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You are forgetting that Metroid Prime's core is actually Metroid Prime itself. The outer exoskeleton of Metroid Prime is simply armor. Though in the US version its stated that it absorbed several defense systems and this could be it, though this is taken away in all other Metroid Prime 1 versions, including the Trilogy version. It could be a positive mutation formed by the large amount of Phazon it consumed. Needless to say, the core "essence" is just the actual Metroid Prime, and the exoskeleton is either a mutation or part of its DNA genome.

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