Part 57 of my Metroid Prime Video Walkthrough.
Now we have another major boss to deal with.
Don't attack him when he has his shield up (the glowing hand).
Wait for him to perform his Thunder Quake (or however it's called), jump over the shockwave and quickly attack one of his four Phazon part (shoulders and knees) with a Super Missile.
Once all those Phazon armors have been destroyed, he'll camouflage himself and call for help.
I made the mistake to ignore the pirates, since I thought the Omega Pirate will appear instantly.
Oh well.
In any case, get rid of the pirates as fast as you can and then switch to the X-Ray Visor.
The Omega Pirate will appear on one of the Phazon puddles to recover his Phazon armor (or whatever that is).
In that phase, his chest is extremely vulnerable. Attack it with Super Missile.
After one hit, he will warp to another Phazon puddle.
Keep hitting him, until he recovers his Phazon Armor. Then repeat until he is dead.
Reward: Phazon Suit
Enjoy!
Credits:
Metroid Prime is © of Nintendo/Retro Studios