This is a large and fairly involved level, with a variety of areas. You begin on a ledge at the west end of a large flooded outdoor area. There's a slow wind which will mess with the aim of some of your weapons. Not far from where you began the level, you'll find the Yellow Door. Take a look just to the right: that inset section is a door that will be open later on, leading to some bonus areas. At the far end of the area you'll find a Green Door, which is actually one of several into this part of the building.
Go up onto the big central construct, work your way to its highest point and collect the Yellow Key. Also, while you're out here, try to clear out the enemies in the building that you can get to through the windows. Most of them will congregate there, and you can make things easier later.
Open the Yellow Door, and enter the complex. To the right you'll come across another Green Door. As an aside, go to the tall room across from this door, where there's a Morph Ovum on a pedestal. You'll get a small ambush when you pick it up. Back in the hall, you'll see a wide section that is dark. Run through this: it's a crusher that will activate when you enter it. On the other side, take a look at that alcove of sorts to your left. The wall will lower when you walk up to it, with a door inside. In here is a bonus area with an item or two; plus, you can clear out enemies in areas you'll get to later. And, you won't have the guys in here shooting at you later on like they would be otherwise.
Back in the main hall, you'll find the Blue Door to the left. Further ahead the hall goes off to the right and continues outside, but the doorway is out of reach above. Back across from the Blue Door, go upstairs to the overlooking side room where the Time Bombs of the Ancients are, find and hit the switch. This raises stairs in the hall to the doorway leading outside. You can also get rid of many of those Gargoyles outside through the windows.
Head on outside: this is a deep courtyard of sorts, with ledges on the opposite side, a tower in the near section and a couple of flooded areas at the opposite end. There are several ways you can go from here. First, run across the gap directly ahead of the doorway you entered the area from, follow the ledge to the far end and collect the Green Key.
Go across the narrow walkway off to the south. Halfway across, two sections of the walkway will lower, one behind you, one ahead. Just stay on this until it goes back up. On the other side, activate the wall where the texture is different: this is a hidden door. Follow this route, across a second walkway, to a room where there's ammo and a Ring of Invincibility. After you get these, jump down to the far area past the second walkway, where you'll find a passage that loops back to the area between the two walkways. Jump down to the icky water and look around the corner to your far left for a switch. Hit this switch to lower the sections on the first walkway.
While you're still down here, go over to the tower. At the bottom, look for a switch. Hit this, and the inside of the tower will lower, where there's a Dragon Claw. To get back to the upper area, take the north passage exiting the area (the one that doesn't have the water in front of it--there are two passages leading out of here). When you go up that step to where the torches are, a lift will lower up ahead and around the corner, behind the Shadowsphere. If you're busy fighting enemies, you might not see it until after it's gone back up. Go back and run across the step again to lower it if you need to. The lift goes up to a side room near to where you found the Green key. You'll find a teleporter that goes to the ledge near the Green Door back in the big outdoor area where you began the level, where there are items. (If you looked in this side room earlier when you got the Green Key, the teleporter would have been covered up.)
Drop back down to where the tower is, but this time take the passage past the water. At the far end of this route you'll come to yet another Green Door. All three Green Doors go to a big temple of sorts. If you go this way, you'll come to a small room with two sarcophagi. Hit the switch to your right, and the one with the Silver Shield will lower, revealing a passage. This goes up to a ledge in the big temple.
Go to the big temple via the Green Door of your choice. In here, you'll find the Blue Key, out of reach on top of a big sarcophagus. Go over to the windows looking out on the big outdoor area, and look for a not-quite-hidden door nearby. Find and hit the switch inside here, and the sarcophagus will sink to floor level. Grab the Blue Key.
A side area: Remember the closed door outside next to the Yellow Door? When you picked up the Blue Key, this opened. Inside here is a flooded room, a few items and a teleporter that goes to the tower in the courtyard. You probably saw through a window into here a moment ago, after you hit the switch to access the Blue Key.
The last crypt
Go back inside the building, open the Blue Door, and follow this path. You'll find Wings of Wrath in the corner on your right. Be careful of those moving pillars: it's easy to get crushed if enemies on the other side impede your movement. When you go up the steps you'll be ambushed, but there are lots of Ethereal Arrows on the two chairs as compensation. Hit the switch, take the opened passage down, and you'll come to another of the crypts this level is named after. First, a bonus area: run up onto the ledge to your left, using the coffin as a step, and follow the hall to where it ends. There's a Map Scroll. Activate the wall at the end, where the texture is different, to open a hidden door that goes back to the main hall just inside the Yellow Door.
Back in the crypt, jump down and go up to where the red coffin is. Where you jumped down is too high to climb back up, but if you want to go back that way, just take the teleporter on top of that other coffin. The level exit is inside the marked door near the red coffin. Before you leave, there's one final bonus area: stand on the red coffin, then go up to the far end of this area. A door here is now open, leading to the ledge where you began the level, plus there's an additional room past here that's now open, with a pile of ammo and items. When you've seen the sights and gotten everything, head to the level exit to continue your mission. Up next is the final level of the episode.