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Instinctively, it was trying to eliminate the Omega Metroid because the Metroids are the natural predator to the X; the Omega Metroid was a greater threat to it. If it had succeded in killing it, it would have attacked Samus after that. Also, they could have been trying to re-create the Super Metroid scene where the Metroid larvae protects Samus from the Mother Brain.

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