To the uninitiated, the Omega Pirate is possibly the most difficult boss in the game. However, if you are quick on your reflexes and wits, it can be a pushover.
The Omega Pirate has 4 points of concentrated Phazon on its armor which you must first destroy before you can attack it directly. Start with the ones on its thighs, and when those are gone, aim for the ones on its shoulders. It may be tempting to destroy these with Missiles, but you should save your ammo and take them out with charged Plasma Beam shots instead. Otherwise, all you have to do is stay back and avoid its shockwave attack by jumping over it, just like you did when fighting the Elites. Shoot your beam at the balls shortly before or after its attacks, or else it will suck them up in its hand.
After the Omega Pirate's armor is destroyed, it will phase out of normal vision, and a wave of Pirate Troopers will come after you. The kind of Trooper you get is random, so pay attention to what color they are to determine their vulnerability. Take them out as quickly as possible and immediately switch to the X-Ray Visor. It may seem as though the Omega disappears in random locations throughout the arena, but in fact it just goes over to the giant pools of Phazon to recharge its armor. This is when you need to aim a Super Missile at its chest. If you're fast enough, you can get multiple Super Missile hits in while it is in its invisible state. Try to avoid the oncoming Pirate Troopers if you can, but if they become too much for you to handle, you'll need to take them out.
Repeat this strategy until it dies. The Phazon Suit will be yours!
Like all bosses, the Omega Pirate is a rare scan.
