This is not a mission location, just a useful reference point for other locations. Main hallway is what I call the large hallway stretching across the map. It has a large slope called Vehicle elevator (don't confuse with Vehicle lift) on the West end leading deep down and connects to the "dig site" location on the East end.
Dig site is a high traffic area. Connects main hallway, cells (S), locked exit (E) and a tunnel leading down to the cave (N), and has a secondary player spawn point.

Series of small rooms and hallways located just on the South side of the main hallway. It has two large tables with documents on them.

Small area just on the East side of the Command post and South of the dig site, that could be confused for being a part of the Command post itself. It has tree side rooms (cells) and a blocked off room in the middle.

Large two storey room with steel walkways at the south-east point of the map. Keep right from the top/South entrance or from the Industrial zone. Be warned that there is another room that fits this description, located on the left path from the top entrance. There are no mission objectives there currently.

This area is a small labyrinth of corridors and small rooms with medical equipment. It includes the mess hall.
Connected to the Cells (W) via a rat tunnel, Dig Site (N) and Storage Area (S).

This is the most confusing one, as everything in the Bunker looks "industrial". It could be more appropriately called "boiler room" instead. It is a dark, medium-sized room with a red blinking light and large liquid tanks everywhere.
Industrial zone is found straight down from the top entrance. Go down the pathway, take right at the fork, go straight at the intersection. You're there.

A tiny room off the top of the slope in the main hallway, opposite of the unnamed room that is similar to the Storage area. Has red blinking light.

Confusingly named Vehicle Lift is a 3 storey drop located all the way at the West end of the main hallway. It leads from the bottom of the Vehicle elevator further down to the military camp cave. Two activated blast doors are located right next to the top of it.

Pipe control room is on the military camp area level, and is found behind the activated blast doors next to the vehicle lift. It's not so much a room, as an appendage/balcony to the pathway leading down from the blast doors to the camp area.

This one is obvious. Large cave at the very bottom/North of the map. It has military camp in the middle and direct sunlight coming through the ceiling.