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.
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.
If you don't know what you're doing then this boss will be more difficult than all the earlier bosses combined, but once you know the proper attack and defense it's not all that bad, still hard but doable.
Part of the problem is that the in-game information on this monster is a bit vague. While it is more susceptible to Missiles than to Beam weapons, Beam weapons still have their place here. So you really need to do some trial and error to find the most effective weapons rather than depend on what the game says. Fortunately we've done a lot of that kind of thing for you.
At the start of the battle the Omega Pirate fights much like the other Elite Pirates you've met. It has four protective shields, one on each leg and one on each shoulder, and you need to break all four of these. So target one of them and after each of its shockwave attacks fire back as you're jumping over it. If you're using plain missiles then you can get a hit in more often, and this may be the way to go for the shoulders since you don't have as many clear shots. As with the Elite Pirates, do not fire when its gathering energy in its hand since it will just absorb it. It takes about five ordinary Missile hits, or two Charged Plasma Beam hits, or one Super Missile hit to destroy one shield. As you're doing this, try to keep your distance and avoid being cornered. If the Pirate does trap you then switch to Morph Ball and Boost away from it. If it fires missiles at you then jump to the side to avoid them.
When all four shields are gone, the Omega Pirate summons some Troopers as reinforcements then it disappears. It seems to be random which Troopers you get, but the first group will probably be all one color and the groups that follow have up to two colors. Switch to the appropriate beam and fire two or three Charge Beams at them to cut their number a bit, but they're not your top priority.
In the time it took to fire those Charge Beams, the Omega Pirate will have found a pool of Phazon to start recharging itself. It's only visible to X-Ray at this time and it's also the only time it can take actual damage, so switch visors and find the monster and shoot it. The Super Missile works very well here if you've pre-charged your Power Beam, but the Plasma Beam fired repeatedly does almost as well. Meanwhile keep weaving to avoid fire from leftover Troopers. If you do enough damage then the Omega Pirate moves to another pool of Phazon so you can do more damage if you find it quickly.
When the monster regenerates its shields it becomes visible and the battle continues as at the beginning. If there are still Troopers around they will quickly fall victim to the Omega Pirate's shockwaves and if you're lucky you may get an Ultra Health pickup. Occasionally you'll meet a Trooper who likes to cling to the walls and you'll need to take it out yourself.
There are pools of Phazon where you're fighting, and you will take damage from them, but it won't be much compared with what the Omega Pirate is trying to do to you, so don't worry too much about avoiding them; if you die it won't be from Phazon poisoning.
There is a technique we should mention, for doing damage using the Power Bomb. The idea is to switch to locate the pool of Phazon where the monster is recharging, approach in Morph Ball form, jump and drop a Power Bomb in the air, then quickly stand up. The last part is needed because the monster is immune to damage while you're in Morph Ball mode. This might work for you but it seems to be version dependent.
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.
When the Omega Pirate was defeated it also lowered a force field blocking access to a small elevator on one side of the room. Scan the panel to activate it and step in to be taken to the upper level of the room. Now follow the catwalk to the exit.
Processing Center Access
An Energy Tank, the last expansion in the game, is waiting here. It will restore full health so it's good timing. Scan the security panel to unblock the passage. You can't do this from the other side, which is why you had to go all the way through the Metroid caves to get to Elite Quarters. Note that even though the floor here is covered with Phazon, you can wade through it without damage now that you have the Phazon Suit.
Phazon Processing Center
You're back in previously explored territory, but you'll find Plasma Troopers in this area now. You now have all the upgrades and expansions in the game, and the next step is to collect the remaining Chozo Artifacts.