From the very start point, follow the hall and turn west, but instead of running down the staircase, climb up and follow along the narrow ledge until its end, and open the southernmost panel for a small elevated room full of armor and health bonuses, a backpack and a chaingun.
At the northwest part of the map, just before one of the blue keycard doors, you will get ambushed by zombies, Imps and a Revenant. Go to the small niche the monsters came from and open the southeasternmost wall to find some health bonuses and a plasma gun.
After opening the door which requires the blue keycard (the one nearest to secret #2), proceed to the dark hall whose walls have brown piping decorative panels. The last panel, right before the staircase, can be opened to reveal some health and armor bonuses, as well as rocket boxes and an invisibility sphere.