Getting the Flamethrower is very quick, so most of this page will actually cover the exploration of the remaining section of the Phazon Mines. The hint system may already be pointing to a room on the third level very close to the Phazon Processing Center. But the way through that room is blocked, so the only way to get there is by exploring the rest of the mines. Get to Main Quarry, save your game if you want, and proceed to the Mine Security Station.
Mine Security Station
Get to the upper level and drop a Power Bomb at the Bendezium wall near the exit. Then scan the panel behind it to lower the force field in the lower level. Go back to the lower level and go through the red door that was behind the force field.
Storage Depot A
The Flamethrower is here in a small room. The Flamethrower is basically a plasma based version of the Wavebuster. It's more powerful but use it sparingly because it also uses Missiles very rapidly.
The next destination is the Central Dynamo; the route has already been covered but there is one change.
An Elite Pirate attacks when you enter the room. The battle is a bit cramped this time so it's hard to avoid its attacks, but you should be able to defeat it fairly easily anyway.
It's a good idea to save now because it will be a while before you have the next chance. Drop a Power Bomb near the door opposite the save station to unblock it and go through. You're now entering unexplored territory.
This room is guarded by four Mega Turrets, but you can get through without taking too much damage. Look for a hole in the floor to the right as you enter, switch to Morph Ball and drop in as soon as you can. Roll through the tunnel under the floor to come out at the other end of the room. Using the wall for cover as much as you can, scan the nearby security panel to turn off the Turrets.
Metroid Quarantine A
This is a large room with Pirates at one end watching over Metroids behind a force field. Don't even bother fighting the Pirates yet, just scan the consoles near the entrance to release the Metroids and they'll do most of the work for you.
Defeat any Metroids still in the Pirate part of the room, then take a closer look at the Metroid part. The floor is covered with Phazon so you'll want to stay off of it as much as possible. Switch to X-Ray to see cloaked platforms hovering from side to side. To reach them, hop on top of the giant mushrooms on the left, then jump to the first platform when it floats into range. You'll need to use in X-Ray vision for this, but switch to normal view occasionally so Metroids don't sneak up on you.
Jump to the ledge on the far side of the Phazon, then to a platform on the right. Look for another cloaked platform and use it as a stepping stone to reach a ledge on the other side of the passage. There are slanted Spider Ball tracks here but ignore them for the moment.
If you look closely at the map then you'll see a passage going from the ledge you're on back toward the start. It looks like a solid wall blocking it, but if you switch to X-Ray you'll see that it's not. Switch to Morph Ball and drop a Power Bomb to clear the wall, go down the passage a bit, and drop second Power Bomb to open the other end. You now see a narrow bridge in front of you with Spider Ball track on top.
Follow the bridge to another ledge, then switch to X-Ray again and ride the cloaked platform up to a higher ledge to collect a Missile Expansion. Either back track or drop down a level and retrace your steps to get to the slanted Spider Ball track again. This is easy to follow and leads to the exit.
Elevator Access B
This is a short passage with Burrowers in the ground. If you try coming this way with only the X-Ray visor then you'd get stuck here at the red door.
Take the elevator to Level 3. As with Elevator A, you can see the Impact Crater through the window.
Fungal Hall Access
There is a Space Pirate below the ledge where you enter. Use the mushrooms to platform up and down here since the floor is covered with Phazon.
There is a Missile Expansion under the large mushroom at the bottom and you need to switch to Morph Ball mode to reach it. It's possible that you're meant to get this later since at this point you'll take some damage getting it. Get it if you're going to and platform to where the Pirate was.
Fungal Hall A
This cave has a ground level which leads nowhere, and an upper level where you need to jump from mushroom to mushroom. Hunter Metroids patrol it so clear them quickly.
Getting to the other end can be a bit frustrating because if you make a mistake in platforming then you'll need to start over from the start. When you get near the end, Grapple the Glider to reach the exit.
Phazon Mining Tunnel
There is a boulder blocking the way and neither a scan nor the X-Ray visor reveal what to do with it. But there's no other way through so your only choice is to drop a Morph Ball bomb. This opens a tunnel into a Morph Ball maze.
You can hear the hum of an upgrade or expansion here, but don't be fooled. The path to it goes through Phazon and you won't have enough health to reach the end and get back without dying. You're not meant to get the item yet, so either don't try or don't say we didn't warn you.
Drop down a bit to a series of floor panels that disappear soon after you touch them. To get across, charge the Boost Ball and zip past them before they have a chance to drop you into the Phazon.
When you come out the other end of the maze you can catch a glimpse of the Chozo Artifact that was making the noise.
Fungal Hall B
This is similar to Fungal Hall A in that you need to platform on the mushrooms on the upper level to get through. There are regular Metroids here instead of the Hunter variety, and it's very dark so you'll need Thermal to see them and where you're going.
Before doing anything else, get to the far end of the passage at ground level and locate the Missile Expansion under the ground. It's surrounded by a ring of small mushrooms and it visible in both Thermal and X-Ray. You only need a simple Morph Ball bomb to break through the ground and get the expansion.
Now go back toward the start and jump the mushrooms toward the end. There is a Glider here as in Fungal Hall A, but there are two doors you can reach using it. Start with the one on the left.
Missile Station Mines
There is a Missile Station here. Note that it only refills Missiles, not Power Bombs.
Fungal Hall B (cont.)
Go back and this time swing to the right exit.
Quarantine Access B
There are cloaked Bombus here, just like regular Bombus only you need to switch to X-Ray to target them. Jump on the mushrooms to stay off the Phazon on the floor.
Metroid Quarantine B
This is the counterpart to Metroid Quarantine A, but they take things a bit more seriously at this end. It's guarded by the last type of Trooper, the Plasma Trooper. There are several here and you'll want to clear them out before doing anything else. Two hits each with the Charged Plasma Beam should do the trick.
Now find the Spider Ball track in front of some Phazon. Follow it around to a platform behind it, then jump forward to a second platform. Use the Grapple Beam to swing across the Phazon to a platform in front of a force field.
You can scan a console to the left to lower the force field, but there are more Troopers on the other side waiting to attack so be ready for them. There is a Plasma Trooper, but also Wave Troopers waiting in the wings.
Once the room is quiet you can start looking for scans and items. Get the last Pirate Data scan from one of the consoles here. In fact, not counting Artifacts, you should have all the scans in the game except for six Creature scans.
There is a canister here made of Cordite, so fire a Super Missile at it to get the final Missile Expansion.
When you've done everything, go through the door on the lower level.
Save Station Mines C
There is a boss coming up and it's been a while, so a save is definitely in order.