Sanctuary Fortress Items
Missile Expansion: Head to the Sanctuary Map Station and ride the beam of light there up to a little room where the missiles await.
Missile Expansion: Head to the Sentinal's Path and use your Annihilator Beam and echo visor to open the sonic door here.
Power Bomb Expansion: There's a sonic door at the bottom of the Main Gyro Chamber, so unlock it and use the kinetic cannon to find the expansion.
Ing Hive Keys and Items
You should actually have all of the items from this section of the game (and should be at 100% by now), so now all you need are the Sky Temple Keys!
Sanctuary Key 8: To get this one, retrace your steps to the Spider Guardian's lair (in Sanctuary Fortress), then head to the locked door where you picked up the spiderball and bust through. The portal within will lead you to the Hive Dynamo Works, wherein you'll need to pass through a little spiderball course to find the Ing cache.
Sanctuary Key 9: This one's located in the Hive Entrance, which is the Dark Aether counterpart to Aether's Sanctuary Entrance. You'll need to Screw Attack your way across to the beam of yellow light, ride up, the Screw Attack back to the far side and grab the key from the cache there.
Now you're ready for the end game!
Sky Temple
When you've gotten all of the items that you want, and are ready to return the keys to the Sky Temple, head for the Hall of Eyes in the Temple Grounds and use the portal there. You might want to hit up an ammo station before you do this, as there isn't one before the final fights.
Before you deposit the keys into the center of the Sky Temple Gateway, be sure to scan anything in the room, if you haven't been here before, as using the keys will retract the pillars and make them unscannable. It'll also open up the path to the Sky Temple Energy Controller, though, so you'll want to do it and head on up. There's a save point in the Controller, so use it before moving on up to the Sanctum.
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