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Horrific as it may sound, there are two of them now.
~ A space pirate log referring to Dark Samus' arrival.

Dark Samus is the central antagonist of the Metroid Prime Trilogy.

She is a dark copy of the hero Samus Aran and the reborn form of the phazon-mutated Metroid Prime.

History

Metroid Prime

After Samus defeated Metroid Prime, it clung onto her 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 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 tonnes 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 didn't get far before she met Dark Samus, and Dark Samus lured her almost to death in Dark Aether, where the Ing attacked, but only stole equipment. 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 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 awhile 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 was. Dark Samus was full of anger and 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 disintegrated and was believed destroyed in Dark Aether.

Metroid Prime 3: Corruption

She serves as the main antagonist. However, her 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 be destroyed, 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, she merges with an Aurora Unit to fight Samus, but is defeated, and is destroyed for good.

Super Smash Bros. series

Dark Samus appears as an Assist Trophy in the video game; Super Smash Bros 4 for the Wii U and 3DS. When Dark Samus is summoned, she unleashed a barrage of Phazon beams, and Phazon Spikes.

Dark Samus also as one of Samus' alternate costumes.

Personality

Similarly to another big bad of the Metroid Series, Ridley, Dark Samus never talks (unless one counts her deep, sinister laugh), this makes it hard for people to analyze her personality, though there are some notable characteristics 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 to win, she once corrupted Rundas, Ghor, and Gandrayda, so that she didn't have to risk getting damaged. The only creatures she is shown to respect are the Metroids. If her greedy and egotistical qualities weren't 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 tries to come in her way, she will instantly try to kill that creature, despite if it is allies or anyone else, 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 psychopath who has no control whatsoever and has a terrible laugh, while in Corruption, she is presented much more sophisticated, which can also make her seem more threatening, considering she can be emotionless while killing people. 

Navigation

           Metroid Villains

Space Pirates
Mother Brain | Dark Samus | Ridley | Draygon | Kraid | Omega Pirate | Phantoon | Ridley Robot

Metroids
Alpha Metroid | Gamma Metroid | Metroid Prime | Omega Metroid | Zeta Metroid | Queen Metroid

Ing
Emperor Ing | Amorbis | Chykka | Guardians | Quadraxis

X Parasites
B.O.X. | Neo Ridley | Nettori | Nightmare | SA-X

Galactic Federation
The Deleter

Chozo
Diggernaut | Ruins Test

Other
Phaaze | Sheegoth | Crocomire | Imago | King Worm | Parasite Queen | Vorash | Sylux | Gorea