Now that you have Morph Ball Bombs and the Amber translation module, the way is now open for you to make your first foray into Dark Aether. The Portal is located in the Portal Terminal which you can reach via Mining Station A and Portal Access A. It may appear there are two routes to this location and if you're coming from the Temple Grounds this seems to be the long way, but the other route is blocked for now.
Portal Access A
Use the Orb Cannon to cross the barrier and proceed to the next area.
Pirate Troopers are waiting for you here; get a scan if you missed it earlier. Soon they will be possessed by Darklings and become Dark Pirate Troopers. Get a scan and don't stint on the Missiles when fighting them because they are tougher than the non-Dark versions.
The portal is at the top of a ramp on the far side of the room. First check behind a sandfall to the left of the ramp and scan the Amber history hologram. Then go up to the portal, but you can't turn it on yet. Start by activating the Bomb Slot that turned itself on when you defeated the Pirates. This turns on some Morph Ball sized conveyors in the side walls.
Before using them though, get a scan of the Pillbugs that have appeared in the right hand wall; you normally can't scan them because they live in tunnels, so this is one of your few chances. Now roll into the conveyor to the right of the Morph Ball slot and follow the path to where it's blocked by a Talloric cylinder. Drop a bomb to clear it and the flow of sand changes, moving a lens and platform into place and releasing some War Wasps. Continue along the path to drop into an alcove in the wall, switch out of Morph Ball, clear the wasps, and hop over the platform to another conveyor, and repeat.
After the second platform there is no conveyor, just a Morph Ball path in the wall. Use Bombs to propel yourself up a level when necessary, and either dodge the Pillbugs or use bombs to defeat them. Destroy the third Talloric barrier to move the final lens in place and activate the solar generator that powers the portal.
Go back to the portal and scan the lower left circle to turn it on. The first time there is a short cutscene where you go through, find yourself in Dark Aether, and notice that as soon as you leave the safety zone around the portal you start losing health.
Dark Agon Wastes
This is the Dark version of the Portal Terminal and while the shape of the room is the same there is much that is different. First, unless you are in one of the safe zones created by the Luminoth, you lose energy fairly rapidly. The good news is that if you are in one of the safe zones then you get back energy, but slowly. The problem with this mechanic is that if you want to maintain a good level of health you need to spend a lot of time hanging around in the safe zones; it might be a good idea to have book on hand to read while you're waiting.
There are no enemies to contend with while you're getting used to surviving the atmosphere, so just get some scans in. First, turn around and activate the portal, but just get a scan rather than going through. There are two types of mechanisms which generate safe zones, one permanent and one which needs to be charged by your Power Beam. There is also a new type of storage unit used by the Ing.
The are two exits, but the one on the right is out of reach until you get your Space Jump Boots back. So go to the one of the left and activate the Morph Ball Slot to open the passage; this opens the corresponding passage in Light Aether but there's nothing you can do about that now. Note that once you drop off the ledge with the portal you won't be able to get back without Space Jump.
Follow the passage until you meet your first Ing. Remember to stay in a safe zone while fighting because the atmosphere will do as much harm as the enemies. Blast the Missile door at the end of the passage.
Save Station 2
Follow the path; there is a Save Station near the end just like the corresponding room on Light Aether. Scan the flying creatures above for a Logbook entry.
As you enter from the Save Station, go to the Light Crystal on the left where you will be attacked by a Warrior Ing. It's relatively tough for this stage of the game, but remember to stay close to the Light Crystal and keep dodging its various attacks and you should be fine. It's more difficult to hit, but you can still get some damage in while it's sliding around in its amorphous form. It may try to possess you but the Energy Transfer Module prevents that.
When the battle is over, follow the ledges to a door blocked by a grate just as in the Mining Plaza. Hop over to the central platform and then cross the bridge. Get a scan of one of the small white critters on way; you can't hurt them and they generate a safety zone so you want them around anyway.
Switch to Morph Ball and follow the tunnel.
Approach the Light Crystal in the main part of the room and the doorway closes behind you. An extra spiky Ing appears and a battle begins.
When the battle is over, grab the Space Jump Boots the monster left behind. The door you came in through, which was blocked during the battle, reopens and you can go back, but you might as well use the Space Jump to complete the loop back to the Portal Site. There is a Missile door here but it leads to the Dark Energy Controller and there's nothing you can do there now. So continue through the door on the other side which is next to the first ledge you can jump to. Don't attempt to go through if your health is low though since there aren't may safe zones for a while.
Follow the passage and use the Space Jump to scale the ledge in the middle. There is a Lightflyer which generates a temporary safe zone when you defeat it.
Portal Site (cont.)
You've now come full circle back to the portal. Stay in the safe zone for a while to restore your health, then activate the portal and return to the Light side.
Expansions (Agon Wastes)
The Space Pirates are still hanging around here so clear them out before doing anything else. Then activate the portal again to get the scan. The door on the left at the front of the room is now open so go through.
Use the Bomb Slot here to open the barrier in the passage and reveal a Missile Expansion.
There are two more Missile Expansions in the Temple Grounds, so head there next unless you want to save them for later.
Expansions (Temple Grounds)
Temple Assembly Site
When you reach the Industrial Site, continue to the Temple Assembly Site as at the beginning of the game. There are stone pillars scattered around the entrance to Temple Transport B and with Space Jump you can now use them to reach a ledge to the left. Follow the ledge, then switch to Morph Ball and follow the tunnel to a Missile Expansion.
The Dynamo Chamber is no longer a dead end so go that way.
The gates that closed behind you the first time you went this way are still closed. But with the Space Jump you can reach the upper passage and get through that way. Don't mind the bugs up there, they won't hurt you much.
Space Jump to the ledge on the left and notice the large glass blister on the ground. Drop a bomb to break it open and collect the Missile Expansion inside. There is a door up here you can reach now but other than a scan which you can get later it's a dead end.
You may remember a platform carved to look like a child Luminoth in Mining Station A. At the time your were forced to pass it by because it was too high for you, but now that you have the Space Jump it's time to investigate.