Plasma Beam, Plasma Beam (Power Bombs), Plasma Beam. I can't stress this enough. Use charged Plasma Shots on his knee and shoulder joints. Super Missiles are decent for damage, but they're unreliable - use them if you want, but the Plasma Beam is a little steadier in terms of accuracy, I've found. Even when he's using his siphon, you can sometimes hit the joints if you're close enough to him. When you've blown his joints away, he'll be weak and call several beam troopers to assist him. At this point, what you want to do is get near one of the Phazon pools around the arena. Draw all of his reinforcements to you and lay a Power Bomb to wipe them all out at once and without needing to worry about the color-coding.* Now - because you're near one of the Phazon pools already, and because he will never teleport to the pool you're standing by, expect him to appear by one of the other two pools (by the way - the second the pirate troopers are dealt with, begin charging a Plasma Shot). When he appears, hit him with your fully charged shot. Fire off into the corner so you don't hit him with the uncharged shot and charge another, but move toward him as you do so. You want to charge the shot until it's almost, but not entirely, fully charged. Hit him with that, too, and hurry back to the Phazon pool you were camping at before. OP will never appear at the same pool twice in a row, so charge another Plasma Shot and aim for the pool that he didn't appear at before. Use the same method to get in two more charged shots. His health should be more than half gone by this point (assuming you're not playing on Hypermode**). This is where it gets tricky. It's possible to finish him off before he restores his armor (just repeat the same method as stated above for when he reappears at the other Phazon pool), but rather difficult. Don't worry about it if he does, though, provided you have enough energy and Power Bombs to survive another round of destroying his joint armor and dealing with the pirates he summons. Once the joints are gone again, you should have ample time and margin for error to finish him off. Enjoy your new Phazon Suit.
* You can also use a well-place Power Bomb to destroy all his armor without using the Plasma Beam, but if you haven't done much backtracking to find PB expansions, you might want to save them for the beam pirates, for which speed is much more important. There are only eight Power Bombs to be had in the game, even if you have gotten all the expansions (which I'm not sure is possible at this point), so my advice is to save them for the beam pirates and suffer through with the Plasma Beam for everything else. Depends how well you place the bombs and how many you have.
** God help you if you're playing on Hypermode. He'll have twice the health and so you'll need twice the energy and Power Bombs to outlast him and his annoying summon magic. This guy gave me some trouble on Hypermode.
Hope this helped. Feel free to ask if you need clarification on anything.
