You will be in a room (A) with four raised teleporters and a switch. Hit the switch and walk into any teleporter. You will be in a small room (B) with some Green Armor, a Super Shotgun, Shells, and a switch. Hit the switch, and the room will lower, revealing a huge room (C). The platform you are on has a bridge running south a bridge running east, and a bridge going north, which has a bridge going east to west crossing it. Each bridge has barred walls except for the platform you are on. In the southwest portion of the room is a small raised platform with two Revenants and a Soul Sphere, surrounded by nukage and Specters. On the north side of this room is a Yellow door (I), and on the south side is the Exit door (L), which is locked. Go forward, and go west along the bridge (D), onto a platform next to a pit with nukage and Demons. Go west through a room (E), raising Commandos which cannot see you at the moment. Go through the southern door, through a hallway (F), leading to a switch. Kill the Revenants, then activate the switch (G), which will raise stairs on the east side of the room you are on. Go back through the hallway, and you will be ambushed by Hell Knights, and the Commandos which couldn't see you. After the fight, go back into the room just east of the one you are in right now. There will be a switch on the northeastern wall of the platform you are on. Hit it, and the wall will raise, revealing a path to the Yellow Key (H). Grab the key and go to the Yellow door (I). Inside the door is a pit with nukage in it, with 4 small platforms in the pit. On the north side of the room is a short raised platform with a window on the east and west containing a Commando, and a switch on the north side of the room. Kill the Commandos and hit the switch, revealing two hallways on the north side of the room that connect, containing Imps. Four windows will open in the room, releasing Barons, which will teleport into the pit. Go into the hallway, and on the south side will be a switch, which opens the Yellow door back up. Go back to the platform you started on in the big room, and go east along the bridge, and turn south, coming to two doors. One door has a lever (I), which lowers itself, revealing a teleporter. Step on it, and you will be next to some stairs you just raised. Climb them, then hit the switch, revealing three Mancubi on the southwestern part of the room, guarding a Blue Key (J). Kill the bad guys, get the key, and jump on a teleporter, which will take you to the center of the two bridges in the main room. Go east through the blue door (K), and climb the stairs across the pit to your right. Hit the switch at the top, which will open the exit door (L). Go through it and hit the switch, lowering the east and west walls, revealing Commandos. Kill them, then go through either hallway, leading to a room (M) with three Seargents, a red teleport pad, and a silver teleport pad (N). Kill the Zombies, step on the silver pad, and hit the exit switch (O).
Once in the main area, cross the bridge leading west (opposite the blue door). In the next room, there will be a brown sludge pit (P) to the right with three pillars in it. You must run (no straferuning is required) from pillar to pillar. The third pillar, which holds a plasma rifle, counts as the secret.
After getting the yellow keycard, drop into the adjacent slime pit. There is a switch on the far side. Flip it, then take the teleporter. Head straight forward and go up the short staircase. To the right is an unreachable platform (Q) with a soul sphere on it. Drop into the slime here, and go through the small passage to the right. There's a newly opened teleporter in here (R); go through to be taken to the aforementioned soul sphere.
From secret #2, drop back down into the slime and go through the opening to the southwest. Take the teleporter closeby, and you'll end up in yet another slime pit. Enter the small alcove across the way and flip the switch to lower a lift (S) that you can ride up to a secret combat armor vest.
After flipping the skull switch behind the yellow door, return to the highest platform of the main area again (the one across from the soul sphere platform). From here, head west down the stairs toward the tan door (T). Before you reach it, go through the newly opened doorway and run along the red-lighted catwalk (U) into the alcove on the far side. It is a lift leading up to a cache (V) of health bonuses. The lift is timed, triggered when you walk down the stairs, so it may take a few tries to get there in time.
This level is the only level in "The Plutonia Experiment" that has its exit as an exit switch. (All other levels, aside from the last level, in which you would destroy the Gatekeeper, all have exits as portals.)