Dark Agon Wastes
You now have all the but the last upgrade you can get in Agon Wastes so it's time to finish up. You will be coming back to Agon for expansions and whatnot but the main story is will be done here when you've finished these last few tasks.
Go back to the Portal Terminal in the Light side and use the portal there. Note, Dark Agon Wastes is, for now, in two sections and you can't get from one section to the other without going through the Light side. So if you're thinking about getting to the Dark side through the Command Center, it won't work. Once in Dark Agon Wastes, return to Judgement Pit.
There's a Missile door here which we skipped before because it was a dead end. It's on the opposite side as you come in from Portal Access. Blast it open and go through.
Dark Agon Temple Access
There's not much here so just follow the passage.
Dark Agon Temple
The first thing you see here is the place where you're supposed to place the keys you've been collecting. There is still one key to go though, so ignore it for the time being. Follow the outer path to the left until you reach a Black door.
The last key is just sitting there, so pick it up and go back.
Dark Agon Temple (cont.)
Go back to where you first came in to find a very sparkly hologram telling you all the keys have been found. Step in to it to open the door. You might as well top off your energy as long as your in a safe zone, then step forward to step into an arena where Amorbis appears and a battle begins.
When the battle is over you can collect your reward, the Dark Suit. This reduces the amount of damage you take from the atmosphere on Dark Aether, so now you lose energy at about the same rate as you gain it in the safe zones. Also, and this is more important than it sounds, it makes you immune to the gas spewed by Ingclaws. A ledge appears which allows you to jump out of the arena and on to the next room.
Dark Controller Access
Use the Bomb Slot to turn the gate.
Dark Agon Energy Controller
This is where the Ing have stored the stolen energy. Step into the room and you automatically use the Energy Transfer Module to collect it. There's nothing more to do here so start heading back.
Dark Agon Temple (cont.)
Warrior Ing have taken the place of the Amorbis, you can fight them if you want, then use the new ledge which has appeared in the arena while you were in the Controller to continue back to the Light side. Dark Pirate Troopers appear in the Portal Site when you reach it.
Agon Energy Controller
When you return to the Light side go to the Agon Energy Controller. You're taking the same route from the Dark Controller to the portal only backwards and in the Light side. Note that you can't leave Agon with the energy you're carrying.
Step into the room and you automatically use the Energy Transfer Module to release the energy you've got into the controller. A beam starts feeding the energy back to the Main Energy Controller. You now need to go check in with U-Mos. So head back to Temple Grounds.
Temple Assembly Site
You're going to be passing through this room anyway and there's an expansion nearby you can pick up now.
Locate the purple crystal near where you come in from the Collapsed Tunnel. Shoot the crystal with the Light Beam to move a wall out of then way and reveal a portal. Now use the Dark Beam to open the portal and go through.
Sky Temple Grounds
Plain of Dark Worship
This is your first time in the Sky Temple Grounds and right now you can't go beyond this one room. Head into the main area. Get the Missile Expansion inside the large Ingworm structure on the far side.
You may wonder if you couldn't have gotten this before now. It would have been pretty difficult because you need the Dark Suit so survive the gas from all the Ingclaws scattered around the room.
Get back to the Light side and return to the Great Temple.
Main Energy Controller
When you go in there is a dialog where U-Mos thanks you for restoring Agon's energy, but warns you that now that the Ing know you have the Energy Transfer Module they will now be out for revenge. He then points you to Torvus Bog.
Note that while you don't really get anything from this visit except for some vague hints, the game prevents you from going on if you try to skip it.