles on the island. There are black and white squares on the puzzle and all you have to do is separate the colors. See the solution for the door below.
Once inside, you will see two sets of puzzles on the wall – one with 5 and one with 4. Starting at the far left work your way though them. Once again, you need to separate the colors but here there are far more colors than just black and white. They aren’t too challenging though. For help, see the solutions below.
Solving these puzzles will allow you to open the door to the laboratory looking area to the right where the rules change slightly.