After you enter the Fire Sanctuary, hit the fruit above the lava pool to create a platform and hop over. Hit the next fruit and ride the platform to the right, killing the two Bokoblins shooting at you. Go around the left to reach a chest with a key. Drop down and enter the door. Head down the stairs and through another door.
Now head right until you reach an opening. Jump down and on top of the platform. The Magmanos will eventually rise it so that you can hop onto the closest ledge. Kill the Bokoblin with your bow then cross the vines to reach the platform on the right. Drop down and enter the door on the left, next to the Bird Statue.
Location: Fire Sanctuary
Attacks: Swipe, Dark Breath
Effective Weapons: Sword
Strategy: Dark Lizalfos have heightened battle skills compared to their standard counterparts. They're still possible to beat, however, provided your own skills are up to the task. They also pack quite a punch and can take a decent beating before going down, meaning it'll take endurance in addition to skill and precision. Be very careful not to get hit by their Dark Breath, as that will block all of your abilities for a rather long period of time.
Once the Lizalfos is dead, enter the next room. On the northern wall there's a lava spring (Stone face) that's blocked. To the left of it, on the west wall there's an opening with a blue rupee, and some bombs behind it. Send your Beetle up there and grab a bomb, then do a circle around the corner and run it into the lava spring to free it up. Hit the fruit above the lava nearby to create a platform, which will now float due to the stream. Ride it to the far west ledge and enter the unlocked room.
Ignore the Mogma for now and just head right. Use the bellows to clear the heated dust and take the small key from the chest at the end of the corridor. Head back and enter the locked door in the previous room. Stab one of the fruits so that it sticks to your sword, then go to the upper level, in front of the frog head, and toss the fruit at it. Enter the next chamber and drop down to start a fight with two Magmanos. Use them to raise either one of the two platforms to rach some water fruit, stick it to your sword, then toss them at them. This will petrify hem allowing you to kill them.
After they're taken care of, go through the door on your level, down the stairs and pull the lever to release the Mogma. He will upgrade your Digging Mitts to allow you to burrow down into underground tunnels.
Nearby you'll find three dirty mounds. Burrow down to enter a small underground section. Destroy the small stones as you make your way to the bomb. Hit it from below to make it roll into the big stone on top. After it's gone, you can reach the ray of light, where you'll emerge to the surface again. Just to the west is another mound you can bury down through. In here go around to the red piston and hit it to open the gate above. Go out and through the newly accessible door.
Turn right and press the switch at the end of the corridor to create a shortcut to previously visited areas. To progress however, you need to go east. Kill the Bokoblins and grapple yourself to the right pillar, then to the other side. Enter the room and go to the south most part to find a mound you can dig down through. Once underground, go all the way down, then right, and hit the piston. Go up now, and make your way to the very top. Hit the piston here to make the gate move down. Head back to the entrance (You'll have to go around, past the first piston, since the second gate now blocked your short path).
You'll now be able to get to a water fruit nearby. Stick it to your sword and toss it at the frog head. Pull the lever in the previously blocked off room to release the Mogma. Get the dungeon map from the chest, then place a bomb at the east wall of the room. Dig down the mound, defeat the centipede by hitting its tail three times then go left and go up to the surface again.
Get the small key from the chest and climb up the vines. Drop down to where the fake wall was. Now head all the way back west, to the room with the bird statue. Enter the locked door and drop the water fruit into the lava ahead of you to cross over. Head up the stairs and enter the west section. Follow the path around the right side and dig down the mound at the end.
Go left and hit the piston. As you enter the upper area the Mogma will start running. Catching him is a tad tricky - try to catch him at an intersection or corner, and quickly run into him. It's frustrating but doable.
Once outside, head left and hit the water fruit above the lava. Go back past the mound and throug the newly opened gate to jump onto the platform and ride it to the east ledge. Go outside an dig down the mound next to the bird statue.
Make your way up, and clear the three stones in the corner in order to be able to toss the bomb at the rock above. Once the lava starts flowing, sprint back. Make use of the stamina fruit. Once you're outside, hit the switch to open the gate, creating a shortcut to the exit.
Go down the stairs and drop the water fruit to create a now drifting platform. Ride it to the central area. Go behind the tablet and jump off the left edge, towards the statue with the closed eyes. A platform will appear in front of it on which you'll land. Enter and drop down to fight two Dark Lizalfos. Once they're dead, sprint up the wall ahead and enter the door. Make your way up the tower and enter the top chamber.
Go down the mound among the statues. Head up to activate the first light pad, and righ to activate the second one. Now head down (Do not cross the light pad above the bomb!) and roll the bomb upwards to clear the rock and allow you access to the third pad (Go around to reach it). Number four is the one next to the bomb, and number five the one on the top left. Defeat the centipede the same way as the previous one, and exit. Head west through the door to get back to the central hub. You can now access the boss room.
After a while he will summon up two swords. From this point onward he will occasionally summon a bunch of flying daggers around you. Depending on whether they're arching above you or surrounding you, do either a vertical or horizontal spin attack to get rid of them. Use your shield to deflect / defend against any daggers he sends flying your way. Once he jumps up into the air, keep running to avoid him coming down on your head. Once he hits the ground is the perfect opportunity to hit him. You can also damage him when he walks up for a sword duel or teleports himself behind you similarly to the first fight in the Skyview Temple. In both of those cases you'll have to watch out for his guard and slice appropriately.