When you have the energy tank, return to the Catacombs and use your gravity boost to get you to the bomb slot under the water. Activating it will let you through the portal above. Your only exit from the Dungeon will take you through a few rooms until you reach Undertransit One, where there's a hidden Missile Expansion. It's on the left side of the central bubble here; you'll need to use your burst to get past one of the gaps in the pipe and jump from there to reach the missiles.
In the Crypt, use your dark beam on the first crystal you see, then jump across the shifting platforms to reach the tunnel beyond the light door, which will take you to the Undertemple Shaft. Your first stop here will likely be the save point at the top of the room; it's in the same position as it is on Light Aether. When you load up on your health there, drop down to the bottom of the room and use the bomb slot to rotate the corridor one turn, so that it lines up with the blue door, then head through to reach the Sacrificial Chamber again.
Boss Fight: Grapple Guardian
The Grapple Guardian is one of the easier boss fights you're likely to encounter in the game, if only because it doesn't move very quickly and follows a pretty strict pattern of attack. The Guardian is essentially an overgrown Grenchler, with an added weakness (the glowing eye) and the ability to grapple you.
The first form is pretty simple to defeat; just use your charge beam to hit the Guardian's eye over and over again. Eventually, you'll anger it enough to force it to use its grapple beam on you. If you're near one of the large crystal pillars, though, you can strafe behind it, which will cause the grapple to lock onto the pillar instead, letting you get behind the Grenchler and unload a super missile on its butt. Repeat the process until you blow the butt off, at which point the Guardian will change its pattern a bit.
The grapple will no longer lock onto the pillars at this point, so you'll just need to avoid it. It shouldn't be much of an issue, though, as you can easily finish off the beast by aiming charge beams down its maw; one or two blasts will be enough to drop its Phazon shield, after which you should have enough time to use another charge beam on it, doing a good amount of damage. Keep this up until the beast is dead, and you'll grab your grapple. You can then make your way back to the Crypt afterwards and warp back to Aether.
When you reach Torvus Bog again, you'll have some running around to do.
1: Grab another Missile Expansion in the Path Of Roots, thanks to your new Grappling Hook.
2: There's another Missile Expansion underwater in the Torvus Lagoon that's accessible now that you have your Gravity Boost.
3: Head to the Abandoned Worksite and grab another Missile Expansion that's now accessible with your Grapple.
4: Head over to the Forgotten Bridge and use the portal there. From the Dark Forgotten Bridge, head south (check your compass on the map screen) until you reach the Venemous Pond, where the last Dark Torvus Temple Key is located.
5: You'll want to grab the Beam Ammo Expansion in Cache A (which is in the same location as Aether's Save Station A.
6: Then head through the portal in the Portal Chamber (you can find a jumping path near the door leading from the Poisoned Bog if you look around) to grab another Missile Expansion.
Now that you have your dark superweapon, it's time to use it on the boss of the Dark Torvus Temple. Make your way back to the Torvus Bog via the elevator near the Portal Terminal. Proceed from there to the portal in the Forgotten Bridge, save your game, and head into the temple for the big boss. Before you use your keys in the center of the Dark Torvus Temple area, though, check out the two offshoot corridors around the keystands, where you'll find an ammo resupply and another energy tank, which should indicate the kind of fun you're about to have.
After you enter the temple, you'll spot a huge cocoon. After scanning it, destroy the four pedestals holding it up with missiles; this will launch you into the first part of the boss fight. This guy can be pretty rough, so if you wish, you can skip down to the next section and follow our instructions to grab the Darkburst before heading in. It's unlocked at this point, but is a lengthy detour, and isn't absolutely necessary for this fight, so we recommend you give the boss a shot before grabbing it.