Phazon Mines
Now it's time to face the Phazon Mines boss and collect the last upgrade in the game.
Metroid Quarantine B
If you're returning here or restoring from a save, Metroids will break out the canisters here. Also, with no Troopers to keep them at bay, Metroids will occupy the part of the room near Quarantine Access B. In addition, the room goes almost completely dark so you'll need to switch to Thermal or X-Ray to find your way. There is a stack of boxes here to top off your supplies.
Go up the ramp near the save station to the exit on the upper level.
Elite Quarters Access
A Plasma Trooper pops out as you enter the main part of the room. Defeat it quickly before you take too much damage.
There is a barrier in front of the exit here, and the controls are frozen in an ice-like substance. As you would expect, the Plasma Beam clears the way.
Elite Quarters
Step into the room to see the Omega Pirate in its cryogenic canister. Get a scan before coming too close because you'll be pretty busy during the actual battle. Get a bit closer and the Pirate will break out, give you a menacing look, and start to attack.
When the battle is over the Omega Pirate keels over and lands on top of you (ew!). Then it kind of melts away into your armor (double ew!). The result of this combination of the Phazon from the Pirate and your armor is the next upgrade, the Phazon Suit.