When you go through the shadow gate that leads to the final area, you'll start in a room with three shadow gates. All three gates will take you to the same place -- another set of those purple islands in the shadow realm. To get out of the area, go through the eastern gate, then the southern gate, and then the western gate.
Fire Spout Section
You'll find yourself at the eastern end of a long corridor. Your objective here is to get to the western end. However, unlike some similarly-themed puzzles in the Shadow Ruins, this one is pretty easy. Simply press the SHIFT key at the templar knight statues (#1) to briefly raise the platforms (#3) to shorten the gaps so you can jump to the west. Complicating matters slightly is that fire spouts line the walls and spew out fire every few seconds, but the fire spouts do little damage, and they're mostly there to distract you rather than hurt you.
If you miss a jump and land down below, you'll have to head north, climb a ledge, and then enter a shadow gate leading to another set of purple islands. To get out of this set, go through the eastern gate, then the eastern gate, and then the western gate.
Finally, if you use the southern templar knight statue (#2), then you'll briefly open a secret door (#2a). To get to the door in time, you'll have to use the northern statue (#1), then use the southern statue (#2), and then quickly jump to the west and run to the door. Inside, you'll find some crates and a level 9 trinket chest.
Once you're finished with the section, head through the shadow gate on the western side (Exit B) to move to the next section.
Shadow Altars Section
Your goal in this section is to acquire two shadow crystals (at #4 and #5) and place them in the shadow altars (#6) in the central room. Once you've done that, light beams will activate the central altar (#7), and a staircase will form around it. At the bottom of the staircase you'll find a shadow gate that leads to the next section.
The eastern shadow crystal (#5) is easy to get. All you'll have to do there is defeat an Athena giant and grab the crystal from its corpse when it dies.
The western shadow crystal (#4) is more complicated. In that room you'll meet a pair of shadow wraiths that can't be killed, and you'll find the crystal floating in the air near the ceiling. The center of the room is actually some sort of weird wind machine, and it will blow you around when you get near it. What you'll have to do is jump towards the center of the room, let the wind machine push you upwards, and then grab the crystal. There seem to be two ways to do this: do a backflip into the machine, or else take a running leap into the machine from one of the platforms in the corners of the room. Once you've grabbed the shadow crystal, you'll then be able to kill the two shadow wraiths if you want.
Shadow Realm (2)
Here it is -- the last set of purple islands in the game! Hooray! This set is fairly large, but if you head through the eastern gate, then the southern gate, then the northern gate, then the western gate, and finally the southern gate, you'll get through it and enter the last section, where you'll find the Lord of Shadows waiting for you.
You'll find yourself in a room shaped like a pentagram, with a "plume of protection" in the center (#10). Nauselom, the Lord of Shadows, will also be there, and he won't be thrilled to see you. At the start of the battle, what you'll have to do is dodge or block Nauselom's spells, and then attack him in between casts. Once you've done enough damage, he'll disappear and drop a shadow stone. You can use this "intermission" to finish killing off any of Nauselom's minions who happen to be left in the room, and to save and heal. But once you put the shadow stone upon a guardian knight statue (#8), one of the walls (#9) will disappear, revealing a new guardian knight statue, and you'll have to battle Nauselom again to get another shadow stone.
After placing five shadow stones upon the statues, two things will happen. The "plume of protection" will disappear and be replaced by the rod of divinity (a Relic of Power), and you'll be able to start fighting Nauselom for real.
Nauselom can be tough to fight. He casts a lot of spells, he summons minions (including wraiths and banshees) to help him, and he's resistant to magic. However, we've heard some conflicting reports about what it takes to kill Nauselom. Some have said that only the rod of divinity works against him, while others have claimed that they've had success with regular weapons. From what we can tell, you have to hit Nauselom once with the rod of divinity (to stop him from regenerating his health), but after that, you can use anything you want to kill him.
Note: You don't have to attack Nauselom's minions, unless you find them really annoying. Nauselom will spray so many spells around that he'll kill them himself.
When Nauselom dies, he'll drop a scepter of shadows. If you're playing the Collector's Edition, then he'll also drop a shadow lord amulet. If you take that amulet to Staroxia in the Forbidden Lands, then she'll offer you a quest to become a shadow lord (a third tier class). Finally, after the battle a "gate of ascension" will appear in the center of the room (#10). You can use the gate to exit from the Shadow Ruins.
Note: In MMXII, the battle with Nauselom is a little bit buggy, and you'll be able to take the Rod of Divinity as soon as you enter the room.
1 - Templar Knight Statues
2 - Templar Knight Statue
3 - Platforms
4 - Shadow Crystal Room
5 - Shadow Crystal Room
6 - Altars of Shadows
7 - Altar of Shadows
8 - Guardian Knight Statue
9 - Wall
10 - Plume of Protection / Relic / Gate of Ascension