Metroid Prime 2: Echoes/Space Jump Boots

Agon Wastes
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.

Portal Terminal
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. 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.

Portal Site
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. 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.

Crossroads
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.