The latest Metroid game, Other M, took some...liberties with the universe's story, and what it did to hero Samus in particular didn't go down too well. Many people blame the game's developers, Team Ninja for this, but that's not very fair.
You need to blame someone from Nintendo instead. Something Team Ninja is only too happy to do.
In an interview with G4TV, Team Ninja's Yosuke Hayashi makes it very clear the game's story was Nintendo's job, not his own studio's.
"The story for Other M was definitely the product of Mr. Sakamoto at Nintendo", he said."We definitely worked with them on the project, but that was all him."
Way to keep it subtle, Hayashi! For reference, and as die-hard fans of the series will already know, that's Yoshio Sakamoto, the co-creator of Metroid itself, and director of games like Super Metroid. So as far out as the story seemed, it's coming from the guy who has had a hand in every Metroid game ever made, so...make of that what you will.