The SA-X is the prime enemy in
Metroid Fusion. It was created when scientists and doctors were performing emergency
surgery on the legendary
bounty hunter Samus Aran (who had been infected by the
X Parasite on a previous mission). The medical team was forced to amputate key sections of
Samus's
power suit after the
X Parasite had bonded to those componants.
Samus survived the surgery and the infected pieces of the
power suit were sent off to a nearby
space station for storage and eventual study. However, something went wrong...
The X Parasite was smarter and more devious than anyone could have known. The infected power suit was teeming with X, and the parasite began to grow and evolve, eventually reaching sentience. It took the form of Samus Aran at the conclusion of Super Metroid - Samus Aran at full power. Armed with Samus's abilities, knowledge, and pieces of power suit, the X began to roam the station and killing and absorbing the resident scientists and inhabitants. The new lifeform was dubbed "SA-X", as in "Samus Aran X". When contact with the station was lost, a weakened Samus Aran was sent to investigate.
After Samus arrived at the station the SA-X began to sabotage her efforts, destroying key systems and manipulating her into unlocking high level security zones. The SA-X began hunting Samus, however it left her a wide enough berth to unlock new areas and accomplish the tasks that it itself could not. At several points Samus and the SA-X crossed paths, causing Samus to run for her life as she was highly vulnerable to the ice beam that the SA-X controlled (a side effect of the vaccine made from Metroids used during her surgery).
Eventually Samus stumbled into a high security zone on the space station and made a horrifying discovery: a secret Metroid breeding program was underway on the station, and the Galactic Federation was planning to breed and hyperaccelerate Metroid growth for their own purposes - the same plan attempted by the Space Pirates in the original Metroid. As Samus fled the Metroid captivity room she encountered the SA-X which, instead of targeting her, began targeting the Metroids. The SA-X destroyed the breeding zone portion of the station, as the X Parasites natural enemy is the Metroid. For that one brief moment the goals of Samus and the SA-X were the same.
With the horrible plan revealed, Samus made preperations to evacuate the station and destroy it before the SA-X and the other manifestations of the X Parasites could spread across the galaxy and consume it. However, the X reproduces asexually and as a result by this time there were an estimated ten SA-Xs aboard the station. Thankfully Samus only encountered one - the original SA-X - and they battled as the station broke orbit and began to drift into a nearby planet's atmosphere. By this time Samus had been restored to nearly full power and was able to make quick work of the SA-X, however it reverted to X form and fled the room before Samus could destroy it.
As Samus made her escape from the station she found that her ship had been set adrift. Suddenly an Omega Metroid (a result of the breeding program) attacked and just before it could destroy Samus, the SA-X reappeared and bonded with her, giving her the power to destroy the powerful Metroid. With the threat of the SA-X eliminated, Samus was able to board her ship and escape just before the station was destroyed.
References:
http://pocket.ign.com
http://www.vgmuseum.com
GameFAQs.com Metroid Fusion message board