Phazon Metroids and how Metroids got out there in the first place
Phazon metroids are created by infusion with Phazon from the egg stage, as any later only generates a fission metroid under normal circumstances. Metroids were brought to Phaaze by Dark Samus during the Phazon crisis, and with the massive amounts of bioenergy available to them in the form of Phazon, they were very successful; with the evolution of metroid hatchers, their numbers multiplied rapidly. Metroids were useful assets to Dark Samus’ army, and she also attempted to make herself some “siblings”- other Metroid Primes which would aid her in her conquest. Those attempts were apparently not successful.
The Metroid Prime never came from Phaaze either, but where it came from was a mystery. Given the supposed impenetrability of the Chozo seal, maybe it was on Tallon IV before the cipher was created. Perhaps metroids were brought from SR388 to Tallon IV to combat the prophecised meteor threat, though the Chozo of Tallon IV loved their world and would loathe to bring such an environmentally destructive beast as a metroid to it. Or perhaps it was an escaped Pirate specimen, which somehow breached the seal on the impact crater.
In any case, the Leviathan summoned the metroid to guard its core, like Mogenar or Helios or Omega Ridley. The metroid, being a metroid, devoured the core instead and essentially replaced it, becoming a bubbling source of Phazon. Exposure to all that Phazon mutated it heavily and transformed it into the Metroid Prime. It poured out Phazon faster than even a normal leviathan core would, having a devastating effect on Tallon IV. The rate of Phazon production caused the Phazon itself to mutate, generating red Phazon inside the crater where Prime was trapped.
Given that nobody else can get into the crater, I think it's weird but plausible to suggest that the metroid got in there pre-cipher. Some of the clearly non-biological weapons it uses could be stolen from the Chozo who attempted to defeat it. I’m open to anyone else’s theories because honestly the Metroid Prime is awesome but its existence is a huge freaking plot hole.
