From the start position, walk straight ahead until you reach a discolored wall behind four health bonuses. Open it (sector 125), run up the stairs for a green armor.
After getting the green armor in secret #1, head outside towards the slime waterfall, and throw the switch. Enter the corridor and walk to the west. As you descend one single stair, open the northern wall with yellow lights at the bottom (sector 356) to find a chainsaw, four health bonuses and four armor bonuses.
After advancing to the point where enough switches have been thrown to raise the steps to the central switch, hitting it lowers the barrier along the center of the area. Enter the northern part, and take the first newly available avenue on the west. There will be two corridors branching off to the south ahead of you; press the wall between them. It reveals a room (sector 903) with a computer area map, two medikits and two armor bonuses.
After collecting the computer map in secret #3, back out of the room, and take the westernmost corridor to find a berserk pack. Open the wall across it to reveal a room (sector 924) with two medikits and four armor bonuses.
Go to the floor north of the central switch that lowered the barrier mentioned in secret #3. Walk to the east, ascending some stairs, passing a room (where you before had to ascend the stairs to the south to raise the northern part of the stairs leading to the central switch) further to the east where you finally end up in a small room. The northern part of the eastern wall looks like a kind machinery. Open it to reveal a room (sector 897) containing three sets of shotgun shells, three rockets and two medikits.
Walking around a certain column near where the Spider Mastermind enters can cause a permanent Hall of Mirrors effect on many of the textured walls. Reloading a save will not fix this bug, neither will quitting to the main menu. Only quitting to the dashboard and reloading the entire game will fix this glitch.
Linedefs 1327, 1337 and 1339 - each one with Action: 90 - WR Door Open Wait Close - have Tag 25, but there is no corresponding sector in the map.