Letters in italics refer to marked spots on the map. Sector numbers in boldface are secrets which count toward the end-of-level tally.
Secrets[]
After you open the door next to the exit door, there will be two brown techno panels at the east wall, bordered by columns of lights. After climbing the nearby stairs, do a running jump at the northernmost panel from a distance, landing in the recess where it sits. Doing this is best done using straferunning. After pulling this off, push on the panel to open it, revealing a medikit and a box of shells. (sector 285)
After climbing the stairs near secret #1, there is a computer panel to the west. Push it, and it will briefly lower, allowing you to access a teleporter which leads to the platform near the exit door. At this spot, you will find a stimpack and a switch. Activate the switch to lower the wall west of the exit door, leading into a room with some monsters and a super shotgun (sector 661), along with another room containing two stimpacks, 16 shotgun shells, and a megaarmor. Stepping onto the cross-shaped platform where the shells and megaarmor sit will cause a compartment full of enemies to open to the south.
On your way to the red keycard, there is a computer terminal with a long, red light at the top, at the south of the hallway around the outdoor section. Press on this panel to open a door at the northwest, where you can find two stimpacks and a box of bullets. (sector 461) This room also contains a vantage point from which you can kill the enemies in the alcove east of the pillar with the chaingun, even before it is opened.
Beyond the red door east of the first hallway, there is a tall mainframe, upon which there are two clips, 8 shotgun shells, and a backpack. At the south of the walkway around the room is a computer terminal with silver borders. Push on this panel to find a medikit and a teleporter. Enter the teleporter to be warped on top of the mainframe, allowing you to gather the munitions there. (sector 517)
In the same room as secret #4, there is a slight recess in the northwest wall on the upper floor, next to the elevator switch. Open it to find another teleporter; enter it to be warped on top of the stack of crates near where you found the red key, from which you can jump into a compartment to the west containing a supercharge. (sector 425)