Up in the room with the rocket launcher, check the three red bars in the walls nearby (linedefs #3331, # 3265 and #3334, third screenshot). They will lower the three bars and grant you the access upstairs. Plenty of goodies, here.
In the octagonal room with the stairs, climb them up and use the wall (linedef #5024) and wear the megaarmor.
Enter the pools of blood near the grinder, grab the plasma gun.
Down in the end, enter the nukage pool and get plasma ammo and health.
Down in the room with the grinder, if you don't cross all the three lines and then hit the switch (linedef #630) to open the wall in front of the lift (sector #215), crossing the last lines will close definitely the wall: the switch is a one-way switch.