The Catacombs (Master Mode)
Red Cave 1
There are two Stones that you can Take if your pants are feeling too light. Go through the right entrance.
Red Hollow
There are two large Red Crystals sticking out of the ground. Use the Metal Bar on them to pry them out. Head back to the Red Cave 1.
Red Cave 1
Go through the left passage.
Red Shaft 1
Go down the ladder.
Pit
Go through the passage.
Blue Tunnel
Go through the right passage.
Blue Cave 1
Use the Metal Bar to chisel out three Blue Crystals, then Go back to the Red Shaft 1
Red Shaft 1
Go through the left entrance.
Red Cavern 1
Use the Metal Bar on the Red Crystal. There's also a Skull in here you can take if you want. Go back to the Red Shaft 1.
Red Shaft 1
Go through the right passage.
Den
Try to Go forward and you'll be accosted by twin gargoyles! Use the Silver Orb on them to release the Lightning Elemental and startle them, and they'll flee back into their hovels. Go through the middle entrance.
Red Tunnel 1
Open the Threadbare Sack on the ground to find the Timeworn Scroll, Tablet, and a Blue Crystal. The Timeworn Scroll is some lore, and mentions the fact that there are some easter eggs from the original Shadowgate and Deja Vu games down here. Only one of which we'll find along the path I'm outlining here. To continue on with the quest, Go through the left entrance.
Red Cavern 2
There's a Skull in here you can Take. Go through the passage.
Cavity
Go up the ladder.
Yellow Cave 2
Go through the passage.
Yellow Passage
Go through the passage
Yellow Tunnel 2
There are three large extra-glowy crystal stalagmites growing out of the ground. If you Look at them, the description reveals that they're translucent black crystals. Use the Metal Bar on at least one to obtain a Black Crystal. You can mine the others if you want to, but they're optional. Go through the middle passage.
Hollow
We need to Take the White Crystal sitting on the floor beside the mirror. You can also Take the Cuthegar I and Cuthegar II Books if you want some lore. The Markings Book and the Glyphs Book are indecipherable, so you don't have to Take those either if you don't want to. The Thin Scroll will disintegrate if you try to Open it, and theDisconcerting Key does not do anything in unless you're going for some hidden deaths. With the crystal in hand, head back to the Red Tunnel 1.
Red Tunnel 1
Go through the right passage.
Red Cave 2
Go down the ladder.
Red Shaft 2
Go through the entrance.
Rendezvous
There's a gong in here that you can hit with the Mallet you picked up in the Music Room, but I don't recommend doing that if you like staying alive. Like other easter eggs to the original game, this has some dire consequences. Go through the right entrance
Red Cavern 3
Another Skull ripe for the Taking. Go through the only entrance in here.
Red Shaft 3
Go up the ladder.
Red Shaft 4
Go through the passage.
Red Cave 3
You can Take the Skull and two Stones in here if you are so inclined. Go through the passage.
Red Mine
Yet another Skull you can Take. Go through the passage.
Red Tunnel 2
Go through the right passage.
Chasm
There's a small rock pillar just before the chasm proper, Go to that stone to reach the Crystal Puzzle.
Rock Table
You need to place certain colored crystals in certain slots to solve this. In Master Difficulty, you start with empty rows of holes. As long as you've collected enough crystals (which you should have if you've been following along), you're all set to solve this. If you're missing any, go explore the catacomb a bit more to mine whatever you still need.
The goal is to match the crystals with the peaks depicted on the mural in the Ornate Chamber. Start by Using the Red Crystals on all of the slots in Row 4. Then Use Blue Crystals on the last three slots on the right of Row 3. Use the White Crystal in the third hole from the right in Row 2, and finally Use the Black Crystal in the third hole from the right in Row 1. Use the Crysalys spell on the Rock Table to complete the puzzle.
Chasm
A fancy bridge of light appears across the chasm, which is something I really Dig. Go across it and through the doorway on the other side.
Yellow Cavern
Open the Torn Bag on the ground to get the Confusing Scroll, Red Gem, Black Gem, Gold Bar, and Bone Key. None of these do anything remotely useful, but it's fun to have things, right? Go through the passage.
Yellow Cave
Go through the passage.
Yellow Tunnel
Go through the passage.
Skull Door
Use the Invokan spell on the obelisk to summon Lakmir for a final time. Note that if you are wearing a goblin disguise, he'll panic and teleport you to the Boneyard. Assuming you're wearing acceptable clothing, he reveals that the Staff of Ages requires an empowerment involving a great sacrifice in order to be fully formed. Use the Silver Orb on Lakmir to capture his spirit within. Use the Stave with the Golden Thorn, then Use that combo on the Silver Orb to create the Staff of Ages. Note that the Silver Orb won't combine with the Stave unless you've first captured Lakmir's power.
Now we just need to open up the door. If you looked at the Tablet you picked up earlier, you'll see that it has a picture of a hand, something that looks like the Bladed Sun, and then four vertical lines. Following those directions, Use the Bladed Sun on the recess located on the ring finger (fourth finger across from the left), then Use the Platinum Horn on Thyself. Assuming the Bladed Sun was properly placed, the door will open and allow you to Go through to the final battle.
Summoning Chamber
The great Behemoth has already been summoned. Are we too late?! The Warlock Lord will summon three glowing orbs that circle and annoy the beast. In order to end Talimar's evil machinations, Use the Staff of Ages on any one of the three orbs to break his spell.
Now just Enjoy the ending!