Near the southwest side of the room you start in is a computer console. Use it, and a crate stack will lower in the southeast to reveal an opening. After raising the lift, take it up, and then jump to the opening to find a stairway leading down to two bulk cells and a plasma rifle. (sector 105)
In the room with the blue sofa, press on the screen in front of the sofa, and it will lower into the floor. After that, open the differently textured wall to the east, and flip the switch to lower yourself into a room with three barrels, a switch, and a door. (sector 211) The switch will lower the floor like an elevator, which does not seem to serve any purpose. Open the northern door to find a room containing a first aid cabinet with five health bonuses in it, a box of ammo, a blur artifact on top of a toxic vat, and a switch. If you fall into the northwest corner of the room, press on the northernmost side of the staircase and a teleporter will open, allowing you to free yourself.
Press the switch north of secret #2, return to the intersection, and head into the northeast room to find a switch has appeared. Press it to be lowered to a passage (sector 152) leading to five clips, four sets of shells, a rocket, a cell, a super shotgun, and two chainguns. Open the southeast door to find twelve stimpacks; enter the southwest door to discover a shotgun; and enter the western door to get two backpacks.
In the room northeast of where you find the blue keycard, part of the western wall fades from green to white. Push the whitest portion of the wall to find a passage (sector 675) leading to a box of rockets and a computer map.
In the computer room north of where you obtain the red keycard, there is a switch. Press it, and go to the southeast hall to find a newly-opened compartment containing a plasma rifle. (sector 492)
In the room southwest of where you find the red keycard, you can find a lift taking you down to a short sewage tunnel. At the end of the tunnel is a control room; hit the two switches at the north, and two Commander Keens will be killed off-screen. Once this happens, a switch will be revealed in the southeast; press it to open another room in the southwest containing two boxes of rockets and a switch. Press the switch, and return to the sewage tunnel to find that the sewage has been drained. Jump down, enter the southern tunnel, and look to the west to find that a portion of the wall is green instead of brown. Open it to find a stone passageway (sector 517) leading to a library. At the end of the library is a megasphere.
In the room accessed by the red keycard, part of the northern wall bears a hazard stripe and exposed circuitry. Push it, and it will lower to reveal an invulnerability. (sector 594)