The three chapels are quite intricately connected with each other; pulling puzzle switches in one chapel may open new areas in other chapels. This can become very confusing; so I recommend that you simply solve the nine puzzles in the order that I present them. This time it's not the best way of doing things though. In many places you can solve more than one puzzle without leaving the chapel, but for the sake of neatness, I'm doing things the long way. Of course, for those of you who want to do things your own way and don't mind getting confused, :) I've included many cross-links in this document.
Go to the west side of the hall where there's a wall with a purple diamond at the top. This is a secret door; open it and pull the switch inside. This is the first puzzle switch in the Griffin Chapel. Besides solving the puzzle, it also opens:
If you've solved the first puzzle in the Griffin Chapel, you can solve the second puzzle in this chapel from here; and if you've solved the first puzzle in the Dragon Chapel, you can also solve the third puzzle.
Turn right when you enter this place, and open another door there. The switch inside is the first puzzle switch in this chapel. Besides solving one of the nine puzzles, this switch will:
The east door leads to a short corridor with two passages on the sides, the northern passage and the southern passage. These will be blocked with iron bars unless you've solved the first puzzles on the other two chapels. If you've solved the first puzzle in the Wolf Chapel, you can solve the third puzzle in this chapel from here.
The west door leads to a short corridor with two pairs of rotating pillars on the north and south sides, which block the passages behind them. You cannot pass these pillars unless you've solved the first puzzles on the other two chapels. If you've solved the first puzzle in the Griffin Chapel, you can solve the second puzzle in this chapel from here. There's a switch on the left wall. This is the first puzzle switch in this chapel. Just as in the other two chapels, this switch also opens:
Go to the Griffin Chapel, and down the stairs on the south side of the hall. Climb up the passage on your right. This leads to an open area with a deep chasm on either side of a walkway. Walk to the end of the walkway where it widens out into a round ledge. When you walk here, a trigger is activated. This is the second puzzle.
Across the chasm on the east side, there's a stained glass wall. If you break the stained glass, a wall will open on the west side across the chasm. This leads to the room with the Porkalator, in front of the ledge. Note that this stained glass takes good aim to break. I've found out that it's possible to break this glass with all the character classes. You need very good aim, that's all. Try strafing to the sides and shooting from different angles if you've trouble breaking the glass. (Thanks to Arco Vermaat for telling me that it's possible with the fighter's hammer.)
Presto! a magic blue bridge appears at your feet, leading to two openings across the deep chasm. If this doesn't seem to work for you (ie., you fall into the chasm and die when the bridge appears, or it doesn't appear at all), note that: you must walk over the edge, not crawl like a coward. There's a small gap between the edge and the bridge; if you crawl too slowly, you'll fall through the gap to your death. Also, you must walk off the edge exactly where the arrow is. If you walk off elsewhere, you'll miss the bridge and die (or the bridge may not even appear).
Now go to the opening on the right first, and press the switch there. This will open the bars that are blocking the opening on the left. After you press the switch, go to the opening on the left and enter the teleport. This teleport takes you to the southwest corner of the chasm, near the bottom. Follow the narrow passage and jump across the small section of the chasm. The passage on the other side leads to what I call the Crazy Walls Room.
There are many walls in this room that move back and forth. If you're not careful, you'll be crushed between moving walls! The puzzle switch is at the far end of the room. But don't run there yet! If you do that now, the ceiling wall fall on top of you and kill you. You must first find four switches in this Crazy Walls Room. The switches are behind walls with a purple diamond at the top. They are located near the four corners of the room.
Note: Several times when I played this level I had problems with walls that seemed to be stuck, and in places close to these walls I seem to be able to "see through" them (DOOM level writers call this the Hall of Mirrors Effect). The reason seemed to be that some ettins are stuck between the walls, and for some reason -- I think it's a bug -- the walls cannot move and this causes the wall-moving script to malfunction (my guess). This is especially irritating when one of the four switches are behind the stuck wall! The way to cure this bug is to either kill the ettin and quickly move out of the way before the wall crushes you, or use the Disk of Repulsion on the ettin. For some reason this kills it, and the walls go back to normal.
After you have activated all four switches, go to the end of the room where the puzzle switch is. The ceiling won't fall down now. After you pull the switch, the "Crazy Walls" move into some fixed position and then stops moving.
At the end of the corridor is a big auditorium, with a triangular symbol at the front and two pillars at the sides. You need to run and jump on both pillars. This solves the second puzzle in this chapel. Before you stop to congratulate yourself, some monsters are jealous of your progress...
Solving this puzzle also raises the floor where the triangular symbol is marked. Now you can jump from this raised floor onto the small ledge with the Krater of Might.
If you have solved the first puzzles in both the Dragon Chapel and the Griffin Chapel, you can enter the Wolf Chapel using the west entrance. From there, enter the first door on the right.
Otherwise, go to the main hallway of the Wolf Chapel and enter the door on the west, where there's a room with a deep pit with a pillar in the middle. (I still don't know what this pillar is for. If you know, please tell me.) Enter the door on the left, which leads to dark corridors. Go left when you enter the door, and go inside another door on the left.
Now you should be in the room with two pillars and some Dark Bishops. The door on the opposite side leads to a room with the puzzle switch. Once you pull the puzzle switch, four platforms at the corners of the room will lower, with some ettins on them. The two pillars in the first room will also lower, with some Dark Bishops on them.
One of the platforms will rise when you step on it, and will take you to a small secret room with an Icon of the Defender.
For those of you who are adventurous, you might want to try exploring other rooms along the dark corridors. There's a room with something that looks like a fireplace. Anyone knows what this is for? There's also a room which has three raised ledges with Discs of Repulsion on them. Each time you take the Disc, the ledge lowers into the floor. Once all three have lowered, Dark Bishops will teleport into the dark corridors outside. By the way, the map seems to show that there's a door from this room into one of the side rooms in the long hallway with stained glass, but I can't get it to open. Anyone has any ideas? Please tell me if you know anything about this.
If you haven't solved the first puzzle in the Dragon Chapel yet, do it now. Go to the west corridor where the rotating pillars are (this is also where the first puzzle switch is). Go past the northern pair of pillars. There's a wall with a dragon symbol on it. You need to open this door by pulling a switch upstairs. Turn right and activate the wall where the texture is different. This lowers an elevator which takes you to the ledge where a slaughtaur was. There's a wall with a dragon symbol on the left: open it and go up the stairs. Now you are on the high ledge in the northwest corner of the chapel. There's a switch near the edge. Pull this switch and the door downstairs that I mentioned will open. Now go back down the stairs and jump down into the main hall of the chapel. Note: don't jump down straight from the high ledge. You'll get hurt.
Now go back past the northern pair of rotating pillars and go through the door that just opened. Go all the way to the end and pull the switch there. This is the second puzzle switch. If you look through the window here, you'll see a swampy pool with lots of goodies. You can get in there from the main hall of the chapel outside. Go to the swamp pool and strike the northern wall (strike, not open). This lowers the pool into this area behind the window.
Go to the east corridor and down the south passage. Activate the wall with the dragon symbols. This is an elevator that takes you to the highest ledge in the southeast corner of the chapel. From there, jump down to the lower ledge on the north (not back into the main hall!). A wall will open on the right, with some baddies. The switch inside is the third puzzle switch in this chapel.
Although this document is supposed to concentrate on the puzzle side of the game, I think a few tips on fighting the Heresiarch should be included here since it's an important juncture in the game.
The Heresiarch has several modes of attack: he can fire a wavy trail of large purple fireballs that are extremely damaging (they explode, too, so stay away from them even when they miss you and hit the floor), or he can summon bouncing blobs of fire that chase you. These blobs of fire look like skulls and stay around for quite a long time before they disappear, if they don't hit you. When the Heresiarch is badly hurt, he'll also summon Dark Bishops to help him. Note that the Heresiarch can freeze into an invulnerable mode (when he has those purple swirly things around him, not necessarily when he raises his arms -- thanks to Arne for correcting me on this point). In this mode, all attacks are blocked, and most magical weapons are actually reflected back at you.
Jump inside the room where the Chaos Serpent was (you've probably seen this place from the outside before). The wall on the corridor behind you will open, and the portal leading to the next episode is standing there, waiting for you. Before you enter, you may want to explore the secret level first. If you're ready to enter the portal, make sure you have enough health and ammo left, otherwise you're not going to survive the next episode (yes, it's that horrible!).