At the end of the hallway in this area, shoot the light in the ceiling of the next room, and a teleporter will be revealed. It takes you to the "cage" over the lava, left side of the picture.

When you make your way through this room, a door opens behind you. There's a few goodies.

Get into the water and shoot the red button at surface level behind the steps. The floor at the side moves, allowing you access to some useful stuff. Can you get out before the lid shuts again? Muhahahahaha!

Opposite the cage the silver key resides in, a pool of light spills from a secret door. Shoot to open.

After grabbing the silver key, make your way to the exit. Get behind the stairs for another secret.

There is a big medikit in the gold key room, high up. You need your kangaroo genes to get there. Or perhaps a bit of rocket jumping.

When you enter the library (Most likely with a few nicks and scratches. The librarian seems more pissed than usual.), one of the books is sticking out. Push it. You'll probably need what's in the secret room.