Great Temple
Your new mission is to start getting back the energy the Ing stole from the Luminoth, and the place to start is the Energy Controller in the Agon Wastes.
Main Energy Controller
Exit and take the lift back to the Temple Sanctuary.
Temple Sanctuary
Now that you can translate Violet holograms you can open the door with that hologram by scanning it. Go through the door behind it, but note that it isn't the way you came in.
Transport B Access
Scan the flying creatures here, then continue to the next door.
Temple Transport B
Scan the control panel to activate the lift and hop on.
Temple Grounds
Temple Transport B
Continue to the next area.
Temple Assembly Site
You're now behind the door you couldn't get through the last time you were here. Scan the hologram to get through the door and you should now be on familiar ground. When you step out into the main area, the Splinter Cocoons open and release a group of Splinters. These turn into Dark Splinter unless you dispose of them quickly.
The Dynamo Chamber, where you went the last time you were here, is now a dead end. But now that you have the Missile Launcher you can blast open the red door near the path back toward the hive.
Storage Cavern B
When you're done make Office Space jokes, grab the Energy Tank to increase your maximum energy by 100. These are the most valuable upgrades in the game since you can run out of everything else, but you can't run out of health.
Go back and continue back to the Industrial Site, the way you came from the first time through.
Industrial Site
There is a Violet Hologram door here which you can now open, but before doing that you might want to get to one of the two save points that are nearby. The first is the Hive Save Station which you can reach by taking the lift down in the Hive Transport Area. The other is your ship which you can reach just about as easily. Go to the Hive Transport Area and open the door with the Violet hologram to get the Hive Access tunnel, the open the similar door there to get back to the Landing Site where you started the game. It doesn't matter this early in the game, but the advantage to going back to the ship is you get an ammo refill along with an energy refill.