Blue Mesa is the last desert zone, and it one of the more confusing ones due to a large number of dead ends, areas, and floors.
While not a secret passage or part of any achievement / storyline, a somewhat hidden area is the containment chamber on Floor -66. While it can be seen from the main floor -66 area along the north west wall, it cannot be entered directly. Instead, from floor -66 you must exit out the passage in the north east corner (do not go in the east passage way) and go up the ladder. Then work your way through the outdoors until you find the helipads. On the corner of the second helipad is an elevator tube which brings you back down to floor -66, this time inside the sealed off area. Follow the west path until you find the containment center.
- Military Shooting Range - Enter the facility, and use the elevator to go downstairs. Once you're on floor -03, head up towards the gigantic freight elevator from the main story (with a dead scientist laying there) to reach the outside lot. Pass the hole in the fence and follow the outside of the subsequent fence. Then turn north along the fence until you reach an eastward passage through an open fence. Head through the satellite communications center towards the backyard, where the shooting ground awaits. You will encounter the crate at the very east of the shooting grounds below the slope.
- Valtain [Floor -66] Torture Chamber - From spawn, follow the road (S/E) until you reach the Gas station. Go inside and make your way (N/E) then (N/W) and enter the staircase. Keep going (W) until you went through the MINE EXIT. Outside, still go (W) until you see the bike, climb down the ladder. Go (S/E), you will see an aquarium and -17 yellow keep on the path and take the elevator. Go S/E, you will see the first -66, at this point you can go (N/E) towards the observation and analysis center. The crate is in the index case's isolation cell. If the corridor is visible but there is a wall in the way, it is closed.
- Coppercreek Mineshaft's Depths - Use the same steps as above to reach the ladder, and once it is reached climb down. Follow the path down and take a left until there is an upward opening at the southwest corner of the mine shaft.
Research workshop blueprint
The blueprints found here will unlock the research workshop (see page for locations). The blueprints look like a broken monitor and test tubes.
Click to enlarge. Map image provided by Elrandira.