The bunker is located at the base of the large mountain where the lasers converge, on the side of the beach.
The principle of the bunker puzzles is grouping like colors and separating the different ones.
Enter the bunker by separating the white and black colors.
The first set of puzzles on the left as you enter, and on the front wall
Once you complete these, you are allowed to enter the room with the flowers with the different colored glass. The principle is that some colors appear the same when seen through a different color light. The only way to solve these puzzles is to group colors that look the same in blue or yellow light.
After this you get access upstairs and you will see two puzzles on the wall with a switch. Flick the switch and the wall will open exposing daylight and the solution to the puzzle. Close this to solve the second puzzle.
Finally, once through the container, make your way to the bottom of the stairs and find the elevator in the red room. There is a pattern on the wall but you cant tell the colors due to the light shade. There are many different patterns that will take you to different floors, however the only pattern you need to enter is this one:
This will take you to the top of the bunker where you can easily activate the laser.
Enter in any other pattern to go back down.