Now that you have the Dark Beam it's time to get its opposite, the Light Beam
Return to the Command Center; this time you can go through the black door instead of going through the floor. Shoot the inactive portal on the far wall with the Dark Beam to activate it.
Dark Agon Wastes
Get a scan of the floating soccer ball-like creature. There are two platforms in the middle of the room; go around to the back of the one on the left and shoot at the darkened light crystal to reactivate it. Then fire a missile at the statue on the platform to reveal a Lift Crystal. Scan and shoot it with the Dark beam to lower the platform. Hop up the platforms, get the temple key on the left, and continue on to the black door on the next ledge. There is another black door behind the key, but it leads to a dead end.
Somewhere around this point you should be at the 40% scans milestone which opens some bonus features on the main menu.
Follow the passage; there are Warrior Ing here to make it more interesting.
There is a portal near the end of this passage, but you'll have to come back to it because you don't have the light beam yet.
Hall of Stairs
Go past the square pillar and activate the lift crystal on the far side to lower it. This time you can scan the other type of lift crystal after you do. Jump on top, turn around and jump to the ledge, then blast the Missile door.
Save Station 3
Save your game if you want and continue to the next room.
Switch to Morph Ball and make your way through tunnel. The well part has Phazon at the bottom and you'll take some damage if you fall in. There is a way to avoid this though. First, get to the upper passage and roll up to the edge of the pit. Drop a bomb and roll back a bit, then roll forward so you're over the bomb as it goes off. If the timing is right then the bomb lifts you into the air while your momentum carries to the other side of the pit. If your timing is off then you land in the pit, but it's no worse that if you didn't try the trick.
Step into the hologram to ride the lift down to the main level. The exit is on the other side of the the room, but you need to find and scan three control panels that open the lock so you can go through. The first, and hardest to find, is in the corner to the left as you come in. It's behind some crates so either destroy them or jump around behind. The second, and easiest to find, is on a ledge to the right as you come in. For the third, you need to hop the series of floating platforms that lead to a ledge above the exit. Timing is needed because the platforms move up and down, and you should definitely keep the light beams active so you don't lose health waiting for the right moment.
First get a scan of one of the barnacle-like creatures on the far wall. They spew toxic gas but there's not much you can do about them because they're indestructible. While still in the safe zone on the ledge at the start, fire at the crystal on the platform ahead to clear it. This attracts Lumites though, so clear them before moving. Now start hopping the platforms, past the Ingclaws where you'll take some damage, to the Missile door. Blast it at go through. If you fall to the floor then look for a ledge next to the crystal you can jump to get get back up.
Follow the passage to the main area, then clear the Nightbarbs flying around so you don't get hit by them as you're moving around here. Locate the lift crystals near the tops of the pillars in the middle of the room. You need to work your way around the edge to the other side to see them. Shoot to lower the pillars and jump along them to the ledge on the far side. Go through the Black door there.
Ing Cache 1
Pick up the Light Beam which is just sitting there.
Feeding Pit (cont.)
The game tells you what you need to do to refill your Light and Dark ammo supplies. Unlike most drops which you get at random, you can only get Light ammo by destroying enemies or containers with the Dark beam and vice versa. So since you're probably low on Dark ammo by now, try shooting some of the Ingblades with the Light beam to get some refills.
Another thing to do here is shoot a Light Crystal and Light Beacon with the Light Beam to create energized versions. Get scans of these; energized safe zones can actually destroy certain enemies.
Shoot the White door to open it and go through.
Feeding Pit Access
Get a scan of the webbing that's blocking the passage, then shoot it with the Light Beam to clear it. Shoot the second webbing to reach the other end. Weblings don't respawn to get their scan now.
Doomed Entry (cont.)
There are Dark Splinters here now. They are much easier to deal with now because the Light Beam will kill them in one shot, though it takes a few seconds before they disappear.
Before heading back to the Light side we'll collect an additional key and open the last White door in this section. Get back up to the platforms and go through the Black door skipped earlier; this was above a White door.
This room has two paths as you'd expect. The upper one is easier to get through but you're forced to use the lower one on the way back.
If you're low on health then recharge in the safe zones for a bit, and might want to try to top off your Light ammo using the Ingblades too.
Drop down to the center of the room where the key is located. Before you can get it though, several Ing Warriors appear and make off with it. You need to defeat them all to get it back. First make sure get a scan of the creature that's blocking the door since it only appears in this battle. The Ing are weak to the Light Beam so use it on them, but an easier way is to energize the beacons dotting the walls and move to their safe zones. If you're lucky you'll catch an Ing inside the zone and wipe it out. Also, while you're in the zone there's a good chance that the Ing will try to attack you, touch the energized zone that way and wipe themselves out.
Get the key and head out through the lower door since the upper one is out of reach.
Double Path (cont.)
The lower path is guarded by tentacles similar to the Reaper Vine of Metroid Prime. Get a scan the shoot them to make them retract. Jump over the poison water to reach the end.
Doomed Entry (cont.)
Continue to Dark Oasis as before.
Dark Oasis (cont.)
Go through the White door skipped the first time through here.
Ing Cache 3
There is an Ammo Station here if you need to top off your ammo. It's probably not much use at this point in the game but we'll add it to the map as long as we're here.
Dark Oasis (cont.)
The portal to return to the Light side isn't in Doomed Entry where you entered the Dark side, but here. Shoot the portal with the Light Beam to activate it and go through.
Expansions (Agon Wastes)
There aren't many new expansions you can get with the Light Beam. There are several purple crystals in the Temple Grounds which you can activate now, including one next to your ship, but the paths they open up are still dead ends for now.
On the map it looks like there's a White door you can explore here, but you can't reach it yet. Instead head back to the Command Center.
Enter Command Center Access through the White door on the upper level.
Command Center Access
This is the upper passage in the room; you went through the lower passages earlier.
Central Mining Station
You're now on the ledge with the turret. You need to use them in a minute, but in the mean time don't step off the ledge because, at least for now, the only way up here is via the Command Center. Switch to scanner and locate the three portable generators scattered around the room; they are stubby cylinders with round tops. The first is under the skiff to the left, the second is to the left of the glowing orange rectangle on the far side, and third is on the ledge on the right. The second one is out of scanning range but you should still be able to see it.
Once you know where the generators are, step into one of the holograms to start using a turret and shoot the generators. When you hit the one on the right more Pirates appear; you can shoot them with the turret or take them out the normal way. You can also destroy the windmills here if you feeling destructive, but there's no reason to.
Now that you've cleared the path you can get your reward. Jump on top of the skiff which is now on the ground. From there you can jump to the platforms in the middle and then to the ledge on the right. Enter the cave and scan the terminals there. Continue behind the orange rectangle to a ledge, switch to Morph Ball, and roll into a small room. Scan the dead Luminoth, and collect the first Beam Ammo Expansion.
Return now to Agon Temple, follow the path to the right and go through the White door.
Switch to Morph Ball and roll into the hologram to be fired across the canyon.
Ventilation Area A
Switch to Morph Ball and roll into the tunnel. Go past a loop patrolled by a Pillbug and a side tunnel which goes behind the screen, on to second loop patrolled by a Pillbug. Drop some bombs to get it out of the way because you may be here for a while. Do a double jump (as for the Energy Tank in the Mine Shaft) to get to the top of the loop. Then do a second double jump to follow the path above. Keep following the path to reach a Missile Expansion.