This is a secret level accessible from Pigsty.
Secret Places (7)
When you grab the blue access card, two hidden doors open. The one without a teleporter behind it has a secret place. Use a jetpack to fly up to the top of the shaft and find the secret.
This area is a sub-floor just below the main floor of the Area 51 building (found before falling down the elevator shaft). There is a switch-like object above the computers (left half of image). You don't have to press it, you just have to jump onto those computers. This activates a secret door in the adjoining room (right half of image).
In the same room as the previous secret, one of the corners is slightly brighter than the surrounding walls (a holoduke is in this corner). Grab the holoduke and press on the corner behind it to open another secret compartment.
On the lowest level of the Area 51 building, behind forcefield 2, is an area with loads of crates. There's a crack in the wall beside the computer. Blow it up to find "Groom Lake".
Within the previous secret area, there's a bloody handprint in a dark corner. Press it to open a teleporter. Travel through the teleporter, then walk across the bridge and get the RPG to be credited for a secret place.
There's a computer back in the room with loads of crates. Press on the computer (not the monitor) to open one of the nearby crates.
Just outside the crate area there is a crane which picks up canisters. Let it pick you up and carry you to the conveyor belt platform. There's a switch here (right side of image) that is used to toggle the conveyor belt. However, it also opens a hidden teleporter (left side of image). (Note: The switch inside this teleporter is the only inoperable switch in the game... they forgot to tag it). The teleporter warps to the interior of the alien ship from "Independence Day".
Unofficial Secret Places
Unlock the blue access switch door and enter it. Behind a counter in this area you will find a computer. This computer opens a hidden door at the other end of the room (beside the combination switch door). The hidden compartment contains a medkit.
These combination switches are on the top floor of the Area 51 building (inside the blue access switch entrance). The correct combination unlocks the elevator shaft door.
Area 51 happens to have the most complicated combination code in the game. This "launch code" has a total of 256 possible combinations (255 if you rule out the null combination). Luckily, the launch code is hinted at in three different places throughout the level. The first two hints could be taken ambiguously, but the third hint makes things quite clear.
The first hint is found on the arm rests of the captain's seat (the seat in front of the blue access card). This would be easy to misinterpret as mere decoration if you've never played the level before.
The second hint is found on the sub-floor just below the main floor of the Area 51 building (before falling down the elevator shaft). It's the same hint as on the captain's seat, although this time it's more noticeable (but still just as cryptic). One thing that has always bothered me about these hints is that they use red to indicate "on", and green to indicate "off". This is just needlessly confusing, since the switches themselves display their status in the opposite manner.
The third and final hint clears up any prior confusion. It's difficult to miss, the yellow access card is right in front of it. The combination colours are still backwards, but at least the red ones are flashing this time to make it more obvious that they need to be activated.
Now for the combination itself. The combination switch sets are found at the end of the level (after using the yellow access switch elevator). Flip the multiswitch once to access the first set of combination switches.
Flip the multiswitch again to access the second set of combination switches. The correct combination will make the launch switches available. Flip the multiswitch one more time to access the launch switches (they are on opposite ends of the room).