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Why the SA-X seems to assist Samus is unclear, but it is likely that the X saw two threats: one with only a few strands of Metroid DNA (Samus), and a full-blooded, incredibly powerful Metroid (the Omega Metroid). The SA-X then attacked the greater threat; if this is the case, then it probably intended to finish off Samus after the Omega Metroid was dealt with. It is possible, however, that Nintendo was recreating the ending of Super Metroid where the Metroid hatchling, after growing a relationship with Samus (its "adoptive mother"), sacrifices itself to save her from the final blow. The SA-X may have done the same thing. Less likely but still possible, after being defeated by Samus the SA-X grows to respect Samus as an admirable adversary and therefore protects her.

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Q: In Metroid Fusion why did Sa-x help Samus to kill The Omega Metroid?
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