When Samus Aran defeated the titular creature of Metroid Prime, it took one last grasp at Samus and, in its seeming death throes, stole her Phazon Suit before it dissolved into a pool of Phazon. After Samus was forced to evacuate the collapsing Impact Crater, Metroid Prime had, unbeknownst to her, survived their battle. Some time afterward, the Phazon Suit's hand emerged from the pool of Phazon, albeit with clawed fingers and an eyeball on the back of its palm. This effectively signaled the rebirth of Metroid Prime as a Phazon-based cyborg: the creature's essence and remnants of Samus' DNA within the Phazon Suit constituted its biological components, while the Phazon Suit itself constituted its mechanical component by becoming the creature's new body. Thanks to these traits, the reborn Metroid Prime managed to acquire all of Samus' abilities, as well as human-level cognition. However, the creature was also obsessed with absorbing Phazon, a trait it retained from its time as Metroid Prime.
Dark Samus, as she would come to be known by the Space Pirates, is first seen by the Pirates in Metroid Prime 2: Echoes. They first believe she is Samus with a new suit and new goals, as she only steals Phazon the Pirates are mining on Aether for her own sustenance. Her actions later result in the Pirates' operation being discovered, leading to Samus' eventual arrival. Dark Samus fights Samus several times across Aether, prompting the Pirates to consider an alliance with her, though this never occurs. Once Samus defeats the Ing and destroys Dark Aether, Dark Samus confronts her for the last time, but appears to disintegrate after losing.
After her defeat, Metroid Prime 3: Corruption begins with Dark Samus' remains being unknowingly collected by the Space Pirates as they clean up their Phazon mining operation, allowing her to reform. She absorbs all Phazon aboard the ship, and in doing so gains further developed cognition alongside a more streamlined Phazon Suit. Thanks to her further developed cognition, Dark Samus corrupts the few Pirates she leaves alive into serving her and sets off toward her new goal: galactic conquest via the spread of Phazon across any and all planets she comes across. In the end, Dark Samus confronts Samus for the final time on Phaaze, first in direct combat and then after merging with Aurora Unit 313. In the end, Samus destroys 313 and, because of its symbiotic connection to both Dark Samus and Phaaze, definitively kills Dark Samus and renders any Phazon inert.
Super Smash Bros. for Nintendo 3DS/Wii U
Dark Samus is an assist trophy in the game. Her design from Metroid Prime 3: Corruption. Some of Dark Samus' attack animations are similar to Samus', such as her down tilt and up smash.
Super Smash Bros. Ultimate
Dark Samus appeared in Super Smash Bros. Ultimate as a playable fighter. She was revealed on August 8, 2018, during the first Ultimate-centered Nintendo Direct, being announced alongside Simon Belmont, Richter Belmont, Chrom, and King K. Rool. According to Masahiro Sakurai, Dark Samus and fellow Echo Fighter Chrom were included because of significant fan demand from overseas and Japan, respectively. Dark Samus' design is a combination of her organic features and color scheme from Metroid Prime 2: Echoes and her redesigned Phazon Suit from Metroid Prime 3: Corruption.
- Dark Samus is the second playable character to be created outside of Japan and the first to be created in the United States.
- Dark Samus is the only Echo Fighter that is a villain since Dark Pit is more of an antihero.
- Dark Samus is the second playable female villain in the Super Smash Bros. series. The first was Wendy O. Koopa.
- However, due to Wendy being an alternate costume of Bowser Jr., Dark Samus is the first female villain not to be an alternate costume.
- Dark Samus is the second clone in the Super Smash Bros. series to be a doppelgänger of the character she is derived from. The first was Dark Pit.
- Unlike Dark Pit, however, she is a cybernetically enhanced hybrid instead of a genetically identical clone.