With the Phazon Suit in your possession, we'll now be able to track down the last few items to be found in the game. Firstly, go all the way back to the Phazon Mining Tunnel. On the way don't be afraid to walk on the Phazon pools, you won't get hurt by them anymore. When you reach the Quarantine Access B tunnel, scan the Metroid floating around to reveal it as a Fission Metroid.
These Metroids are a pain, as after taking enough damage it'll split in two, cloning itself and creating another Metroid. You'll then have to use the correct Beam Weapon corresponding to the color of the two Metroids to defeat them. If they bug you too much, use a Power Bomb to incinerate it on the spot.
Keep going to the Phazon Mining Tunnel, way down at the base of this narrow winding shaft you'll locate the final artifact, the Artifact of Newborn. Now we'll be able to access the Impact Crater - the resting place of the monstrous creature the Pirates were talking about in various Pirate Data entries.
Also go back to the Fungal Hall Access room, just below the large mushrooms at the base of the shaft you'll find Missile PM.07 (deal with the invisible Pulse Bombus first). If you run into trouble on the way through the fungal halls with all the Metroids everywhere, drop a Power Bomb to send them packing. With these two items in hand, go back to the Elite Quarters (reload your missiles along the way) and ride up the elevator to the upper level of the room.
Go over to the door on the right and head through. Inside you'll find Energy Tank PM.02 - the final one. Scan the button ahead to open up the gate. The next gigantic room has a few surprises. Don't worry about the Metroids floating around, as they'll come too close to the Phazon pools in the floor and explode! Watch out for the various Turrets in this room as you ascend.
Also remember to track down Missile PM.05 in this room - the very last Missile to find and your very last item, grab this to score a 100% item pickup. Even with the destruction of the Omega Pirate there's still a few Pirates left in the area, deal with them as you climb up. Climb all the way up to the top of the room to find a door there leading to an elevator going up to Magmoor.
Say a well-deserved goodbye to the mines and return to Magmoor from here. With all the items and artifacts tracked down it's time to return to the Tallon Overworld. Hopefully by now you should have roughly a 94-95% logbook entry rate, if you've missed any non-critical stuff to scan go and scan them now.
We're now near the end of this long journey. Save your game back at Samus' gunship, with all twelve artifacts in hand we can go and unlock the seal at the Artifact Temple to gain access to the Impact Crater. Head on over to the Artifact Temple and look down through the window overlooking the open area when you get there. Everything looks normal below, but it won't be soon.
Walk down the ramp and go over to the central pillar where you found the first artifact. All twelve pillars will activate and begin powering up the central pillar. A beam of light will shoot out of the central pillar into the air and the ground below it will glow. But just before the entrance can open, the last remaining soldier of the Pirates will turn up - Meta Ridley!
This time he's found you and it'll be a showdown to the death. Ridley will swoop down and destroy the central pillar, shutting off the gate. He'll drop a few bombs towards the exit which is now blocked by a force field, so you're stuck out here. When you return to Samus' visor quickly scan Ridley for your logbook and refer to the bosses guide for tips on sending this old fiend back to where it came from.
With the defeat of Meta Ridley you'll witness an interesting event. The Chozo said in the Chozo Lore entries that they'd never leave this place until the poison was gone - they're not joking. After taking down all of Ridley's health, the numerous huge bird-like statues above the temple will come to life and begin glowing red.
Each one will fire down an energy beam into Ridley's chest, eventually knocking the dragon down into the crater below where he finally meets his end in a spectacular explosion. Twelve Chozo Ghosts will then appear where the pillars once stood, but these are the real Chozo spirits.
They'll use their power to open up the gate leading down to the Impact Crater for you, from now on the glowing energy field in the center of the platform will take you down to the crater. With the Pirates finally defeated, you now have to face off against the source of all the Phazon.
Before going down you might want to save your game back at Samus' gunship, but there's also a Save Station and a Missile Reload Station down in the Impact Crater (dunno how they got there).