All the keys reside in the Dark Aether version of the room the bodies of the warriors lay. With the Dark Visor, you'll easily be able to locate them all. You may remember seeing a warrior's body near your ship at the Landing Site, so let's go for that one first. Return to the Shrine Access area and look for a green door nearby.
Blow the blast shield off the door with a Super Missile and enter beyond. Drop into the main chamber of the Defiled Shrine to be greeted by four Warrior Ing - these creatures must know you're after the keys now. Show them who's boss by shooting one of the Light Beacons with the Annihilator Beam, easily defeating the quartet.
Now for the key. If you look around the chamber you won't see much, they trick here is the Dark Visor. Switch it on and look up at the south-western corner of the chamber. See that ugly floating thing visible now? Shoot it until your visor goes white, then switch back to the Combat Visor to see that it's now visible. Scan the object for your Logbook to reveal it as a Flying Ing Cache. It won't attack you at all, so open up on the ugly eye to blow it apart, revealing the blue Sky Temple Key 8 within. Jump up to claim your prize - only eight to go now.
You've now cleared out this portion of the Sky Temple Grounds, so return to Aether by way of the portal at the Base Access area. Back at the Temple Grounds, we've got two more keys to locate here (and you may as well clear the area of its remaining items before scouring Agon, Torvus and Sanctuary). For now, travel to the eastern side of the grounds to the Temple Assembly Site.
There's an inactive Dark Portal hiding in a small alcove here near the southern door, use it to travel to Dark Aether. Once in the Plain of Dark Worship (the site of a missile you picked up what seems like an eternity ago, if you don't have it yet go grab it from the tall mutated Ingworm structure ahead), use the Seeker Launcher to bust open the purple blast shield on the door nearby.
Proceed through the twisting tunnel beyond, shooting the overgrown Venom Weed to clear your path. Beyond this tunnel lies the Accursed Lake - the location of another Sky Temple Key. Step forward to the edge of the sickly lake and defeat the Hunter Ing emerging from the depths. Scan one of the Dormant Ingclaw around you for your Logbook, then switch on the Dark Visor.
You'll spot the Flying Ing Cache way over on the other side of the lake. Either jump in and wade across or take the path around the left cliff side. Watch out for a second Hunter Ing emerging from the lake, take it out then blow open the Flying Ing Cache to claim Sky Temple Key 9.
Only one more key to find around here. Return to the Plain of Dark Worship and transit back to Aether. From there, travel to the Sacred Path region and look for an inactive Dark Portal hiding in an alcove above (and beside) a War Wasp Hive. Once on Dark Aether, you'll be greeted by two Dark Pirate Commandos. Boy do the Ing love these creatures. Energize the scattered Light Beacons with the Light Beam to try and catch them off guard.
With both targets down, let's pick up the item hidden behind the sealed door at the mutated Ingworm structure. Does the door look familiar? Yep, it's another sonic security system. Switch on the Echo Visor and break out the Annihilator Beam. Shoot the door to hear the sequence of tones, then look for the emitters and input the correct sequence to open access to the final Beam Ammo Expansion!
With Beam Ammo Expansion TG.01 secured, let's move on to that Sky Temple Key. Beyond the Profane Path lies the Phazon Pit. A Dark Tallon Metroid will greet you from the Phazon pit below, take it out with Super Missiles and the Light Beam (or give it a Power Bomb if it grabs you). Screw Attack or Grapple across the pit to reach the door ahead and move on.
Outside is the huge open Phazon Grounds area. Take care around the numerous Phazon deposits. Before leaving here, take a look out over the cliff beyond where the GF ship rests on Aether. See those Dark Tallon Metroids floating about? (one's carrying a dead Space Pirate around) Use the Dark Beam on each, freeze them with a charged hit and send a missile their way to finish them.
With all targets cleared out, look out over the cliff again at the structure way off in the distance. Clear off the Dark Tallon Metroids hovering over the gap, then Screw Attack across the gap to reach Missile TG.09 waiting there. Screw Attack back to the mainland and exit the area by way of the purple blast shielded-door on the southern end.
Beyond here lies the Reliquary Access - a cave filled with tiny and deadly Ing particles. Scan them for your Logbook if you haven't come across them yet - these Ingstorm will render this area impassable unless you have the Light Suit - scan the two unfortunate Luminoth bodies nearby to learn of their fate here.
With the Light Suit equipped the Ingstorm are harmless, so proceed on (touch the tiny red particles to see them pop). Beyond this cave is the Reliquary Grounds - almost there. Switch on the Dark Visor to see in this surprisingly dark area. Step forward to the open area to be ambushed by a whole group of Warrior Ing. Deal with them all before moving on.
Climb up to the only other door in this area and step inside the following grove. Inside you'll find a dead-end filled with Ingstorm particles, so you know what to do. Switch on the Dark Visor to see the Flying Ing Cache, then bust it open to claim Sky Temple Key 7.
With this task complete, you'll have now secured all the items to be found at the Temple Grounds and Sky Temple Grounds (sans two items) if you've been following this guide. Otherwise, go and pick up the Sunburst and anything else you've missed. Return to Aether by way of the portal back at the Profane Path. There's now two more keys to find in each of the three major regions of Aether, so seeing as we're nearby the Sanctuary Fortress lift let's head there first.
Proceed onward to the Fortress Transport Access and make your way through, dealing with the dual Luminoth Turret defenses. Down the end of the corridor you'll spot that giant yellow light beam that previously only gave you temporary blindness if you stepped through it. Not anymore. Step into the beam to be teleported up to a hidden chamber (thanks to the Light Suit) where Energy Tank TG.03 awaits. With that you'll have cleared out the Temple Grounds so let's move onto the Sanctuary Fortress.
Once back in the fortress, travel to the Reactor Core and take the left door down the passage into the Sanctuary Map Station. See the giant yellow light beam down the ramp ahead? Step inside it to be teleported instantly up to a hidden chamber where Missile SA.09 awaits. With this item secured travel back to the Reactor Core and make your way to to the Hall of Combat Mastery. Once there, use the portal terminal to transit to Dark Aether. Now let's go look for another Sky Temple Key.
Proceed through the door on the western side of the Culling Chamber to locate yourself in Dark Aether's version of that area where the four rotating gyros were. Except this time you're looking at not much more than a massive chasm between your ledge and the doorway ahead. Only one thing to do now, switch on the Dark Visor to reveal a sneaky invisible platform hovering back and forth across the ravine. Use it to reach the door ahead and move on through.
Beyond here is the Hive Reactor. Descend to the bottom of the shaft and deal with the Dark Ingsmasher lying in wait. Deal with the monster (and any annoying Inglets), then fill up your payload at the Ammo Station down the right tunnel next door. Save you game also down the left path before moving on if you wish. Demolish the yellow blast shield on the door at the southern end of the room with a Power Bomb and proceed through.
Beyond you'll discover a large chamber where a Nullified Light Beacon resides. A swarm of Nightbarb will streak around it, so do the sensible thing and energize the Light Beacon to rid the chamber of those pesky bugs. Cross the chamber (carefully) and proceed through the tunnel beyond. Watch your radar near the end of the tunnel, as a swarm of small creatures will pour from ahead, intent on flying into your face.
Quickly scan one for your Logbook, these Ing Larva Swarm won't be much of a hassle, so take them out with ease. Exit the tunnel ahead to locate the Hive Entrance - a massive chasm where no bridge exists. The Flying Ing Cache hiding here is directly above you - reaching it will be tricky. See that tall yellow light beam on the structure way across the chasm? That's where you need to go. Firstly, hit the Light Beacon here with the Annihilator Beam and scan the Super Crystal for your Logbook if you haven't done so already.
Clear the way to the structure by locking onto and destroying all the Dark Preed floating about. Now for the tricky part. You'll need to Screw Attack across the chasm now, try to launch from one of the two small platforms jutting off the edge. It might take you a few tries to clear the gap, once you do jump in the light beam to be teleported above.
Now for the return trip. If you look back at the fortress and switch on the Dark Visor you'll see the Flying Ing Cache way over ahead of you. Screw Attack over there and blow it open to recover Sky Temple Key 5. With four keys now recovered overall, let's go hunt down the second one in the fortress. Carefully climb down and return to the Culling Chamber.
Once there, return to Aether and take the lift nearby up to the second floor of the fortress. If you check your map, you'll probably notice a tiny room attached to the Dynamo Works which is yet to be explored. That's where we'll be going next. Travel around to the Sanctuary Temple and follow the path towards the Worker's Path, the same path you took earlier when going to fight that horrible Spider Guardian.
Once inside the Dynamo Works, travel through the network of tunnels until you reach the chamber where you scored the Spider Ball some time ago. Blow the yellow blast shield off the door before you with a Power Bomb and enter the chamber beyond. You'll discover an inactive Dark Portal housed within the large chamber. Energize it and transit to Dark Aether. Once there, exit the room and roll through the tunnel to find a very different area of the Hive Dynamo Works.
Switch on the Dark Visor and look over at the platform on the far side - there's the Flying Ing Cache. Climb up the Spider Ball track on the wall beside the door, then boost yourself across to the hovering sentry pod. Boost across to the other pod at the right time, then boost across to the next Spider Ball track running along the northern wall. Follow it to the platform, then deal with the Flying Ing Cache to retrieve Sky Temple Key 6.