The Omega Pirate was created by injecting Phazon into Pirate embryos, one of which was successful, the others became Elite Pirates and became psychotic. But the Omega Pirate was a success, he was equipped with missile shoulder pads, gigantic claws, accelerated recovery process, and the ability to summon other Pirates and use Phazon to heal his injuries.
Preparation for war
So the Pirates believed they had it made with their project, and protected the Omega Pirate in a dark room of the Phazon Mines. But Samus Aran came and gatecrashed their project. She killed many Pirates, hacked their computers, got their data, freed many Metroids to kill their masters, and on the way she finally met the Omega Pirate.
The Omega Pirate was a challenging enemy, because he could turn invisible due to the Phazon qualities he had injected into himself, and he roared as Samus approached. The Pirate then broke out of his tank in one smash, and walked round the room, smashing Phazon shockwaves at her. He also launched rockets from his backpack. Samus had to Bomb each of his feet and Super Missile his shoulder pads, and his knee joints, to make him vulnerable. Then, when he went into a Phazon pool to recover, she had to switch to X-Ray visor, because he was invisible, and then she had to fire a Super Missile at his chest, wounding the beast. The giant Pirate would summon smaller Pirates to defend himself and distract Samus, but this didn't matter because she was armed and dangerous. She focused on the Pirate and eventually bought him down, but he didn't go quietly, he stood over her, sneering, and then collapsed on Samus herself, disintegrating him into a pool of Phazon, which bubbled all round her, yet his remains turned into a Phazon mould round Samus, giving her the awesome Phazon Suit.