Sky Temple Grounds
Now it's time to go collecting the keys you need to get to the last Dark energy controller and meet the boss Ing that control it. If you played the previous game you may remember there was a similar section where you had to chase down Chozo artifacts. The first step is to get clues to the locations of the Key Bearers, Luminoth who managed to locate the keys. You get the clues from A-Kul, the one Key Bearer who managed to survive long enough to bring a key to where it's supposed to go.
War Ritual Grounds
Go to the Hall of Eye, which was on the route to Torvus from the Temple Grounds, and use the portal there to get to Base Access, and from there go to the War Ritual Grounds. We where there previously to get an expansion. This time continue through to the next area.
Follow the Morph Ball tunnel to reach the main area which is guarded by Corrupted Sentreyes, which you may remember from the Abandoned Base, but which you can now destroy with a charged Light beam. There is both a Green door and a Purple door here, but for now we'll just do the Purple one.
Get past the Darkling Tentacles to the other end of the passage.
Sky Temple Gateway
This is where you'll eventually take a lift to the Sky Temple, but first you need to get the keys. Scan the tops of the pillars to get nine clues, and scan the Luminoth at the base of the tenth Luminoth's (who left the clues) testament. If you're going after 100% scans and have already gotten some keys then you have to be careful to get the clues before placing the keys; once a key has been placed the corresponding clue can no longer be scanned.
Aside from two missing testaments, which we'll get shortly, this should complete the Lore section of the Logbook.
We'll do the keys in order from 1 to 9 which isn't the most efficient order but it will keep things tidy at least. For each key you need to locate the Key Bearer in the light world using the clue, then look for the key itself in the corresponding room in the Dark world.
Central Mining Station
First we look at J-Stl's clue which says, "Noble J-Stl. Lost his soul before a fortress in the scorched land." The scorched land is obviously Agon Wastes and the fortress there is probably the Space Pirate area there. Sure enough, we've already gotten the J-Stl's Testament in the Central Mining Station on the way out after getting the Light Beam; J-Stl was in the shielded alcove across from the cannons. Optionally, go back there and switch to the Dark visor to see the shadow of something floating just outside the shield. We need to go to the corresponding location in the Dark world.
Battleground (Dark side)
If you're coming from the Temple Grounds elevator, follow the path through Agon Wastes almost straight ahead. Get to the Command Center and use the portal to get to Doomed Entry in the Dark world; the location we want is Battleground, which, you may remember, was also the location of one of the Dark Agon Temple Keys. You need to enter from the upper passage coming from Doomed Entry. Switch to the Dark Visor and notice the invisible platforms floating around. Hop these in sequence, using a ledge to reach the last one, and hop over to another ledge opposite to where you came in. You'll find a flying shape that's only visible in the Dark Visor, and it's location is exactly where the shadow was in Central Mining Station. Shoot it once to make it visible, get a scan, and keep shooting at it until it breaks open to release the key. This should complete the Reseach section of the Logbook.
The next clue is for B-Stl which says, "Gallant B-Stl. She lies deep in a fortress of dry land." This clearly refers to the Pirate section of Agon again, but it's a bit more vague. Her scan is a harder to find, and you would only come across it if you came into the Main Reactor through the White door from Ventilation Area A, or if you used the Spider Ball to get out the same way. The shadow is perhaps easier to find since it's floating in the main room of the reactor.If you're continuing from the first key, backtrack to the Dark Oasis which is nearby.
Dark Oasis (Dark side)
Get to Dark Oasis, the Dark version of the Main Reactor. Scan to find a weakened section of rock made from Benzium just as you come in from Oasis Access. Blast it with a Power Bomb to find a pool of poison water. Above the water there are poisonous little particles called Ingstorm which will swarm you and do heavy damage until you get the Light Suit. (We've been avoiding areas with Ingstorm until now for just that reason.) The key isn't visible right away since it's under water, so jump in and search around with the Dark Visor until you find it. Don't forget to scan an Ingstorm. If you missed the B'Stl's Testament scan, take the portal to the Light version of the room and jump from the ledge in front of the black door to the top of the Phazon tank in the middle of the room. The B'Stl scan is across right behind the grate.
The next clue is, "Brave S-Dly. Beside the marsh of a raining land she laid her body forever." The raining land is clearly Torvus and is says 'beside' instead of 'in' so it's somewhere on the boundary. The Torvus Lagoon is one of the first places you see when you enter the bog and in fact you should already have the scan from when you first entered. The shadow can be spotted underwater near where you picked up the Missile Expansion. Note that if you're getting the keys in numerical order, if you arrive in Torvus via the elevator from Agon, it may be more efficient to get the fourth key and then backtrack to this one.
Poisoned Bog (Dark side)
The nearest portal from the Light world is probably Forgotten Bridge. Get to the Dark world and go to the Poisoned Bog. This is the Dark version of the area, so jump in the water to find the next key.
The next clue is, "Gentle G-Sch. With a Bearerpod he sleeps in a flooded temple." You may remember finding a Luminoth in one of the underwater areas with a lot of Bearer pods, namely the Catacombs. Head down there and you can see the ghost underwater near the Grey door.
Dungeon (Dark side)
In this case there's a portal right in the same room so there's no extra travel to get here. Jump into the pool of poison water and you'll find the path to the key is blocked by a new creature. Get a scan, then force it to move by activating the light beacon above it with the Light Beam. There are two of them so repeat and get the key at the end of the passage. Get out the same way.
The keys in Sanctuary Fortress are a bit more difficult and involve some unexplored areas.
The next clue says, "Loyal S-Jrs. He no longer breathes, looking down at the great bridge of a holy fortress." This is the bridge at the entrance to the Sanctuary Fortress and you may remember the Luminoth found while getting the Power Bomb Expansion there. If you go back you can see the ghost nearby next to the Orb Cannon.
Culling Chamber (Dark side)
We need to get to the corresponding Dark side location, but we haven't covered this part of the Ing Hive yet. Go to Hall of Combat Mastery and use the portal there to get to the Culling Chamber. We've been putting off seeing what beyond the far exit there, but it's time for to do that now.
You need to cross a wide chasm here, and you can either switch to the Dark Visor and hop the invisible platform or use the Screw Attack. If you decide on the platforms then remember that they are a bit closer to you when they are going right to left. (There really isn't any reason to come here before getting the Screw Attack though so it's a bit pointless to put the platform here in the first place.)
Drop to the lower level where a Dark Ingsmasher is waiting; get a scan if you haven't already since this is probably your last chance. Note that since you now have a good supply of Power Bombs you can use one to dispatch the monster quickly and easily. There are three exits and we'll cover the Red door first.
Hive Save Station 1
Save if you want to, but the Ingsmasher is probably the most dangerous thing in the vicinity.
Go back and through the Blue door opposite the Save Station.
Hive Cache 1
There is an Ammo Station here. There is a beam of light here as in the Map Station in the Light side, but it just causes a bit of damage.
Go back and blast open the Yellow door.
Hive Reactor Access
There is a swarm of Nightbarbs blocking the way here, but all you need to do is shoot the disabled beacon in the center with a Light Beam to activate it; most of the Nightbarbs will vanish when they enter the safe zone. The Annihilator Beam would work better for this except that the shots track the Nightbarbs instead of hitting what you aim for, so just use the Annihilator or Missiles to mop up the stragglers.
Entrance Defense Hall
As you get about a half way through the passage a swarm of baby Ing comes toward you, so get a scan since this is the only place they appear, and either power through them or defeat them somehow. One way is to simply back up into the safe zone here and let them destroy themselves lemming style.
You're finally in the Hive Entrance so (going by the ghost) now you need to get to the ledge above. There is no direct way up so you need to cross the chasm. First get rid of the Dark Preed floating around so they don't interfere with your flight. Then Screw Attack across; the ledge sticks out a bit farther on the left so you'll want to aim for that. Now step into the beam of light to be transported to the ledge above, and finally use the Screw Attack to cross the chasm back and onto the ledge with the key. Drop back down to get back to the entrance and head back.
The next clue is, "Judicious C-Rch. In a small corridor within the depths of a high fortress, he lies silently." This refers to the Luminoth in the Dynamo Works. In this case the ghost isn't visible since it's located in the Morph Ball section. Go around, through Sanctuary Temple to where you fought the Spider Guardian, and follow the maze to the small room where you picked up the Spider Ball upgrade. Blast open the Yellow door here.
Use the portal here.
Hive Cache 3
Go on to the next area.
Hive Dynamo Works
Follow the tunnel to a ledge, then you must cross a chasm to reach another ledge where you can see the key with the Dark Visor. The Screw Attack won't work because of the difference in height, so you must follow a course of Boost jumps similar when you got the Energy Tank in the Reactor Core. Get the key when you reach the other ledge and use the Screw Attack to get back. This should finish the exploration of the Sanctuary Fortress and the Ing Hive.
The clues now move to the Temple Grounds and the first one here is "Steadfast D-Isl. Who shall disturb you among the trees of holy ground?" This turns out to be an area we haven't covered yet, a small room off the Communication Area. Go there and get to the highest ledge, the go through the door
Storage Cavern A
There's no reason you couldn't have come here any time after getting Space Jump except there wasn't anything here but a dead Luminoth. Get the scan and locate the ghost nearby.
This is the last Lore scan and the last scan you can get before the final bosses, which means if you've gotten everything so far you should have 96%.
Phazon Grounds (Dark side)
To get to the corresponding area in the Dark world, you need to come through the Phazon Grounds, which means using the portal in the Sacred Path. Go through the Purple door here.
The passage is blocked by Ingstorm if you don't have the Light Suit, in fact the whole area ahead is pretty infested with Ingstorm. Continue to the next room.
Defeat the Ing, then get to the highest ledge as in the Communication Area.
This place was hard to reach, but now that you're here getting the key should be no problem.
The next clue takes you back to the beginning with, "Fearless M-Dhe. The one who shall move the pillar of holy ground will see your soulless body." This refers to block you have to move to get from your ship to Service Access. The ghost is next to your ship.
To get to the corresponding area in the Dark world you need to get back to Shrine Access, so go back to the portal in Hall of Eyes. There was a Green door in Shrine Access we skipped earlier and it's time to go through now.
Once you've dealt with the Ing here, get the key from the lower part of the room where your ship would be in the Light world.
The last clue is, "Mighty J-Fme. In the last, what did you see? Was it one of our gates closing, sealing the scorched land from our holy ground?" This refers to the gate blocking access to the Agon Wastes which you had to scan to open after getting the first translator module. This is in the Industrial Site and you may remember the Luminoth just inside the gate. The ghost is above the start of the ramp to the right, near the metal bridge.
Plain of Dark Worship
To get to the corresponding area in the Dark world you need to use the portal in Temple Assembly Site to reach Plain of Dark Worship. Open the Purple door here.
The tunnel hasn't collapsed in this world, and remember you can shoot at the Venom Weed to keep it from slowing you down.
There are some Hunter Ing you'll want to deal with first here; a Light Crystal is in the passage on the left which will help you. The key is just past the crystal, but when you shoot the container it starts hovering above the lake. This means that when you release the key it will be difficult to get without landing in the water.
Sky Temple Gateway (cont.)
Now that you have all the keys it's time to place them in Sky Temple Gateway. Return there, though you might want to save your game first, then step into the light in the center and the keys will be placed. A platform is raised and a beam of light appears in the center. Step into this to be taken to the Sky Temple.