We're going to cover an optional upgrade, the Ice Spreader, at this point, and explore a shortcut from the Phazon Mines to Magmoor Caverns in the process. This means taking a rather roundabout route to the next required upgrade, but having the shortcut and a few more expansions won't hurt.
We're going to start where we left off near the Central Dynamo.
If you're entering after restoring from a save, or coming back after getting the Power Bomb, there will be a group of Ice Troopers waiting for you here. There are boxes here to restore supplies and the chances are that one will have a Power Bomb Ammo refill so get a scan. There should be only one Research entry still remaining.
You can now clear the Bendezium rubble blocking the white door opposite the save station, but surprisingly this is a dead end for the moment. (Eventually the hint system will point you back to a previous area.) So don't even bother clearing the Bendezium now. Instead, you need to get back to the door you came in through. There are platforms with a glowing blue mist above them, and you can use them with a bit of platforming skill to get to where you need to go.
Backtrack to Omega Research.
The Elite Pirate in the damaged canister is now free and breaks through a force field to attack. Get a scan if you missed it in Elite Control, and defeat as before. When you come back to this room it will have the same Troopers which were here when you came through the first time.
Scale the ledges where the Pirate was to the upper level. Then jump to the platform floating in the center of the room and on to the ledge on the far side. A pile of Bendezium blocks the door there, so set off a Power Bomb to clear it and go through.
Map Station Mines
This is a tiny room with the Phazon Mines Map Station. Download the map to find out how much is left to explore in this area, it turns out you're only about half done. Unlike the Chozo Ruins and Phendrana Drifts, there is very little of the area not covered by the map. Tallon Overworld and Magmoor Caverns don't even have map stations.
You can now see the overall layout of the Phazon Mines. There are three levels. You've already explored most of Level 1, about half of Level 2, and Level 3 is completely unexplored at this point.
Continue to the Ventilation Shaft.
The good news is that you can get an Energy Tank here. The bad news is that once you get it the Puffers go away so no more free energy and ammo refills. You now have a save station not too far away so on balance it's probably better to get the Energy Tank.
Locate the Bendezium grate on the floor and use a Power Bomb to break it open. Drop into the hole; the camera shifts and it's a bit disorienting, but the tunnel actually goes into a small side room under a giant fan. Stand up and scan the control panel here. This turns on the fan which blows the Puffers into the grate on the other end. The grate breaks open revealing the Energy Tank.
Do a half-pipe jump to continue backtracking.
The last time you were here you fought an Elite Pirate and some Ice Pirates. These have been replaced by Shadow Pirates so switch to Thermal and clear the room.
Get to the lower level and go through the white door there to a new room. (The hint system tells you to continue backtracking, but we're going after a different upgrade now.)
This is a Morph Ball tunnel. You have to drop a Power Bomb in the middle to clear some Bendezium debris blocking the way.
Phazon Processing Center
If you check the map here you'll notice that you're now in Level 3 of Phazon Mines. This is a large room with several levels; the floor is covered with Phazon. Space Pirates attack when you enter but they should be easy to defeat by now. There are also two Mega Turrets here, one on the ceiling which you might as well clear now, and another near the floor which won't bother you unless you fall.
There is a red door at the bottom but this is a dead end even if you were willing to wade through the Phazon to get to it, and able to get through it. If you fall to the floor, then quickly jump to one of the platforms scattered around, then to one of the ledges under where you came in. Now scale a series of ledges and platforms that wind their way around the room to a Spider Ball track over the red door. Follow the track, then a recess in the wall where several Morph Ball jumps are required, to get back to the ledge where you started.
There are two pillars here with Spider Ball track spiraling around them; you may have noticed something similar in the Great Tree Hall. The one on the right as you enter is a dead end, so start up the one on the left. Follow the track to a ledge a level above where you started. Follow the platforms up here which gradually get higher and higher until you reach the top one which is at the same level as a platform sliding from side to side. Jump to the sliding platform and ride it to the edge of the room, then jump to a passage there to find a door.
There is Phazon covering the floor of this passage. Jump to the platform in the middle, and from there to the door at the far end.
Transport to Magmoor Caverns South
Take the lift.
Transport to Phazon Mines West
The lift takes you here. Follow the passage to the exit.
Bendezium rubble blocks the passage, so drop a Power Bomb to clear it. There are Zoomers patrolling here.
You're now back in previously explored territory. Your next destination is Shore Tunnel, just fast Fiery Shores. Note that, now that you have the Ice Beam, you can take out Magmoors very easily and you can freeze those annoying jets of flame scattered around.
This seems to be an empty passage, but a scan of the floor reveals that the the frame is made of Bendezium. Set off a Power Bomb to break through the walls, then go under the passage to find the Ice Spreader.
Continue to Monitor Station.
Get to the bridge leading to Transport Tunnel A. Jump to platform above and to the left, then to a second bridge above the one you were just on. Go back to the roof of the central structure and activate the Spinner there to raise a partial bridge. Then jump from there to a ledge and follow it to a door. (If you've gotten the Artifact of Strength already then you're already familiar with this.)
If you haven't gotten the Artifact on the statue here already then you might as well do it now. There's still more to do here though; scan the steps in front of the statue to reveal the hatch cover here is made of Bendezium. Drop a Power Bomb to clear the hatch and drop in.
You land in a hidden side room of Fiery Shores. Jump up to the ledge to collect your first Power Bomb Expansion. These increase the number of Power Bombs you can carry by one. You start with a capacity of 4 and there are 4 expansions, so your maximum capacity at the end of the game is 8.
Jump into the Morph Ball tunnel here to get back to the main part of the room.
There is one more expansion to get before returning to the Phazon Mines. It's actually on the way assuming you're getting there via the Great Tree Hall.
Get to the Furnace, defeat the Chozo Ghosts that have started to appear there, then look up at the system of Spider Ball tracks that was unreachable the last time you were here. You may notice one of the tracks is next to one of the walls, and if you scan the floor under it you'll find a section made of Bendezium. So drop a Power Bomb there to remove that section of floor and reveal a half-pipe structure.
Do a half-pipe jump to reach the Spider Ball track and start eliminating the Plated Parasites that are patrolling it. To do this, just drop a bomb in their path and move away before it explodes and knocks you off the track. When the parasites are gone, or at least sparse enough for you to move around, get to the top of the track on the left end and drop a bomb to jump to a section of track above.
Follow this track until it goes over a horizontal beam and drop down onto it; look for your shadow on the beam to tell you when you're lined up. Follow the beam, dodging and/or bombing the parasites circling it, to another Spider Ball track. This passes over yet another track and you must drop down in front of it to stick there. Again, use your shadow to tell you where you will land.
This tracks takes you over a second horizontal beam so drop down on it as before; you're higher up this time so the shadow isn't as visible, but you can see it if you look. Follow the second beam to still another Spider Ball track, and this one takes you to a Missile Expansion.
Continue back to the Main Quarry in the Phazon Mines. The X-Ray Visor is actually not too far out of your way, so skip to that page if you want to get it now. But it's just as much on your way coming back after you get the Grapple Beam.