In the large open area in the northwest corner of the map, push the button in the middle and drop down into the hall with the Arch-Vile. Go down this hall and into the room with a four-square set of white teleporters. In the back left corner, one of the boxes is gray (most of them are brown). Press use to lower the gray box and pick up a blue armor (#1).
When first entering the UAAF building, proceed until you are about to exit the building through a platform (which has some revenants on it). Just north of that exit is a window looking out west. You have to press the 'use' button at the base of the window facing outside. This will lower a platform in front of you (#2) with another blue armor.
Upon entering the room with many "hiderooms" with UAAF logos on them, turn left and then turn right. The first right hideout will have a single UAAF logo. Open this wall (#3) to find a backpack and partial invisibility.
Upon reaching the room with a poison pit with a bridge operated by several lifts moving at random, drop into the pit, turn left (north) and go to the end. You will see on the north side a recessed wall with a stone floor. Open this wall for a curved hallway (#4) containing a backpack. Open the silver wall behind it and another hall (#5) will open in front of you, with six armor bonuses and a soul sphere.