User blog comment:Majora's Warth's Reincarnation/Metroid Prime conterversy/@comment-1660176-20100906145656

Well, it's possible that Metroid Prime was a Phazon Metroid exposed to critical amounts of Phazon, because similar skins are found on Phaaze. The scan even says so. Then again, the other three Leviathans had guardians that were from the environment. It's unclear if the pirates even cracked the Cypher, (how a Metroid could have gotten in) as it's different in the PAL and NTSC versions of the game.

As for how the Metroids got on Phaaze, it's extremely likely that the Pirates brought them.