The Vault of Riches
The Vault is where you're finally going to obtain the Screw Attack, but not until you maneuver your way through a lengthy puzzle. To begin with, drop down behind the Screw Attack's little prison and use the bomb slot; this will turn on a series of lasers that you'll need to reorient with spinners. Secondly, scan the panel at the bottom of the vault to lower a bridge that'll lead to a dark portal, then head on through to the Vault Attack Portal, where you'll need to grapple across the chasm, turn around to scan the Dark War Wasps, then activate the second portal here that'll take you back to Aether.
Back in the Vault, you'll find that you have access to the four laser stations now, so kill the Rezbits and use the spinners until each of them locks into place. When that's done, return to the portal, grapple back to the other portal, and return to the bomb slot and use it again. This will unlock the vault, giving you access to the Screw Attack.
Although the Screw Attack can be used to hurt things, in the context of the game, you're mostly going to be using it as a movement aid. To begin with, you can use it to reach the door of the Vault; by continually hitting the B button after you jump, you can greatly extend the distance of your leaps. The trick is to not tap it too rapidly, though; just hit it, then glide for a bit until you start to fall down, then hit it again, and so forth. You can only hit it five times, so you'll need to time it right to get across some of the gaps, especially the one in the Grand Abyss.
Now that you've looted the Sanctuary Fortress, it's time to find the keys to the Dark Sanctuary Temple and finish off the beast that lies in wait there. To begin with, though, let's grab some more expansions in the area. First off, return to the Watch Station and use the portal. The Missile Expansion immediately next to the dark side of the portal requires a new technique; if you scan the wall here, you'll note that you need to use the Screw Attack to bounce off the walls to reach it. The timing for this can be difficult; you need to actually be in a Screw Attack before hitting the first wall, then hold down your jump button after you make the two jumps to reach the missiles.
After you obtain those, head to the Central Area Transport West. Another set of Missile Expansions await you here. If you drop down from the upper level to the one beneath it, you'll notice a series of three ball tubes nearby. Drop down the leftmost one, then head right twice to find a Missile Expansion.
At the bottom of Transport West, you'll find yourself back in Main Research, where you'll need to step through the portal and find the blue door on the dark side to reach Central Hive West Transport. You'll need to wall jump up the entire vertical length of this passage with your Screw Attack to reach the first Dark Sanctuary Temple Key.
The second temple key is accessible via the portal in the Hall of Combat Mastery. Head there to wind up in the Culling Chamber, where the key is held at the end of a spiderball track.
Lastly, the third key can be found off of the Hive Dynamo Access, accessible via the elevator just off the Culling Chamber. You'll need to blast your way through another sonically-locked door to reach the Hive Gyro Chamber. You'll need to spiderball your way from the bottom of the chamber to the very top to reach the key, being careful to avoid the Darkling Tentacles on the way.
The Ing Hive is very close to you; it's located past the blue door on the southern side of the Gyro Chamber here, in fact. Before you head in, though, blast through the northern blue door to find an ammo station, then missile the red door to save your game.