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It is never explained, though it could easily be interpreted that the baby metroid, being the very last one of its kind, was heavily experimented on/used by the Pirates to start multiplying it and creating more metroids by exposing it to unknown substances (mutating it into the giant form in the process). Another factor could be that since the metroid is not in its homeworld, it can't molt into its next stage in its evolution (it could be missing some substance only found in SR 388), and thus can only grow in size while staying in its larva form.

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