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 Final phase has the Metroid Queen mixing up the direction of her fire attacks by lighting the ceiling and wall on fire. She'll unleash more green fireballs and try to blow you into the wall so use the Spider Ball to power through those attacks. And that's about it!

Only the Charge Beam and Screw Attack can damage the SA-X, though Ice Missiles can temporarily immobilize it. The Screw Attack is also ineffective, as Samus will take damage as well, even while the SA-X is frozen. The SA-X has a tendency to use its own Screw Attack as a counter-attack whenever Samus lands a blow.

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.