The SA-X (named by Adam and presumably short for Samus Aran-X) was the main antagonist of Metroid Fusion and the eleventh boss Samus faces on the Biologic Space Laboratories research station. It is an X Parasite mimicking Samus Aran and her Power Suit.

You know that the SA-X reproduce by asexual division. Because of this mechanism, there are now no fewer than 10 SA-X aboard the station." Adam: "Samus, you must go. Get out.

Stick to the low ground and fire charged beam shots directly at the SA-X to destroy it. Your beam must be fully charged to damage it. As it approaches, Space Jump over the SA-X to the other side of the floor while charging your beam, and release the shot when you land.

It's because the x in general and the metroids are mortal enemies. When the SA-X arrived at the battle between Samus and the Omega Metroid, It saw a powerful member of it's mortal enemy, and a weakened Samus. It just decided to first fight the bigger threat. Helping Samus was just a side-effect.