Clyde32 said:
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Not sure.
I read a theory that said Dark Samus's motive was to protect her species (the metroids) from Samus (with her intelligence she forsaw the demise of her species at the hands of Samus). She wanted to create an environment where her species thrived, which was Phazon. She wanted to create more highly evolved metroids, so she wouldn't be alone anymore (the only intelligent metroid).