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Mike321 said:
Other M is a terrible game, unfortunately it exists and it's canon, most importantly makes the prime series (one of the best trilogies period) non-canon. But instead of getting the metroid franchise back on track, nintendo decides to make a spin-off (btw at the very least it looks bad). Great work with one of your best franchises nintendo

Without wishing to restart a long standing debate, I'm pretty sure Other M doesn't make the Prime games non canon. I've heard that a lot, and it's an assumption I've never really gotten the reasoning behind.

The most common places it seems to come from are a Go Nintendo article reporting on an interview with Sakamoto where he basically calls the Prime games "side stories" and says they aren't connected with the story of Other M. Translation's a bit of an iffy prospect, but the vast majority of Japanese speaking people who I've seen comment on this claim that his words lean much more towards the Prime games essentially not having a whole lot to do with Other M rather than taking place in an entirely alternate universe.

Second place I've seen this assumption arise from is a cutscene from Other M where Samus says that the Bottle Ship stuff was the "first joint mission" with the Federation since becoming a bounty hunter. And that's perfectly fine. Escorting troopers in Prime 3 to blow up some door isn't really a full blown mission as much as it was part of a mission that she was doing mostly independently, and there's no point in the Prime series (or any Metroid game before Other M chronologically) where she's shown working jointly with the Federation.

I'd be curious on hearing your thoughts; I don't want to defend Other M's plot, but I haven't seen anything to really suggest that it makes the Prime games non canon outside of a clarified interview and some seemingly shaky assumptions about one line of dialogue in the game.