Parasite Eve Museum Secret Rooms
The Museum is filled with a bunch of secret rooms, this page covers all the ones that I have managed to find within the area. I checked the entire Museum thoroughly and I'm fairly certain I didn't miss any secret rooms. If I did though, please feel free to leave a comment below and let me know what I missed!
This secret room is found just off the room where you turn off the alarm in the Museum. You'll want to travel as far right as you can in the room (past the alarm panel there's kind of an alcove), Aya is standing in front of it in my screen shot above.
When you run around in that area you'll come across an elevator with on option to take you 1F, 2F, 3F or 4F. If you try any other floors but 2 and 4 you won't be able to leave the elevator, the 2nd floor is the floor you start out on, where the computer room is with the alarm, and the 4th floor is where you'll find the store room with all the loot in it.
As far as I know, this store room is the only place you can get a Shotgun at before the Chrysler Building and/or before you give 300 Junk to Wayne. The Shotgun found in this storeroom is the M500, mine came with an Attack of 59, Range of 63 and Bullet Capacity of 7.
Museum Secret Room #1
In the Museum's Nature exhibit run along the far side, right hand side of the screen to find a secret alcove which leads you to a store room. If you can't find it use my screen shot above that's on the right hand side to figure out where you're going.
There's a few treasure chests inside of that store room - with an additional secret storeroom found off the southern end. In there you'll find even more goodies for you.
Museum Secret Room #2
Nearby the stairs that lead to Eve you'll find a secret room by traveling through the broken glass on one of the enclosures. You can see the secret area in the left screen shot on the far left side of the screen. Use the screen shot on the right for help identifying what room this is.
Items in chests:
Tool
Handgun (M9-3) with "Enter two Commands" as a bonus effect
Museum Secret Room #3
Another location in the Museum that's out of your line of sight containing an item is the large tent marked "Museum Shop" you find it early on while adventuring through the Museum and in order to obtain the Tool that's hidden inside of the tent, you'll need to run around inside mashing the X button.