Lacking the Super Missile for now, you can't penetrate the green door on the west end of this area. Head back to the Doomed Entry region for now. When you enter the Double Path corridor via the lower hallway, scan one of the tentacles madly lashing about from the walls to reveal them as Darkling Tentacles. Shoot them once to force them back inside their alcoves to allow safe passage.
Once back in Doomed Entry, follow the path you originally took to reach the Dark Oasis room (use the Light Beam on the Inglets along the way - it literally disintegrates them). Once back in the Dark Oasis, head through the white door on the western side of the room to locate an Ammo Station, step in to replenish your stock. Go to the far side of the Dark Oasis and from there you can wave goodbye to Dark Aether by energizing the Light Portal hiding in the corner with the Light Beam.
Once back in Agon, you'll need to re-enter Dark Aether via the Portal Terminal. For now go back to the Command Center and leave via the white door you previously were unable to access. Follow the corridor beyond to find yourself back in in the Central Mining Station. From up on this ledge you'll be able to jump in one of the Vigilance Class Turrets.
From inside the turret you can spot several large devices scattered around the area that weren't there before (they show up blue when using your Scan Visor). See that large red pulsing force shield way over on the other side of the area? You'll need to shoot the containers with the turret to easily destroy them, creating a crude but effective pathway to reach that ledge.
As you destroy some of the them two Pirate Troopers will emerge and fire at you, quickly take them out before they drain the turret's energy. With the area clear jump off the turret and climb atop the Pirate Skiff over on the damaged storage racks on the left. Jump atop the next platform and across to the small cave. Scan the two terminals inside (one for your Logbook), then follow the path up to the force shield.
Scanning the shield reveals that it's something your weapons can never penetrate, but if you'd taken out the generator device over in the corner you'll see a small tunnel uncovered. Roll through it with the Morph Ball to discover the remains of a Luminoth warrior, plus a very handy Beam Ammo Expansion.
Scan the Luminoth warrior for J-Stl's Testament - you'll find out later why some fallen Luminoth warriors have Logbook entries. With your newly increased payload, return to Mining Station A. Once there, use the Dark Beam on the dual Pirate Aerotroopers to easily knock them out of the sky. Before heading south to the Portal Terminal, we'll stop by the Agon Temple to pick up a now-accessible Energy Tank.
Proceed to the Temple then take the left path around (destroying the obstruction along the way with a Morph Ball Bomb). One the western side of the temple you'll find a black door, use the Dark Beam to get through. Inside you'll find a narrow tunnel, go inside with the Morph Ball to find a large network of tunnels winding around a circular region. Directly above you is Energy Tank AW.03, but you'll need to work through the tunnels to reach it.
Head left and watch out for Pillbugs (drop a bomb to dislodge them, then use a second to send them off). At the first tunnel opening you'll need to use the double bomb-jump (see Secrets and Tips for more info) to reach the tunnels higher up. Practice a little to get up there, then traverse the area all the while sticking to the uppermost tunnels (watch out for the numerous blocks that tend to disappear as you cross over them).
If you fall at all just head back to the right to eventually reach the start. Once you've scored the Energy Tank return to the Agon Temple (the other exit from here is blocked by a purple blast-shielded door, you'll find out how to open it later). Back at the temple, return to the Mining Station and head for the Portal Terminal.
At the Portal Terminal, walk past the attacking War Wasps and scan the terminal beside the portal to fire it up. Before stepping into the Dark Portal scan it for your Logbook, then head on through. Once in Dark Aether, head up to the Duelling Range first (beyond the Save Station), as we'll pick up one final item before taking the plunge at the Dark Agon Temple. Deal with the two roving Warrior Ing in the Duelling Range before opening up the black door on the western end.
Inside you'll discover a short canyon inhabited by Inglets and abruptly ending in a dead-end. You'll find Missile AW.06 tucked away in a well-hidden alcove directly below the Light Crystal beside the door you entered via. With the missile tucked away return to the Duelling Range and make your way across to the Judgement Pit.
Once there, climb up around the walls and look for a black door. Open it up to discover a Save Station tucked away inside. Save your game here before moving on. Proceed to the temple to discover a large circular glowing portal before the locked panel.
Stand in the portal to unlock the door with your three Dark Agon Temple Keys, opening access to the temple beyond. You'll now see before you the open arena of the temple, with three safe zones positioned around a dark and very large mass in the center. Walk forward to face the guardian of Dark Agon - Amorbis. Refer to the bosses guide for tips to take down this gargantuan slug.
With the first major guardian defeated, you'll be granted a handy item - the Dark Suit! With this funky new outfit the damaging effects of Dark Aether's atmosphere won't be as caustic as before. You'll also be granted stronger defense against regular attacks. With Amorbis gone and the path ahead now clear, you're free to enter the Agon Energy Controller and reclaim Agon's planetary energy. Climb atop the platform recently rising out of the ground to reach the door ahead.
Inside you'll discover a (corrupted) temple security station; use the Bomb Slot to access the door ahead. Once inside the Dark Agon Energy Controller, you'll see the stolen energy present in the chamber above the device. Walk forward to the interface module and a cutscene will play as Samus channels the planetary energy into her suit (that suit can do anything), reclaiming it from Dark Aether's twisted world.
The sky itself will turn a blood-red colour, so you'll know that taking back the energy is not going to make the Ing happy. It's now time to leave this twisted realm and return the energy to its rightful place on Aether. Return to the Dark Agon Temple, once there you'll see the entire area is awash with a red tinge. Take out the three Warrior Ing trying to ambush you, then return to the Portal Site and leave this place. Along the way you'll face a horde of various Ing, just ignore them as you proceed.
Once back at the Portal Site you'll face a trio of Dark Pirate Troopers - use the Light Beam to deal with them. Blast the Light Crystals with the Light Beam if they wander inside the safe zones. Return to Aether and head to the Agon Energy Controller. Once there, step forward to watch a cutscene play as Samus returns the energy to its rightful place. You'll see a beam reconnect this Energy Controller with the one in the Great Temple as U-Mos watches on. With the hologram of the amber Luminoth guardian showing their thanks with a courteous bow, you'll have cleared the Agon Wastes area and are ready to expand your expedition of Aether.