this nice little bit of info from wikipedia is quite interesting... I suppose that metroid prime could have been captured according to the pirate logs... but the chozo logs say otherwise..
Both could work, "Prime" crashes into Tallon and creates a crater. The Pirates contain it, and it escapes absorbing weapons and terrorizes the planet. The Chozo as great and mighty as they are, capture and seal the "Great Beast" away.
The Chozo sealing Prime happened at least like 20 years before the Pirates came along. =/
better yet come to think about it, I figure that its more along the lines of, the space pirates came into contact with it. It grafted some of the weapons into itself while the space pirates encountered it in the phazon mines or the "series of tunnels". And sometime after that the space pirates managed to seal it off in the impact crater somehow with the artifacts.
As far as I gathered, the Chozo imprisoned Metroid Prime some time before the arrival of the Space Pirates, but the Phazon that it had created slowly killed them off, corrupting their spirits and turning them into malicious phantoms. Then the Space Pirates excavated the site and encountered the creature in the chamber where it was imprisoned and were able to capture it. It absorbed several weapons and defensive mechanisms during their studies on it.
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English please. LOL
Well think about this then... There are Chozo logs that mention the Chozo seeing the invaders (pirates). The series of tunnels mentioned by the pirates, sound like the tunnels within the crater itself. Heres someting else to look at too, the pirates were mining into the ground and when you are in the phazon mines you take an elevator ride; well look out the window and you can see the artifact site . So, theoretically the priates could have encountered Prime as they were mining; which would still leave Prime contained under the artifact site. Another thing to look at is, the doors in the impact crater. Those are space pirate doors down there and how the heck would an "ammo station:" end up down there too. LOL
Just a thought
It is quite possible that 'The Worm' was a seperate entity from the Metroid Prime when the Leviathan Seed first impacted. What the Chozo call The Worm could in fact be the core of the Leviathan Seed, which is what generates the Phazon or 'Great Poison'. The Metroid Prime, in which case would likely be the guardian for said core. When the Chozo trapped 'The Worm', the Metroid Prime could be elsewhere, and therefore not sealed. The Space Pirates would then be able to later capture the Prime, have it escape, fuseing with some of their tech in the process, and retreat into the Leviathan Seed. Once there, it would absorb the source of the Phazon on Tallon IV, as it seems to have some sort of addiction to the substance, and then start producing a different form of Phazon, the 'Red Phazon' seen in the impact crater, and only on the Tallon IV one.