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.
At first glance, the SA-X looks exactly like Samus in her iconic Varia Suit. The only differences are that the armor in the SA-X's cranial section is a darker shade of red, and its eyes are blank without any pupils.
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 be 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, she evaluates the nature of the SA-X, stating that it is, essentially, a heartless and evil version of her, and knows that she has to stop it before it realizes what it is capable of, even though she can’t combat it in her current condition.
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 are 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 knows that would allow the X to wreak havoc on the universe, and explains they don't expect her help to contain the SA-X. as they knew she would try to destroy it, and for that reason, they stopped providing her with support data. When Samus calls the computer "Adam", as a tribute to her late commanding officer, Adam Malkovich, it reveals that it has his persona, 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. Luckily, she has enough weaponry to fight the fiend. After a fierce fight, Samus barely defeats the SA-X. However, its 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 back 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, piloted by the Etecoons and Dachoras that she released from the Habitation Deck earlier, returns; she immediately boards the ship and escapes from the station just before it crashes into SR388 and explodes, destroying the planet, and the X parasites.
During the boss battle with the SA-X in the Operations Deck, the SA-X's primary means of attack are the Ice Beam and Screw Attack, though it will use Super Missiles if Samus hangs from a ledge in an attempt to make her lose her grip. The Charge Beam is the only weapon that can actually hurt the SA-X; Ice Missiles can immobilize it temporarily, allowing Samus to inflict damage while the beast is frozen. However, the SA-X will retaliate with the Screw Attack after taking a hit. If Samus tries to use her Screw Attack on the SA-X at the same time, they'll both take damage.
As the SA-X takes more and more damage, its body starts to become distorted. It eventually falls to its knees and transforms into a gigantic monster that appears to be a cross between a Hornoad and Samus herself, as the X that infected Samus on SR388 had previously infected a Hornoad, with multiple Arm Cannons on its right arm and multiple visors on its head. In its monstrous form, the SA-X jumps around, trying to stomp on Samus. Again, only the Charge Beam can hurt the SA-X. In this part of the battle, it's possible for Samus to attack the SA-X with the Wave Beam from one of the upper ledges, where it can't reach her.
- Chronologically speaking, SA-X is the second doppelganger/clone of Samus Aran, with the first being Dark Samus. While created through different means, both are shown to be powerful adversaries who tested Samus' abilities. However Dark Samus was shown to have more personality, while SA-X was simply an X mimicking Samus at her full power.
- Interestingly, both Dark Samus and SA-X granted Samus a beam upgrade of some kind at some point. Samus gained the ability to use the Hyper Beam after Dark Samus infected her with Phazon (albeit through the PED Suit the Federation gave Samus) and the Ice Beam (in addition to the Unnamed Suit) after Samus absorbed SA-X.
- Ironically, the SA-X belonged to a species which had been preyed upon by the species Dark Samus originated from.
- The SA-X can only chase Samus into certain rooms; if Samus enters a room where the SA-X can't follow her, it disappears. This is most notably displayed in the first Sector 2 encounter: if Samus survives exiting the room after being spotted, the SA-X doesn't follow, and is mysteriously absent when reentering.