Northeast of the level is giant, grey, and empty room, which is unreachable unless you are using the noclip cheat. The intended purpose of this room is unknown.
At the start of the level, open the discolored section of the northern wall to find a box of bullets, a box of shotgun shells, an energy cell pack, and a plasma rifle. (sector 201) This secret consists of three sectors, including the room itself, the door that leads into it, and the small space directly behind the door.
See secret #1. (sector 217)
See secret #1. (sector 220)
In the passage to the northeast of the nukage pool opposite the blue key door, open the discolored part of the wall across from the eastern side of the passage to gain access to the pool. (sector 29) on Hey, Not Too Rough or lower, you will find an imp, a box of shotgun shells, and a supercharge. On Hurt Me Plenty or higher, you will also find an energy cell pack and a baron of hell. On Ultra-Violence or higher, there will be an additional energy cell pack, and a box of rockets.
Following the blue key door, there is a dark alcove in the southern side of the room, unaffected by the light shining upon it. Enter it to find a zombieman, a medikit, two energy cell packs, and a BFG9000. (sector 139)
The cage you enter to escape from the zoo when pursuing the "Hard Way" through the level counts as a secret. (sector 186)
The door accessed from that cage is also flagged as secret. (sector 188)
The passage beyond that door is considered a secret as well. (sector 187)
Finally, the teleport pad found in that passage is marked as secret. (sector 179) It is thus impossible to register unless you use the noclip cheat.
One baron of hell (thing 196) is placed in the void outside the level, and thus cannot be killed. As a result, only 98% Kills is possible.
Because one secret cannot be obtained without the noclip cheat, you can only get 88% Secrets in this level.