- They supposedly found it wandering around in a tunnel while they were drilling. This opens up the rather large plot hole of why didn't they just keep on drilling if the crater barrier isn't as impassible as previously thought, which is probably why it was changed in the European and Trilogy versions...but then that opens the plot hole of why does Prime have obviously artificial weapons (missile launchers etc.) on its first form if none of the technologically-advanced races made contact with it?
- The first form you see isn't the first form they saw. Wasn't there a log that said it assimilated their weapons? And since they were developing Beam Troopers at some point, and the pirates with packs have missiles...
- The problem is that that log was changed in the EU version and Trilogy, which means that canonically, no, the Pirates never directly encountered it and thus it couldn't steal their weapons. That's why this particular JBM discussion is even taking place.
- Could just be that a few Pirates got lucky and stumbled across it, but were killed and had their weapons stolen. That would explain why they never logged about finding it: they never survived the encounter.
- The easiest explanation to the North American is that the pirates found it but it escaped. Then the Chozo sealed it away under the temple that contained the bulk of Phazon.
- Nah, the Pirate Logs show that the Chozo were long gone by the time the Space Pirates arrived, with the Temple and Artifacts already identified as blocking the Impact Crater prior to the encounter with Metroid Prime.
- Except the Chozo came back briefly to seal away phazon and their own logs detail the pirate's failures. The Chozo just left because they couldn't handle being around phazon too long. Further the pirates do talk about encounters with ghosts, they don't realize those "ghosts" are the returning Chozo.
- It makes a lot more sense that the pirates' weapons were involved in Metroid Prime's armor, since they match, but since you find identical discarded armor on Phaaze, it's clear that's no longer canon. Instead that's just a natural part of the Metroid Prime life cycle.
- The Space Pirates didn't create Metroid Prime's carapace in any version. Even in the original NA version, it was specifically a phazon mutation.
- However, it has just occurred to me that A) phazon can affect machines as well as animals and B) phazon turns out to be one huge spanning conciousness. Maybe it just copied the pirates' weapons remotely and started adding it to each new phazon metroid. It'd explain those fission metroids that have weaknesses to specific samus-beams.
- Or it just grabbed some Chozo weapons when it fought them. That also has the advantage of explaining why it's beam weapons have the special effects when the Space Pirates were never able to copy those.
Headscratchers / Metroid Prime
In the NA version of Prime 1, some Space Pirate logs talk about the Metroid Prime, discussing the armor they made for it, its morphology, etc. However, the Metroid Prime lives in the Impact Crater, and the Space Pirates never make their way to the Impact Crater itself, thanks to the Chozo Artifacts. So how do they even know about the Metroid Prime?