Samus is going to do the dramatic in-character reveal later this week, but here's the short version for people who are omniscient/sick of dealing with crazy randomness. :/ I delayed the payoff far too long, I know.
Samus hasn't been abducted by the Pirates, there's no mind-control device, there's no nerve gas and she isn't enmeshed in a secret government conspiracy any more than she normally is. She's got Phazon Madness, and she's got it bad.
Wikipedia's article on
Phazon is kind of terrible, but the short version is that she's been exposed to massive amounts of radiation/mutagenics/eeeeevil, and it's taking its toll on her. The GF have a treatment, and she'll be fine in a couple of days, but right now she's in a medical facility, babbling into her suit in the Chozo language. The Chozo may or may not be taking advantage of the opportunity to say some things.
Thanks for your time, apologies to everyone who's been bored to death with mind-control plots. :P