Remember, the X and Metroids are "natural" enemies. In Fusion, the SA-X was willing to die in order to destroy the Metroid lab and an X core willing to blow up BSL along itself. Later, a SA-X "saved" Samus from the Omega Metroid which in reality was just a self-preservation method.

Chronologically speaking, SA-X is the second doppelgänger/clone of Samus Aran, with the first being Dark Samus.

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.

The Metroid franchise has never been too cheery, but GBA's sole new Metroid entry cranked the spook factor up to eleven.