Welcome to this episode's secret level. The first part of this level consists of several irregular-shaped outdoor areas, with tombstones scattered about. Most of the enemies here are of the "ghost" variety, which will be harder to take out with the Crossbow. You'll come across the Yellow and Green Doors. (One of those clusters of spores is hiding a Morph Ovum.) Clear out the enemies, and look for a pathway leading up to a big square building, with a Blue Door on each side, in the middle of a big outdoor area.
First, you need to find the Yellow Key. Look along the south outer wall across from the blue-door building for a door. At the far end of the room inside, behind the pedestal, is the Yellow Key. Hit the switch on the back wall, and the pedestal will lower, with a Tome of Power. Before you leave, look on the wall opposite the door for a section of that patterned texture with the more plain texture on either side. This is a hidden door with a secret area and item inside.
Go back down to the Yellow Door. Inside is a huge area with a building in the center, surrounded by platforms that randomly raise and lower. Look around those covered sections in the corners of this area. Just outside one of them is a switch: activate this to open the door to the central building. Inside is the Green Key. (You may need to wait for the platform in front of it to lower. It's behind the platform that goes twice as high as the others.)
Find and enter the Green Door. Inside is a unique-looking chapel of sorts of several levels, that looks something like a snowman on the automap. There is a great deal of ammo and items in here. After clearing out the enemies, go down to the lower level and look behind the columns near the stained-glass windows. On the back of one is a switch. Activate it, and a door near the entrance opens. At the far end of the corridor inside here is the Blue Key. When you pick it up you'll get a substantial ambush, but the extra ammo and items inside those compartments make up for it. (You could see evidence of this along the corridor.) The corridor now continues to a window overlooking the lower level of the chapel. You'll find Wings of Wrath here. (This window is hidden from the chapel side. While you were down there you were probably being fired on by enemies hiding inside.)
Now that you have the Blue Key, go back up to the building with the Blue Doors. Inside is a corridor in a loop with stairways leading up to a central room. Go upstairs, find and hit the switch. This opens four side areas (the silver panels) with enemies inside. When you step inside any of these areas, the big column in the middle of the room will lower, with the exit portal inside. One side area has a Map Scroll, in case you think you may have missed anything. When you've flown around and seen everything you want, return here to the level exit, which goes to E1M7: The Crypts. You should be better supplied now, especially with all the Claw Orbs that were available here.