Yanno, Metroid Prime: Federation Force raises an interesting question: How did the Pirates successfully capture Samus for brainwashing in the first place? One of the less dumb points of criticism against the game is, as cool an idea as having her as the final boss sounds on paper, the setup required just doesnt't seem plausible.

The more realistic theory is she was still working through the aftereffects of the Phazon infection and subsequent withdrawl, giving them a chance to ambush and knock her out successfully, while only losing a few dozen soldiers in the process instead of like, a hundred or more.

The sillier answer, that I personally subscribe to, is the Phazon withdrawl thing, but also that in her moment of weakness and loosened judgement, they figured out how to deliberately weaponize her item-collection OCD to lure her into an inescapable trap.