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For unexplained reasons, the Omega Metroid attacked Samus despite the latter having Metroid DNA, whereas the other Metroids in the Restricted Area ignored her. This may be because the Metroids in the Restricted Area were preoccupied with the SA-X. Not to mention, the SA-X approached the Restricted Area and started to attack the Metroids. One of the Metroids (which transformed into the Omega Metroid) probably took Samus as the SA-X, due to the similar appearance. Or, it just may be a generally violent creature, and therefore attacked Samus. Or perhaps it saw Samus as competition, as there was no Metroid Queen aboard.

Taken from [1].

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