Upon sending it back to whatever twisted realm it came from, the Dark Alpha Splinter will drop a glowing sphere of blue energy. You Scan visor comes up empty - it doesn't know what the object is. Pick it up anyway - your suit doesn't know what it is but it has no negative effect (you'll find out more later). With the Temple Sanctuary now clear it's time to move on. The door you entered via and the exits to the left and right are all blocked by the mechanical hologram-adorned gates, so there's only one way forward.
Exit the room via the door ahead. Inside you'll locate an offline elevator. Power it up by scanning the terminal nearby and step into the hologram to ride it skyward. Step through the door above to locate the Main Energy Controller - and a new face. Beside the giant device in the center of the room you'll meet U-Mos, sentinel and leader of the Luminoth (the moth-like humanoids you've seen the remains of earlier).
Listen to his story, upon which you'll discover Samus' new purpose on this world. The Ing have invaded from Dark Aether, and naturally only Samus can stop them after their generational war with the Luminoth. Now that you've secured what is identified as the Energy Transfer Module just as the Ing were about to take this temple (now THAT's good timing), Samus can infiltrate the temples on Dark Aether and take back the light world's energy.
With his story complete U-Mos will grant you the ability to access objects adorned with violet holograms, such as the many mechanical gates you've seen before. Your first temple to visit is in the Agon Wastes. If you're ever confused about what to do next, just return here and good old U-Mos will give you a handy hint. Before leaving, make sure you scan the Energy Controller, U-Mos and the rotating violet hologram (these units contain Luminoth Lore) on the wall near the exit for your Logbook.
Scan the giant energy sphere in the center to learn more about the planetary energy it contains. Exit the room and head back down to the Sanctuary below. Of the three exits from there, you'll only be able to scan the violet translator gate. Scan it to open up the gate and head through the door there.
The door identifies this path as leading straight to Agon, so you're on track. Once inside you'll discover two floating gold energy balls, scan one to reveal them as Lightflyers. Keep your distance and take them out from afar. Deal with the two nearby and cross the corridor, taking out the third down the other end. Along the corridor you may hear that warm humming sound indicating that an item's nearby, but you'll need the Morph Ball Bomb to pick this one up.
Cross the corridor and exit via the door down the end. Once inside the next chamber, scan the control terminal to activate the elevator then ride it back down to the Temple Grounds.
Head outside at the base of the shaft - you'll find yourself back in the Temple Assembly Site where you passed through earlier. Scan the translator gate to open up access to the compound (you'll get a friendly Luminoth message every time you scan a gate, no wonder they were buddies of the Chozo).
Walk forward to find yourself attacked by a group of Splinters again, and naturally Ing Darklings will promptly appear and try to possess the creatures. Very quickly take them out as you'll have a chance to stop the Ing from possessing them. With the area clear destroy the red blast shield on a door nearby to locate Energy Tank TG.01 hiding snugly inside.
With your first Energy Tank locked away, return to the Temple Assembly Site and head right, returning to the Industrial Site area. Once there you'll be clear to open up the violet translator gate. Open it up to discover a fallen Luminoth warrior on the other side. Scan it to learn more of the Luminoth's struggles against the Ing. Also keep in mind the locations of where all the fallen blue Luminoth you encounter lie, they'll come into play later on.
Enter the door ahead and cross through the pretty observation tunnels overlooking the huge canyons below (don't forget to do some sightseeing ). Beyond this tunnel you'll discover an offline elevator beside a cliff. Take a look around, the view from here is pretty snazzy (just don't fall off). Scan the visible rotating violet hologram off the right side of the cliff for your Logbook, then take a look at the Splinter web nearby.
Blow it open to reveal Missile Expansion TG.01. Grab your prize and scan the control terminal nearby to fire up the elevator. Step into the hologram to gain access to the Agon Wastes. Once at the base of the shaft, turn right and scan the blue Agon Bearerpod for you Logbook. Exit the room and take in the dry sights ahead. Scan one of the small flying creatures to reveal them as Lumites. Don't forget to also scan the fallen Luminoth warrior nearby. Deal with the Lumites and watch out for energy blasts they emit. Scan the Sandgrass ahead for your Logbook before proceeding.