Your new mission is to start getting back the energy the Ing stole from the Luminoth, and the place to start is the Energy Controller in the Agon Wastes.
Main Energy Controller
Exit and take the lift back to the Temple Sanctuary.
Now that you can translate Violet holograms you can open the door with that hologram by scanning it. Go through the door behind it, but note that it isn't the way you came in.
Transport B Access
Scan the flying creatures here, then continue to the next door.
Temple Transport B
Scan the control panel to activate the lift and hop on.
Temple Transport B
Continue to the next area.
Temple Assembly Site
You're now behind the door you couldn't get through the last time you were here. Scan the hologram to get through the door and you should now be on familiar ground. When you step out into the main area, the Splinter Cocoons open and release a group of Splinters. These turn into Dark Splinter unless you dispose of them quickly.
The Dynamo Chamber, where you went the last time you were here, is now a dead end. But now that you have the Missile Launcher you can blast open the red door near the path back toward the hive.
Storage Cavern B
When you're done make Office Space jokes, grab the Energy Tank to increase your maximum energy by 100. These are the most valuable upgrades in the game since you can run out of everything else, but you can't run out of health.
Go back and continue back to the Industrial Site, the way you came from the first time through.
There is a Violet Hologram door here which you can now open, but before doing that you might want to get to one of the two save points that are nearby. The first is the Hive Save Station which you can reach by taking the lift down in the Hive Transport Area. The other is your ship which you can reach just about as easily. Go to the Hive Transport Area and open the door with the Violet hologram to get the Hive Access tunnel, the open the similar door there to get back to the Landing Site where you started the game. It doesn't matter this early in the game, but the advantage to going back to the ship is you get an ammo refill along with an energy refill.
When you're done saving, return and unlock the door with the violet hologram, then get the scan of the dead Luminoth and go through.
Agon Transport Access
This is just a bridge to the transport.
Transport to Agon Wastes
There's more than just a lift here so don't rush through. First break through to webbing on the left as you did at the very beginning of the game and pick up the first Missile Expansion. These increase the number of missiles you can carry by 5 and are important early in the game because you only start out with 5 when you get the Missile Launcher.
Now go out to the edge of the cliff and look to the right to scan another Luminoth history hologram.
You may be wondering what happens if you fall off a cliff like this since they didn't have them in Metroid Prime. You do fall but after losing a small amount of energy you are returned. This will come up later in the game where you'll be asked to do some acrobatics over long drops like this.
When you're ready, scan the control panel and step into the hologram.
Before the cataclysm that hit Aether this was lush forest, but now it's desert with little but sand and rocks.
Transport to Temple Grounds
Get a scan of the sack-like plants here. They are actually for storage and you can shoot them for health and ammo refills. There are many types storage in the game and you've encountered some of them already, but this is the first type with its own Logbook entry.
Scan the flying insects here; they aren't dangerous here but in sunlight they become invisible and more aggressive. The most boring scan in the game is here as well — the grass. It's pretty much just decoration but for some reason it gets a Logbook entry. When you're done, continue to the end of the passage.
This is the first large room in Agon and you get an overview as you enter. To go forward you're forced to cross a low, sandy patch where you'll meet a Sandigger. It's a two headed worm (one at each end like a disturbing pushmi-pullyu) and you have to defeat each end to get rid of it. Get a scan, then keep moving to dodge its charges and green venom while you shoot at its eyes.
When the worm is gone, look up and scan the flying creatures overhead; these are Sandbats and while it's possible to have scanned them earlier it's much easier to do it now.
To the right is a Missile door, blast it open and go through.
Save Station A
Save your game if you want. There is a Morph Ball tunnel here which leads to river of sand. If you follow this upstream you can scan the small trees here for another Logbook entry. Like the grass, these are just decoration, but they are poisonous and that makes them at bit more interesting. The door at the end is a dead end for now, so follow the river back and return to the plaza.
Mining Plaza (cont.)
There is a second low, sandy area beyond the save station door and you'll meet a second Sandigger here. Continue to the far end, then double back to the right along a ledge. (To the left is a door with Amber hologram and you can't open it yet.) You come to a pillar of rock and a scan of the base reveals that it's made of Brinstone. This means that it's vulnerable to Missile fire, so give it a blast to knock it down and create a bridge to the central platform. You pass by an Amber hologram to another pillar of rock; knock it down the same way and cross to another ledge.
Follow this left past a door blocked by a grate; the grate is indestructible so don't worry about the door for now. When you have a bit more altitude, jump back to the central platform to land on a higher part of it. Now jump toward the three red disks on the left, then cross the bridge to the exit.
Mining Station Access
Switch to Morph Ball and follow the tunnel to the exit.
Mining Station A
This is another large room and the first time you enter you meet your old acquaintances, the Space Pirates. Get a scan and shoot Missiles or Charge Beam blasts at them until they are gone. When you come back they will be replaced by War Wasps.
Cross to a ledge with a rotating wheel under it, then follow the ledges right to a door. Get a scan of the crab-like creature on the ledge here, the go through.
Portal Access A
There is a structure blocking the passage here, but you can get past it by switching to Morph Ball and rolling into the hologram at the base. You are fired into the air twice and land in a tunnel, which you can follow to the end and drop down to ground level.
On the other side is a dead Luminoth. Staying in Morph Ball mode, roll to the left of the Luminoth avoiding the hologram, then roll to the center of the structure to pick up a Missile Expansion.
The way ahead is a dead end for now, so get back over the structure the same way and return to the station.
Mining Station A (cont.)
Follow the trail of platforms, clearing the Brizgees if necessary with a Missile followed by Power Beam. It ends at a door with an Amber hologram, but you still can't open these so continue left along the ledge. The rivers of sand can sweep you back down to the ground so it's better to jump over them. Go past a platform carved to look like a child Luminoth to a stone pillar like the ones in the Mining Plaza. Knock this down as before, the blast open the Missile door.
Be careful going through this passage because it's guarded by Shriekbats, those annoying flying creatures from Metroid Prime. Approach slowly enough so you can get a scan while they're still perched, then shoot before they can dive bomb you.
This is a suspiciously large, open room so get ready for a boss battle. There are passages left and right but they are dead ends for the moment, so the only way to through a kind of arena in the middle. Of course as soon as you step in the gates close and trap you inside, then the battle starts.
The monster drops the Morph Ball Bomb upgrade so pick it up. The gates keeping you in the arena are made from Talloric alloy, and now you can drop bombs to clear them.
Continue to the next area. Note that when you return here there will be War Wasp Hives around the edge of the arena.
Use the Bomb Slot (here called a security station) to turn the gate around.
Agon Energy Controller
Go behind the controller and scan the yellow hologram next to the dead Luminoth. You hear the last message of I-Sha, who greets you and tells you you must now go to Dark Aether via a nearby Portal. (Most of the message is information we cover elsewhere so there's no need to go into detail here.)
Your health is restored and you are given the Amber translation module so you can start translating the Amber holograms. Start by scanning the history hologram in a side passage near the door.
You can now go back to Mining Station A; at this point there will be Lumites there.
Expansions (Agon Wastes)
Before continuing on we'll cover the expansions you can get now that you have Morph Ball Bombs and the Amber translation module. These are optional and may take you out of your way, so you want to combine trips by skipping some or all now and coming back for them later. You could skip them altogether but when it comes time to fight a major boss you may want the extra health and firepower.
Mining Station A
Return to Mining Station A and follow the ledge to the door with the Amber hologram; scan to open it and reveal a door.
Grab the Missile Expansion that's just sitting there.
Mining Station Access
Go back, return to Mining Station Access, and switch to Morph Ball. As you follow the tunnel you'll cross a stone block over a pit with an Orb Cannon hologram at the bottom. Drop a bomb to break the block and fall through to the hologram and you'll be fired back though a vertical tunnel. Follow this to a small room with an Energy Tank.
Continue back to the Mining Plaza. Go to the central platform where you can now scan the Amber history hologram. Go right and drop down in front of the door with the Amber hologram and scan to open it revealing a chunk of Talloric rock. Drop a bomb to clear it and follow the tunnel.
Agon Map Station
Step into the hologram to down a map of the Agon Wastes.
Return and continue back to the Temple Grounds
Expansions (Temple Grounds)
Hive Transport Area
If you haven't already, scan the door with the Violet hologram to open the way back to Hive Access Tunnel
Hive Access Tunnel
Again, scan the door with the Violet hologram if you haven't already. As mentioned above, the Landing Site where your ship is located is only one room away in case you want to save, or refill you health and energy. Follow the path and drop down the hole as at the beginning of the game.
Hive Chamber A
There's a dead trooper an the ground here which comes to life when you get close and a battle begins.
When the enemy is defeated, pick up the Missile Expansion and continue as you did at the beginning of the game.
Hive Chamber B
Right next to the tunnel leading to Hive Chamber C is another one blocked by a Talloric wall. Drop a bomb to clear it and roll inside to get another Missile Expansion.
Continue following the route you took at the beginning of the game to the Temple Assembly Site. Enter Temple Transport B and step on the lift.
Expansions (Great Temple)
Transport B Access
The next room when you get off the lift is Transport B Access. Look for a groove in the wall on the left that's just big enough for a Morph Ball to fit. Drop a bomb to propel yourself up to a horizontal path. Now drop another bomb to go up another level and follow the tunnel as it winds around to a Missile Expansion. When you pick it up you drop down to the main passage.
The Temple Sanctuary has another Amber Hologram door you can open now, but it leads to a dead end for now. So just head back to Agon Wastes as before.