There is an optional upgrade to get; the charge combo for the Light Beam. Again, it's purely for battle since it doesn't unlock any new areas or allow you to get any new expansions.
Get to the Windchamber Gateway via the Path of Eyes. Use the Orb Cannon to get over the chasm, then blast open the Yellow door.
Note, it looks like you can get to the next room via the GMFC Compound as well, bit this doesn't actually work; you need to come from the Path of Eyes to do what you're going to do there.
This is a room with deep chasms like the Windchamber Gateway. Defeat the pirates and activate the portal here and go through. (If you can't get to the portal then you came in through the wrong door; see the previous paragraph.)
Ing Windchamber (Dark side)
There are four platforms around the central structure, and you can get from one to the other going counterclockwise using the Orb Cannons. Each of the platforms has a Spinner, and the idea is to use them to rotate the rings in the center. Each ring has a position where it glows blue and another where it glows yellow, and you want to get all four rings glowing the same color. So pick a color, either blue (really more of a bluish grey) or yellow (actually a shade of tan). Use a spinner to move a ring into position, then use the Orb Cannon to get to the next platform and spinner; keep going until all the rings are done.
If you did yellow, then get to the ledge with the portal and notice the four glowing purple dots lined up on the rings in front of you. Use the Seeker Launcher to shoot all the dots at once. This causes two arms on the central structure to be raised, and the corresponding arms in the Light side are also raised. If you did blue then do the same thing only you need to be on the ledge opposite the one with the portal.
Now you need to do the same thing, only with the other color, so get to work on the spinner again and when the rings are in position use the Seeker Launcher to raise the remaining two arms. The rings fall away.
Your job is done here so use the portal to get back to the Light side.
Grand Windchamber (cont.)
The four arms you raised each has a Grapple Hook on the end, so you can now grapple from platform to platform. Get to the one opposite the portal and use the Orb Cannon there to be shot up to the top of the central structure. Get the Sunburst there and when you do some Pirates appear for you to practice using it on. The Sunburst uses five Missiles and 30 Light Beam ammo per use, similar to Darkburst, and it will kill the Pirates with one shot each though they don't die right away. The Sunburst shot itself moves very slowly, so it's not much use against quickly moving targets.
We'll continue on to the Sanctuary Fortress, but first we'll open up some shortcuts in Temple Grounds and grab some more expansions in Agon Wastes. First get to platform to the right of the one with the portal and use the door there.
This is just a tunnel connecting the Grand Windchamber to the GMFC Compound. Blast open the Yellow door at the end.
Continue through to Trooper Security Station.
Trooper Security Station
There is a gate blocking this passage that was impassible until now, but you can clear it with the Power Bomb. This is the last step step to complete a loop that circles the Great Temple.
Expansions (Agon Wastes)
Mining Station A
Continue on to Agon and get to Mining Station A. Scan to find the weakened section of wall under the ledge with the statue and use a Power Bomb to break it down. Roll into the Orb Cannon and use the Spider Ball to grab onto the track you hit. Now its a short and simple Spider Ball maze to reach a Missile Expansion.
Mining Station B
Get to Mining station B via Agon Temple. Locate the weakened section of wall and use a Power Bomb to break it as in the other mining station; a new door is revealed.
There's not much here but a Missile Expansion, so just grab it.
The next stop is the Sanctuary Fortress, but as long as we're in Agon we can open a shortcut there from here. Cross the Agon Temple and the Sand Canyon to reach Ventilation Area A.
Ventilation Area A
Head into the side passage to reach a Yellow Door and blast it open.
Transport to Sanctuary Fortress
Activate and use the lift here.
Transport to Agon Wastes
Continue through the door here.
Agon Transport Access
Defeat the Quad here and continue to the next area
Hall of Combat Mastery
You're in a small side area, but you'll notice a tube going across it. Set off a Power Bomb in the vicinity to destroy the tube a open the way to the main room which should already be familiar.