SA-X

The Samus Aran-X (or SA-X for short) is the main antagonist of Metroid Fusion. It is an almost-identical duplicate of Samus at maximum strength.

After being attacked by an X parasite on SR388, several pieces of Samus's Power Suit were infected and surgically removed and sent to the Quarantine Bay on the Biologic Space Labs (BSL) research station. It was there that the SA-X spawned. With the use of a Power Bomb, the SA-X escaped from the Quarantine Bay, and also released several X-infected specimens from SR388, starting a massive infestation.

History
After escaping from the Quarantine Bay, the SA-X roams the BSL station undetected for the time being. It is first seen after Samus descends the Main Elevator to go to Sector 1 (SRX); it blows up the wall on the left side of the elevator, walks into the room, stops and faces the screen, which zooms in, showing the entity's white pupiless eyes, before jumping over the elevator shaft and blowing up the hatch and leaving the room.

The computer onboard Samus's ship finds out about the SA-X when Samus goes to Sector 2 (TRO), and warns her to be on the lookout for it, because it possesses all of Samus's weapons and abilities. On top of that, Samus is still very weak from her surgery, and the Metroid vaccine she was given to cure her X-infection has given her the Metroids' weakness to cold temperatures, meaning she can frozen just like a Metroid. Therefore, the computer advises Samus to run or stay hidden if she comes across the SA-X and avoid fighting it. During her trek through Sector 2, Samus has two separate encounters with the SA-X, one after acquiring bomb data, and another after defeating Zazabi and regaining her High-Jump and Spring Ball. As Samus leaves Sector 2, Samus evaluates the nature of the SA-X, stating that it is, essentially, a heartless version of her, and knows that she has to stop it before it realizes what it is capable of.

From then on, Samus has several encounters with the SA-X, and they mostly involve Samus running and hiding from her doppelganger and/or uncovering a passageway to escape.

While trying to find a way out of Sector 6 (NOC), due to the SA-X hunting her, Samus comes across a Restricted Laboratory, where the Galactic Federation had been working on a top-secret Metroid breeding program. The SA-X follows her into the lab and attacks the Metroids, triggering an emergency lock-down. Samus narrowly escapes while the lab detaches and self-destructs. However, the computer tells her that there actually 10 SA-X in the station, due to the X's ability to reproduce asexually.

Later, the computer tells Samus that the Galatic Federation believes the SA-X could be a useful bioweapon, much to her disbelief, as Samus knew that would allow the X to wreak havoc on the universe, and explains they don't expect her help, and for that reason, they stopped providing her with support data. When Samus calls the computer "Adam", it reveals that it has her late CO's personality, and tells her to go to the Operations Room and set the station's orbit to intercept SR388, destroying all the X on the station and on the planet.

At the Operations Deck, Samus encounters an SA-X, most likely the same one at the Main Elevator. Fortunately, she has enough weaponry to fight the fiend. After blasting the SA-X several times, it transforms into a gigantic monster; nonetheless, Samus triumphs. However, the SA-X's Core X escapes before Samus can absorb it. Upon returning to the Docking Bay after initiating the propulsion sequence, Samus is ambushed and attacked by an Omega Metroid. Fortunately, the recently-defeated SA-X appears, reassumes its original form, and attacks the Omega Metroid with its Ice Beam, who slashes the SA-X in retaliation, causing it  to go to its Core X form. Samus immediately absorbs the SA-X, regaining her energy, Ice Beam, and original Power Suit. Using her Ice Beam, Samus defeats the Omega Metroid, after which, her ship returns, piloted by the Etecoons and Dachoras; she immediately boards the ship just before the station crashes into SR388, destroying the station, the planet, and the X parasites.