Federation Force spoilers (a real thing that can happen), but my new headcanon for the Samus boss fight is that the mind-control was entirely a body-puppeting situation, and the way the pirates messed up was using morph ball in the first place. I like the headcanon that Samus uses astral projection to control the ball while her body is energy, and so in using morph ball, the pirates inadvertently brought Samus back to consciousness while they were puppeting her body. Cue Samus wrecking the pirates immediately after. This is also why Samus is able to break her way out of a rock collapse.
My other headcanon is the pirates only captured her because she was suffering from long-term side effects/tiredness of phazon corruption (despite the phazon being gone but like viruses take a toll on your body, think similar to that). Unfortunately for the space pirates, it's Samus Aran, and she was too much of a threat to break down mentally, so they just "brainwashed" her (body puppetering). This is probably mother brain's doing, as FF is before her return in Super.
