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.

Less sturdy and possessing weaker shielding than the Power Suit, the Fusion Suit takes heavier damage from enemy attacks and is initially unable to protect Samus from extreme cold, to which the Metroid vaccine has left her vulnerable.

The trick is to always make sure that the SA-X is frozen. Hit it, jump over it if you need to, turn around and freeze it again. Take a step or two, turn around and hit it.

For unexplained reasons, the Omega Metroid from Metroid Fusion attacked Samus despite the latter having Metroid DNA, whereas the other Metroids in the Restricted Area ignored her. This may be because the Metroids in the Restricted Area were preoccupied with the SA-X who admittedly was attacking them at the time.