Yeah, not only did she cause the destruction of their secret Metroid breeding facility, she is also the last living thing with Metroid DNA. They definitely want her. Actually an idea I had before was that they should start the next Metroid game with "The last Metroid is in captivity. The galaxy is at peace." and then pan the camera down to see Samus in Federation custody, imprisoned before the game begins. This would be the explanation for why she doesn't have any powers at the start too
This is what I thought the game was. According to the website, there is a blurb that says trapped on a mechanical alien world, so it doesn't seem to be the case though just going off that. I could be wrong though, but if I'm not, I definitely would've wanted them to take it the GF direction. ---