As an interesting aside, go to the north part of the Seminary (the far end), where there's a hole in the ceiling with a roughly square wall under it. This is a magical area; stepping close to the wall lowers it and randomly teleports monsters and goodies into the area enclosed by the wall. To get the goodies (some of them are quite worth the trouble... such as Kraters of Might), you must get inside the area enclosed by the walls before the walls rise again, because after they rise, they won't lower again for quite some time. Once inside, you can collect all the stuff, and the walls can be opened from the inside when you want to get out again. (Note: if you are low on life/ammo, you shouldn't try this because the monsters that teleport in are among the tougher ones.)
OK, back to solving the puzzle. The five planets that you need are not found in the Heresiarch's Seminary itself, but on two sub-levels:
In some difficulty settings, there may be a nasty surprise waiting for you when the elevator reaches the bottom, so prepare your weapons... At the bottom, you'll see the portal leading to the Silent Refectory. The switch on the wall is to lower the elevator so that you can get out when you come back from the Silent Refectory.
The Silent Refectory looks like some kind of storage area with piles of wooden boxes. But the name is misleading, though... just take a few steps forward and you'll see what I mean :)
After you step off the marked boxes, go west and turn right (face north). Climb over the box in front of you and go all the way to the northern wall. Turn left and jump on the box that's also marked with a symbol. Walk on the boxes into the small at the back, and pull the switch there. (If I've lost you, this switch is on the northwest corner of this storage area.) Now, a door is open on the northern wall next to the marked box. Go into the room behind this door, which has windows looking into some kind of dining room. Enter the dining room and go to the southern end. There should be an opening here (the switch you pulled in the room with the spiral staircase opens this). This opening leads to an ascending passage which has windows looking into the room with the spiral stairs (you've probably been shot at from here when you were in that room).
At the end of the passage there's a switch that opens a door on the east side of the dining room. Pull the switch, go back to the dining room and enter the opening on the east side. There's a large pillar rising from the pit in the middle of the room. When you approach the edge of the pit, the pillar begins to open, and reveal a Sapphire Planet on a smaller pillar inside. To get the Sapphire Planet, aim carefully and jump onto the pillar. Don't panic! The pillar will start to lower when you jump on it. (I guess this is for those who missed and fell into the pit). Just wait a while and it will rise again. Jump back out, and return to the dining room.
As an aside, go to the northern wall of the dining room and push the wall with a purple dot a the top (push, ie., walk against it). If you push far enough, you'll see a small hole on the right with an item in it (I think it's a Banishment Device).
That's all for the Silent Refectory. Now it's time to go to the Orchard of Lamentations. Note: if you go to the room with the lava pool, notice that one of the dark openings is taller than the rest. This is a hidden passage that leads right back to where you first enter this level. Go to the portal now and get back to the Heresiarch's Seminary.
Now, a similar room will open on the other side (the WEST side) of the Seminary. Go west (outside the Seminary) and enter the room there. Go down the stairs, and follow the zig-zagging passage. Note that this passage is magical; after going along it for a distance you'll find yourself on the ledge at the east side of the Seminary, at the end of the southeast corridor, where the slaughtaurs are. (Actually what happened is that in the middle of the zig-zagging passage there is an invisible teleport that warps you to a similar passage behind the ledge where the slaughtaurs are.) There is a switch on the ledge; pull it, and a door will open on the wall in the area below the ledge. The portal behind this wall takes you to the Orchard of Lamentations.
Now you have to very, very fast in making your moves. Pull the switch, which you lower the platform at the end of the path. Quickly jump down and run as fast as possible to the nearest corner, before the entire floor rises and crushes you to death! Now you'll be in a small room with a switch that lowers the floor again. Your goal is to reach the middle, southern room in this place (look at the map). You do this by pulling the switch in each of the rooms and going quickly from room to room as the floor lowers and rises. When you reach the middle, southern room, there should be two switches. The switch on the east wall opens the central room in this crushing-floor area (look at the map and you'll know what I mean). Once this is opened, you can reach it from any of the seven rooms. There are also two switches in this room; one of them activates something on this level, and the other lowers the floor so that you can get out.
Once you pulled the switch, lower the floor and run to the north side where the exit is. Go back to the area with the slaughtaurs on the two ledges. The high place on the east has lowered; climb all the way up until you reach the slimy river at the very top. The Emerald Planet you're looking for is near the edge of the slime-falls (don't fall though, it hurts).
If you're greedy, or feel like bashing up some baddies, notice that the northern wall here has opened. Get your weapons ready, and go grab the porkalator. Monsters will appear at the sides where two other walls will open.
Whether you're greedy or not, notice that the east side of this area is also open now. Go down the stairs into the misty passage. This is another of those magical passages. It teleports you to the other ledge with the slaughtaurs. The Sapphire Planet is here. Grab it, and jump down the ledge.
There's nothing much else to do here, so go back to the portal and return to the Heresiarch's Seminary.
At this point, you should have found the first two parts of your fourth weapon. Go to the end of the southeast passage in the Heresiarch's Seminary. There's a switch here that you must pull: see if you can find it! (no, it's not the one on the ledge that opens the portal to the Orchard of Lamentations.) Hint: remember the first thing you did when you entered the Darkmere in Episode 2? (Remember what those trees looked like??) This switch will start rotating the four doors along the passage. Two of these doors lead to the ledges with the Chaos Serpents overlooking this area. The door we're interested in here is the southwestern one.
It leads to a room with many pitchers. The last segment of your fourth weapon is in this room. The pitchers also have lots of ammo in them. But watch out, though. One of them contains no ammo but a nasty, nasty surprise (I won't tell you which one it is: find out yourself... hehe)
So, you're greedy to get the Icon of the Defender. Well, go through the northwestern door on the southeast passage in the Seminary (see the previous section). This leads to a U-shaped passage that goes around the area with many Chaos Serpents (you've probably seen them through the window from the main hall of the Seminary). At each end of the passage there's a wall with a purple gem at the top. Activating either of these walls lowers elevators around the passage that takes you right into the room with the Chaos Serpents (have fun!). The Icon is on the water in the middle of the room.
Once you've fitted in all the planets, go to the north part of the Seminary where the magical area is. Doors will open on the side walls and on the wall behind the area. The door behind the magical area leads to a room with three portals and nine panels on the wall. Now, it's time to solve the next puzzle in this episode: the puzzle of the chapels.