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The Pirates were formed soon after the Galactic Federation. The Pirates made it their goal to raid Federal ships, kill the crews, and steal whatever loot they had. Often it was the fuel or weapons they stole, sometimes armour, and sometimes the ships themselves.
The Bounty Hunters were created as a team to combat the Pirates; one of these Hunters became Samus Aran.
Attack on K-2L
On planet K-2L, an outpost of planet Earth and a Galactic Federation and Chozo settlement, a young girl named Samus was living with her family, and the Pirates suddenly ambushed and attacked the whole planet, leaving no survivors, and Ridley arrived and killed Samus' parents in front of the girl. Samus, before her father was killed, tried to befriend Ridley because she was so young, but Ridley laughed at her and tossed her aside, before burning her father to death. Then, the Pirates burned the planet to the ground and destroyed all civilization. Samus was left a distraught orphan and the Chozo adopted her and raised her to be a fearless Hunter.
The Space Pirates had found planet Zebes, a planet rich in energy, and they invaded, killed the native Chozo, and, led by Ridley, they founded a post on Zebes, and also bought a new and deadly bio-weapon: the Metroids, which were airborne, life-draining parasites which could also grow into adults and become dominant predators. Faced with this devastating threat, the Federation sent their warriors to fight the Pirates and stop the Metroids from escaping. Samus, on her first mission, went after the Pirates and killed Kraid and Ridley, avenging her parents' death, but then she faced Mother Brain and her Metroids. She fought and defeated them.
Zebes malfunctioned and the entire planet began to blow due to the symboiotic link Mother Brain had with her computer systems embedded to the planet's core. So Samus had to run for her ship, and she escaped - along with two other Space Pirate ships - the Frigate Orpheon and the Sol Paragon Frigate. Frigate Orpheon went to planet Tallon IV; another Pirate outpost.
On this planet, the Pirates were investigating a vast Chozo empire which had crumbled due to a strange element - named Phazon, it was one which had sentience; it possessed and infected life forms, and made them hostile and barbaric. The Chozo had died off when their members had become infected with Phazon and killed each other. The Pirates ruthlessly tore apart the Ruins of the Chozo empire and they tried their best to open a portal to the Impact Crater, where the meteor carrying Phazon had hit. But the Pirates were unsuccessful; they needed twelve Chozo Artefacts to proceed. Samus, intercepting a signal, came to the planet, chased a resurrected Ridley, found all twelve Artefacts, and was stopped by Ridley just as the gate opened, but he destroyed the gateway. Samus fought Ridley and killed him again with the help of the temple's defense mechanisms, leading to him falling several stories and dying in a fireball. But Samus went into the Crater itself after the Chozo Ghosts opened the gateway for her, and met the source of the corruption - a massive, mutated Metroid named Metroid Prime, which had Pirate armour. She killed it and although it seized her DNA and her suit, she ended the biological threat to Tallon.
The Pirates operation in this sector was a disaster; Samus destroyed months and possibly years of their research - and destroyed the Metroid pods and the creatures themselves.
The Pirates were hunting in space when a Galactic Federation ship ambushed them, they crashed on a planet named Aether. Fifty years ago, another Phazon meteor had hit Aether, tearing apart dimensions. The surviving Pirates went through portals and found a dark dimension, inhabited by demons named Ing, who possessed some Pirates; the remainder went back to Aether to report. Their greatest discovery was loads of Phazon.
Samus made planetfall and hunted them down, they were disturbed by her ruthless manner and her new black suit - but they found out, when they saw two Samuses, that the dark one was not Samus, but a clone of her. They offered the clone their services, but Dark Samus ruthlessly killed the recruiters, showing she had no time for the Pirates either.
This was possibly the greatest disaster in Pirate history; Samus destroyed their labs and Dark Aether too, robbing them of precious Phazon.
The Federation Attack
Dark Samus brainwashed the Pirates in the Phazon Crisis and amassed armies of them to take over the universe. But Samus managed to stop them after much effort; even though the Pirates injected Samus with Phazon, turned the other Bounty Hunters against Samus, and took over a whole Federation planet and vessel. The Pirate seige was initially successful; but they failed when the Federation came to planet Phaaze, the source of all Phazon, and destroyed it.
In this operation, the planet Urtraghia was revealed. It was called "the Pirate Homeworld" by the Federation. Considered to be all Pirates' birthplaces, it was later revealed to be just one homeworld they had invaded and that they were galactic nomads.
The X Parasites
Later, the Pirates found a creature called the X, which was a parasite and could clone its victims. An X Parasite wrought havoc on the Federation; but Samus defeated it when it assumed a clone of her.
It is unknown what the Pirates' schemes will be in the future, but in the Bottleship Incident the Zebesian Space Pirates had been cloned by the Federation, who sought to create armies of them for some evil purpose. Later revealed to be the return of Mother Brain and the return of the Pirates.
Metroid Prime 3: Corruption