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Horrific as it may sound, there are two of them now.
Dark Samus is the central antagonist of the Metroid Prime trilogy. Her name comes from how she is a dark copy of the hero Samus Aran and the reborn form of the Phazon-mutated Metroid Prime.
After she defeated Metroid Prime, the Metroid Prime clung onto Samus's Power suit and tore the Phazon suit off of her in a desperate move to save itself. After Samus leaves the planet, the DNA of Metroid Prime combines with the DNA of Samus and the Phazon Suit in order to reincarnate itself as Dark Samus.
Metroid Prime 2: Echoes
Dark Samus serves as a central antagonist and final boss. She left planet Tallon IV and she traveled the Universe in search of Phazon, driven by her instincts from Metroid Prime. Samus eventually found a planet named Aether, which had suffered a war with a dark dimension when strange dark creatures had invaded Aether and its native species, the Luminoth. Dark Samus traveled through Aether and found portals to a dark dimension which she entered, and to her delight, she found tons of Phazon from the meteor impact. Coming and going through the portals, Dark Samus ate all the Phazon she wanted, and grew in power, regenerating herself after her defeat on Tallon IV.
The Galactic Federation, who would later be her enemies, came to Aether and were attacked and killed by the Ing. Dark Samus later found her old nemesis, Samus Aran, come to Aether, in search of the Troopers. Samus did not get far before she met Dark Samus, and Dark Samus lured her almost to death in Dark Aether, where the Ing attacked, but only barely missed the bounty hunter. So Dark Samus traversed Dark Aether for awhile.
Samus later met Dark Samus again when she was in the Agon Wastes. Dark Samus was feeding off of Phazon crystals, and Samus entered, unaware of who Dark Samus was. She soon learned she was the Metroid Prime when she used Phazon to attack. This became a fight to the death which Samus won.
Dark Samus exploded into blue particles upon "death". However, it was just a maximum overload and she repaired herself. The particles reached the Torvus Bog, where she solidified and laughed at Samus before flying off. Dark Samus then returned in the Sanctuary Fortress, where she was seen sadistically laughing after gunning down some Space Pirates trying to protect their Phazon. Samus challenged her to an epic elevator battle, which Dark Samus became invisible after a while due to all the Phazon power. Later, rather than admit defeat, Dark Samus committed suicide by jumping off the elevator tower and falling into the city below.
Dark Samus was unseen through the rest of Samus' adventure, but right at the end, she made a surprise return. Dark Samus returned and she was now skeletal, bereft of armor, and her organs resembled Metroid Prime's, thus confirming who she truly was. Enraged, Dark Samus blocked off Samus' escape from Dark Aether by gliding and firing Phazon missiles at her, Samus noted that if she repelled them back at Dark Samus it would cause another overload. After enough hits, Dark Samus crashed to the ground and crawled towards Samus, trying to absorb her Light Suit, but she disintegrates and was believed destroyed in Dark Aether.
Metroid Prime 3: Corruption
Dark Samus serves as the main antagonist. Despite her disintegration, Dark Samus' particles re-formed in space around Aether. In Metroid Prime 3: Corruption, on the planet Phaaze, the source of all Phazon, she controls the Leviathan Seeds: living creatures that are spawned from Phaaze and contain rooms within their bodies, and carry massive amounts of Phazon.
She plants a seed first into the Pirate Homeworld. Then, Dark Samus, along with the help of the space pirates, leads an attack on the Galactic Federation and manages to implant one of the gigantic Seeds in the planet Bryyo.
Samus manages to stop one seed from crashing into Norion, a planet important to the Galactic Federation. Dark Samus appears then and hits Samus and her bounty hunter allies and implants Phazon within their bodies. Soon after, a Seed is implanted into the planet, Elysia. The Seeds begin to corrupt the planets and the forms of life (In Elysia's case).
To destroy each of the Leviathan Seeds, Samus enters them and must destroy a monster who is powered by the Phazon energy inside (probably inside a lung-like cavity). Every time she destroys a monster, the Phazon released begins to corrupt her even further.
In the end, Dark Samus merges with Aurora Unit 313 to fight Samus, but is defeated, and is destroyed for good.
Super Smash Bros. series
Super Smash Bros. Brawl
Dark Samus appears as a Trophy and a sticker, the latter of which can be equipped to increase Samus' resistance to battering attacks. An enemy called "Dark Samus" appears on "Co-op Event 7: Battle of the Dark Sides" allied with Dark Link, but it is just a black silhouette of Samus rather than her Phazon doppelganger.
Super Smash Bros. for Wii U and 3DS
Dark Samus appears as an Assist Trophy in the game. When Dark Samus is summoned, she unleashed a barrage of Phazon beams and Phazon Spikes. Dark Samus is also one of Samus' alternate costumes. Players can defeat Dark Samus by shooting her enough times before she disappears.
Super Smash Bros. Ultimate
Dark Samus makes her playable Smash Bros. debut in Super Smash Bros. Ultimate as a playable character. As Samus's Echo Fighter, Dark Samus plays nearly identically to Samus, except her attacks have a shadowy effect, as well as levitating in her idle animation. She was added in the game due to high requests from fans. Her Classic Mode campaign "The Great Poison Given Form" is based on team battles against heroes while allied with dark, evil, or corrupted variants of the heroes, such as Luigi in an alternate costume resembling Waluigi while fighting against Mario, Peach, and Daisy. The only exceptions are the penultimate battle, which is a free for all against Ridley and Samus, and the final battle against Master Hand and Crazy Hand.
Similarly to another villain of the Metroid franchise, Ridley, Dark Samus never talks (unless one counts her deep and sinister laugh), this makes it hard for people to analyze her personality, though there are some notable characteristics that she has.
Her name is quite telling, she is extremely ruthless and cruel, as she will do anything to win a battle, even risking her allies lives just because she wants the advantage. She once corrupted Rundas, Ghor, and Gandrayda, so that she did not have to risk getting damaged. The only creatures she is shown to respect are the Metroids. If her greedy and egotistical qualities were not shown enough yet, she is very materialistic for the Phazon, most likely because of her origins as Metroid Prime, she wants to grow and grow and become more powerful, if anyone tried to get in her way, she will instantly destroy the threat, regardless if they are friend or foe, even fellow space pirates get killed if they even try to question her goal. While she has always been insane, her character changes a lot depending on the game, which might be related to her growing from the Phazon, in Echoes, she is a complete maniac who is completely out of control and has a terrible laugh, while in Corruption, she is more of a psychopath; presented much more sophisticated, which can also make her seem more threatening, considering that she can be emotionless while killing people.
Dark Samus in Metroid Prime 2: Echoes.
Dark Samus in Metroid Prime 3: Corruption.
Dark Samus as she/it appears in the manga.
Dark Samus in Super Smash Bros. For Wii U and Super Smash Bros. For 3DS.
Dark Samus in Super Smash Bros. Ultimate.
Dark Samus' Super Smash Bros. Ultimate splash screen.
Dark Samus' voice consists of distorted unused recordings of Samus' grunts and screams.
In Echoes, Dark Samus is labeled as a class Platinum-AAA threat level by the Space Pirates.
Dark Samus will always attempt to deflect Missiles with an energy wave.
In the Super Smash Bros. series, Dark Samus is the second character, besides Little Mac, and the only villain that appeared as an Assist Trophy before becoming a playable character in later games.
Despite being referred to as a "she" in various media, her bio in Ultimate initially referred to her as an "it," which may have been due to her being composed of Phazon. Her original self, Metroid Prime, was also referred to as an "it" before becoming Dark Samus.