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The end battles of MP3 consist of a battle with dark samus followed by a battle with aurora unit 313, the stolen unit from the valhalla ship.

If you mean in the bonus ending with 100% completion where the mysterious ship follows Samus, that would be Sylux (believed to be Sylux) piloting (most likely) the Dialanche. Sylux was one of the bounty hunters from Metroid Prime Hunters who you would fight whenever you ran into him. Like the other hunters, he was after the false "ultamate power", which was really a monster called Gorea. Sylux hates the Galactic Federation and steals prototype equipment from them, such as his main weapon and his suit.

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