Before getting on with the main story, there is an optional upgrade to get now. It's the charge combo for the Dark Beam, just as the Super Missile is the charge combo for the Power Beam. It's purely for battle since it doesn't unlock any new areas or allow you to get any new expansions.
Go to the Mine Shaft as before but this time continue to the Purple door at the other end and blast it open.
Mining Station B
This is a large and complex room and to get through you need to solve a puzzle. First drop down into the main section and get a scan of one of the bugs here. This is a bit tricky because they keep phasing into another dimension.
Look for a small side section with a half-pipe and scan the control panel to activate the Orb Cannon there. Use it to get to a high ledge and scan the history hologram. Drop down and go back to the main area, then activate the bomb slot there. The giant propeller-like drill starts to spin and you have a limited amount of time to to back to the Orb Cannon, get fired back to the ledge, and get to a second Bomb Slot there to activate it. If you make it time then the drill will rise and break through a chunk of rock revealing a portal. (We got the scan ahead of time because you have enough to do before the timer runs out.)
The drill locks itself into a new position so it's now impossible to jump onto it. Instead, go back to the half-pipe and boost up the the ledge on the left. Follow the Morph Ball track into a tunnel and drop through the center of the drill onto the blade. From there you can hop to the warp portal.
Dark Agon Wastes
Look for a crack in the wall and go through, the jump up the ledges in the cave and follow the ledges to reach a door.
Dark Transit Station
Switch to Morph Ball, then follow a tunnel and then an elevated track to the next room.
You're in a small section behind iron bars. Use the portal here.
You're now in a similar small section. (You may have noticed this section near the beginning of the game, and now you finally find out how to get there.) Use the door here.
Switch to Morph Ball and follow the track and tunnel back, the reverse of the route in the Dark side.
Mining Station B (cont.)
This is a ledge high above the main area. Grab the Darkburst upgrade and immediately some Pirate Aerotroopers appear for you to practice on. To use it, switch to Dark Beam and fire as you would a Super Missile. Note that the Darkburst uses 5 Missiles like the Super Missile, but also a whopping 30 Dark ammo, so use it with discretion.
Drop down and go back to the ledge where you originally came in. There is a second control panel you need to scan to activate the Orb Cannon which allows you to get back.
It's time to get back to Torvus, but there's a new shortcut available. Get back to the Transport Center and boost up the half-pipe to the lower of the two ledges. Blast open the Purple door and go through.
Transport to Torvus Bog
Scan the panel to activate the lift.
Transport to Agon Wastes
Blast open Purple door here to get back to Torvus Temple.