You begin this level at the top of a long elaborate hall that descends ahead, down several landings and stairways. Directly behind you is the Blue Door. There are a bunch of floating spores that you can set off to clear out many of the enemies that will show up when they hear you. Near the lower end you'll find the Yellow Door on the left and the Green Door on the right. After you go down the last set of stairs to the lowest level, a hidden door will open. Go back up to the second-highest landing and look in one of those side areas: a hidden area has opened here, with a lot of ammo inside.
Go down to where the stained-glass windows are. On either side are doorways leading to dropoffs into a very large chapel-looking room. If you push the spores over the edge, more will spawn. If you stand in just the right place, the spawning ones will immediately fall over the edge. This doesn't serve any purpose, but they're fun to play with. When you've had your fun here, jump down into the big chapel. You'll see that most of this room is taken up by a huge formation of ice: this level's namesake feature, the glacier. Walk and slide your way along the ledges and platforms to the top, and collect the Yellow Key. The teleporter nearby goes back up to the main hall, but there are several bonus areas down here in the chapel worth looking at.
When you pick up the Yellow Key, two doors on either side of the stained-glass windows will open. There's a dimly-lit loop passage inside. Around back you'll find a flashing alcove. Look for a hit a switch along the passage, and go back to the alcove. The floor has lowered here, leading to a dark passage. Watch out for the Weredragons in here. Take the teleporter at the end to a pentagonal room with Wings of Wrath, other items and another teleporter. This teleporter goes back to the great hall. Go back to the chapel and walk in front of the stained-glass windows. Several will open, leading to a long room with a lot of ammo and items. Back in the chapel, you'll see a large stained-glass window well up on a wall, with an Inferno Orb and Greater Runes on the ledge. You can get to this most easily with Wings of Wrath, but can jump for it too. You'll need to get a long running-start to get up enough speed to reach the ledge. The window is a hidden door that opens, with an enemy in the room inside. (If you see you're missing a secret when you exit the level, go back and enter this room. The room itself counts as a secret, even though only the Iron Lich was inside.)
Long icy room
When you're done in the chapel, teleport back to the main hall, and enter the Yellow Door. In here is a long room, with an ice formation spanning the room in a sunken section of the floor, and several smaller rooms along either side. (Possibly, this complex is meant to be under an ice-covered region, which would explain the ice, although you'll come across a lava pool later. This is also one of only a handful of levels in the game that's completely indoors; i.e. you won't see the sky anywhere.) At the far end you'll see a dark room through a window. There are Disciples of D'Sparil hiding in the dark in here which will fire at you. Watch out for enemies in the side rooms that see you when you walk by: it's easy to get ambushed.
After clearing out the enemies, explore the side rooms. Have a good weapon ready: there are Weredragons lurking around, and there isn't much room to maneuver. In the first room that was on your right when you first came in here, you'll find a dark pillar that looks like it should lower but never does, at least not in single-player mode. In the second right-hand room is the Green Key. (Be ready for a nasty ambush when you pick it up.) The rest of the rooms have Time Bombs of the Ancients.
Lava and empty rooms
With the Green Key, go back to the main hall and open the Green Door. A corridor goes up a stairway, overlooks a large, tall hall with a big lava pool and fenced-off area, and continues down and around a corner. Go down to the lava hall. In front of the fenced area you'll find the Blue Key. You'll see some interesting things inside the fenced area. You'll be able to get into here in a bit. Collect the Blue Key, but before leaving, go to those big decorated-metal columns on the other side of the lava pool. Activate the wall between the torches on the right-hand one: this is a hidden door leading to a teleporter. Take the teleporter to a small room with a semi-hidden door in a nook. Turn around and look behind you: the section of wall with the patterned texture is another hidden door to a room with a Phoenix Rod. The door in the nook goes out to the big chapel with the glacier. (You probably saw what looked like a hidden door between the torches. You now see that it is, but it only opens from inside.) Take the teleporter you landed on, and activate the wall ahead: you'll be back in the lava room; from inside the other column.
Go back up to the corridor, and continue beyond the lava room, down and around the corner, to a series of empty rooms. First, look for the misaligned texture on the wall across from the doorway, near where the floor turns into dark metal: there's a hidden compartment inside with an item. Explore and follow the series of rooms to the end, where you'll get a Mystic Urn. Look to the right of where the Mystic Urn was for a section of wall with a misaligned texture. This is a door to a hidden room with a weapon. Once you've seen all these, you're done in this area.
Go back to the upper end of the main hall, where you began the level, and open the Blue Door. Note the wall with the gold symbol ahead. The switch to the left opens the door with the exit symbol. Inside is the exit portal. But don't leave yet: there's more to see. Open the exit door, fight the enemy, then step inside the room and back out. When you stepped into the room, that wall with the gold symbol opened. There are two teleporters inside. The right-hand one goes to that room behind the window in the long room with the ice floor. There's a Map Scroll and other items in here. The left-hand teleporter goes to the fenced-off area in the lava hall, where there are more items. The switch in the lower center area activates two lifts, allowing you to get to either of the two upper areas. The teleporter in the upper area opposite where you entered leads back to near the exit room.
When you're finished and have seen everything you wanted, go back to the exit room and enter the exit portal to resume your main mission with E2M5: The Catacombs. (Take a look at the inside of the exit-room door: the texture is misaligned. This is a rare error in this game's levels.)