Metroid Prime and its alternate form Dark Samus is the main antagonist of the Prime subseries. It is a strange, black-carapace, red-eyed creature with a humanoid face within its shell and the ability to control and horribly mutate anything it attaches to. Metroid Prime appears in Metroid Prime as the final boss, and after its defeat, reforms itself by stealing Samus' Phazon Suit to become Dark Samus, a black-colored doppelgänger of Samus.

Metroid Prime appeared in Tallon IV shortly after the impact of the Leviathan, a living Phazon meteor, fused with a Metroid unfortunate enough to cross its path. It caused severe damage to the Chozo colony before the Artifact Temple was built to contain Metroid Prime inside the impact crater of the Leviathan. According to the NTSC version of Metroid Prime, Space Pirate miners eventually discovered the creature, eventually dubbing it Metroid Prime after containing it with security units and drones brought to their laboratories to perform experiment

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