Just past the portals is a tall antechamber. The doors ahead will open after a few seconds. If you go for the Crystal Vials on the ledges, watch for an Afrit ambush from above.
Chapel[edit]
The main chapel is a very large, tall, elaborate room that's divided approximately in half by a low-ceilinged section spanning the room. The circle of torches just inside will be lit if the first puzzle-pieces in the other two chapels are completed, and a Krater of Might will spawn after a few seconds. (Not all forces are malevolent here, it seems.) There are many high overlooks plus four towers throughout the room, where Slaughtaurs will be firing at you.
Two corridors and first puzzle-piece lever[edit]
Go up onto the low platform at the far side of the chapel, and step onto either of the uppermost sections on either side of the muck pool. When you do, those two columns on either side nearby will open, releasing some enemies.
The muck pool is also the entrance to a bonus area. Shoot at or strike the wall with the candles, and the pool lowers. (You very likely activated this already while fighting the Stalker.) Past here is a muck-filled chamber with many items. A long wrap-around window above looks into a corridor, where there are enemies. To exit, shoot at or strike the muck surface where you entered, and the pool/lift will lower again.
Next, go to and step onto one of the spaces where the columns on either side of the muck pool opened. The two spaces have items including a Mystic Urn. When you do, hidden doors at both ends of the low-ceilinged section dividing the chapel will open. Past each is a corridor. If you've solved the first puzzle pieces in the other two chapels, rooms at the far ends of both corridors will have opened, releasing a bunch of additional enemies.
Go to the west corridor--this is the side that was to your left when you first entered the chapel. On the wall to your left is the first puzzle-piece lever. This solves one-ninth of the puzzle, plus opens the side areas in the Wolf Chapel, and opens the center bars on the right side in the Griffin Chapel. At the end of the west corridor, on either side (to the south and north) are two rapidly-spinning columns.
At the end of the east corridor are barred-off passages to the left (north) and right (south). The first puzzle piece in the Griffin Chapel moves one of the spinning columns on the south side back, allowing access to bonus areas, and opens the south-side bars, allowing access to the second puzzle piece. The first puzzle piece in the Wolf Chapel moves one of the north-side spinning columns back, allowing access to the third puzzle piece, and opens the north-side bars, with bonus areas inside.
Second puzzle piece: south side areas[edit]
Go to the east corridor, and down the passage past the south-side bars. Activate the wall with the design on it to the right, and a big lift lowers. Ride it up to the higher of this side's two overlooking areas, and jump down to your right to the lower overlook. A dark room to your right will open, releasing enemies. Inside is a lever that solves this side's ninth of the puzzle. Be sure to jump over to the tower in front of the overlook, here and the other three in the chapel. There are many items on them.
Bonus areas[edit]
Past the south pair of spinning columns is a tall room, with two sections of wall that have the gray rows of stones. These are both hidden lifts that go up to the overlooking areas in the near corner of the main chapel. There's no easy way to jump down from the highest overlook without taking damage, but you might be able to reach the lower overlook from up here. The tower nearby can be reached most easily from the lower overlook.
Third puzzle piece: north side areas[edit]
Go to and past the north pair of spinning columns, and look for and activate a section of wall with the gray sections in a nook to the right. A hidden lift lowers, leading up to one of the overlooking areas in the main chapel. (One of the towers is accessible from here.) Activate the wall with the design on it to your left to open a hidden door. Follow this route to a higher overlook, find and pull the switch, then return to the room past the spinning columns. A hidden door here has opened. This route leads down to that corridor you saw from the secret area below the muck pool. At the end of the corridor just past here, find and pull the lever to complete this area's ninth of the puzzle.
Bonus areas[edit]
Go down the passage past the north bars. On the landing above the second stairway is a hidden lift to the right, leading up to one of the high overlooks. At the lower overlook at the top of the stairs, another dark room will open to your left, with enemies and items. One of the four towers is reachable from here.