You appeared in a room with three portals - to the two remaining chapels and back to the Heresiarch's Seminary. Get out in the open area and kill all the monsters there (mostly Centaurs and Slaughtaurs). If they bother you too much, you can also kill the Dark Bishops behind the bars in the chapel itself. Explore the whole area, you'll see that it goes around one big building, the Wolf chapel. Amongst all the stone doors that cannot be opened (they open when a certain switch is pulled somewhere), you'll find only one wooden door to be opened (it is in the south-western corner of the chapel). Go there and pull the switch inside.
Now the main entrance to the chapel (on the south) opened, leading into a big pillar-room filled with Chaos Serpents. Get rid of them. There again, you'll see that out of all the doors there, only two wooden ones can be opened (they are in the eastern wall of the room, on the south and north). The northern one leads to two rooms with Slaughtaurs and some mana, the southern one into a small room with some Dark Bishops and a chain switch, the first ninth of the puzzle to be solved. Pull it and as all the other doors are closed, go to the Dragon Chapel.
Some new doors are now open on this level... So go into the pillar room. The central door in the eastern wall is open now (leads to a room with some monsters and flechettes) and - whoch is more important - the western door opened there as well. Go there into a room with a big pit in the middle. Walk carefully around it - beware of the Dark Bishops that are going to fly out of the pit. When you kill them, open the door on the north. It leads into a circular (or rather square-shaped) corridor with ettins along the way. Describing doors as they come when you go from the pit room to the north: 1 + 2 = big room with some goodies and Dark Bishops. 3 + 4 = another room with Dark Bishops. 5 = two small rooms. At the end of the second is another switch, which would be the fourth part of the puzzle (almost half of them done!). When you'll be going back, the pillars will lower and some Dark Bishops and ettins will attack you. After killing them, notice that the pillar in the north-eastern corner of the further room leads to another ettin and an Icon of the Defender. The most important thing - pulling the other switch - has been done but if you want to, you can still go to the room around which the square-shaped corridor goes. This room, however, contains only some monsters and a fiery altar (I found no way of using it whatsoever).
Now it's time to go to the last chapel, the Griffin one...
Get back to the pillar room. The main door, the one to the north is now finally opened. Get there. If you want to gather some more goodies (they might be useful, the upcoming fight is going to be tough), go to the rooms to your right and left (east and west). But be careful! Upon entering them, some ettins are going to jump through the ceiling Then take the main corridor right in front of you. Again, ettins are going to break through all the painted windows in it. Kill them and get to the big room at the end. If the third segment of the fourth weapon wasn't collected in the Heresiarch's Seminary, it will appear on ground where the symbol is. Kill all the monsters (still not THE big fight of the level). Now the platforms in that room form something like stairs. If you run along the ledge of the uppermost platform, you should be able to jump on the two pillars on each side of the room. First, it lets you take the goodies there but it also counts as the eigth part of the puzzle. When you'll complete that, the lights will change, the symbol on the ground will rise and a lot of Dark Bishops are going to teleport in (the big fight). When you'll have killed them, you can jump from the symbol into the niche with the Krater of Might (previously inaccessible). That completes this level and you can go back to the Dragon Chapel where the last part of the puzzle is waiting for you.