Your mission for the Galactic Federation may be done, but you will soon meet one of the surviving inhabitants of Aether who has something else you can do.
Scan the body to he left to obtain the last trooper log, then roll down the tunnel to the right to get to the lower floor. Scan and defeat the War Wasps which attack. These normally come from hives but in this case they're flying free. Look up and scan the control panel on the far ledge to activate the Kinetic Orb Cannon, then Morph Ball and roll into to be fired to the exit.
As mentioned, War Wasps normally come from War Wasp Hives and there are several here that will start spawning wasps when you get near. Get a scan of one, then take them out with Missiles while you're not fending off the wasps they've already produced. There are three visible, and it's easiest to spot them with the Scan Visor, but there's one above a ledge to the right and it's impossible to see it even though it keeps spitting out a wasp every so often. So you'll just have to do the next part taking a bit of harassment from them.
With your Scan visor, look for a weak section of wall above you and to the left as you enter. Fire a missile at it to weaken it. Now locate the Kinetic Orb Cannon further down the slope and scan the control panel nearby (located in a nook just to the left) to turn it on. Switch to Morph Ball and roll into the cannon to be fired through the wall onto a ledge. Now you can finally see that last wasp nest so take it out.
Roll through the tunnel and along a Morph Ball track to get to the door on the top ledge. There you'll find the corpse of a Luminoth. As you will soon learn, they are an advanced race on a similar level as the Chozo, but while the Chozo resemble birds, the Luminoth look like giant moths.
Temple Transport A
Scan the control panel to activate the left, then step into the hologram to be carried to the Great Temple.
The Great Temple is high building supported by a tower of three pillars rising from the Temple Grounds. You might have seen it in the distance in the Temple Assembly Site. It functions as a hub within a hub since it connects different parts of the grounds.
Transport A Access
As you step into this room you'll see a swarm of Sand Bats coming out of a hole on one side. It's very difficult to get a scan of them now, but there will be plenty of other opportunities later. Note that once you drop over the ledge here you won't be able to go back since you don't have Space Jump. In the left wall is a Morph ball tunnel to a Save Station. Save your game since there is a battle coming up, then continue on.
There are more doors with holograms of different colors, though you still can't do anything with them. Scan the objects inside the walls to learn they are Luminoth in suspended animation. When you step into the center of the room a shield will rise locking you in the and a battle starts.
What would a boss be if they didn't drop some kind of reward that you can't finish the game without? In this case it's a glowing ball of light but your Scan Visor can't identify it. But since the wall around the middle of the room won't lower until you do, pick up the object. At first all you learn is that although it's merged with your suit, it's not doing any harm.
The walls around the middle of the room have now been lowered, but a new hologram door has appeared blocking the way you came. There is only one door available so go through.
Scan the control panel to activate the lift and step into the hologram to get to the top floor.
Main Energy Controller
When you enter you are greeted by the Luminoth U-Mos who tells you the backstory of the game. The Luminoth have been fighting a decades long war with the evil Ing to control the energy of the two parallel versions of Aether. The Ing stole an Energy Transfer Module, but now you have it; it's the unknown technology you just picked up. U-Mos begs you to use the module to restore the energy the Ing have taken from Aether, otherwise the Ing will win the war and may spread to other worlds.
The there are three energy temples and the procedure is similar for each one. First you need to go to the Light version of the temple and speak to its Luminoth guardian. You then need to collect the keys needed to enter the Dark version of the temple. Once you have the keys, you can enter the Dark temple and collect the energy stored there. Finally, you need to take the energy to the Light temple and restore it.
Finally, U-Mos updates your Translator Module so you can read the Violet Holograms of the Luminoth. You energy is completely restored and the Energy Transfer Module is added to your Data Network under Suit Expansions.
Get the scans here: U-Mos, the Energy Controller, and the Violet hologram on the wall near the door. (The holograms on the walls are backstory information only, similar to the Chozo Lore in Metroid Prime.)