In the room following the starting area, a portion (sector 257) of the northern wall in the northwestern compartment can be walked through to obtain a soul sphere.
From secret #1, return to the passage connecting the aforementioned room and compartment. After opening the western door, climb up the stairs to the computer panels and look to the east to find that two of the metal panels are situated lower than the rest. Open these to find an invulnerability (on easy) or a partial invisibility (on medium and hard skills) (sector 105).
Approaching the blue keycard from the east triggers an ambush. The southern monster alcove has a lightning bolt symbol in its southeastern corner. Approach it to be lowered into a room (sector 170) containing a trooper and two boxes of rockets. (On medium and hard skills, there is also an imp and four armor bonuses.)
Return to the door you passed to enter the blue keycard room and wait five seconds. Run down the southern stairway, enter secret #3 as quickly as you can to grab a newly revealed rocket launcher (sector 171). (Stepping from the third to the fourth stair from below triggers the pillar surrounding the rocket launcher to lower.)
Inside the library, the westernmost shelf bears a painting on its western side. Stepping on the chair's lowermost platform from the north darkens the whole library, so step on it from the northwestern or northeastern side. Grab the chainsaw on the chair to lower the painting as well as the southern wall, releasing (skill dependent) none/four/eight spectres and four imps(, also revealing three armor bonuses on medium and hard). Return to where the painting was to find a secret alcove (sector 275) containing a light amplification visor (not on easy skills).
From the red keycard, drop off the northwestern side (thus lowering a lift) and run northwards following the passage. After the bend to the southwest at its northernmost point (where the second lamp is) look out for a recess in the southern wall that you enter. The recess in fact is a lift: it takes you up to a vantage point (sector 248) from that you can jump to the item situated on the pole: a soul sphere on easy or a BFG9000 on medium and hard skills.