I've seen a lot of people not understand what was meant by "joint mission" in Other M, and Samus saying that it was her first time since her Federation days that she was following the orders of a CO, claiming that it breaks canon with Prime 3 (because she was working with the Federation and Admiral Dane in Prime 3). In Prime 3, Samus and the other Bounty Hunters were hired as a 3rd party to assist the Federation. They weren't under Federation Jurisdiction, but they still had rules to follow, such as when Rundas said "I just received word that the Federation is allowing all Bounty Hunters to use ship-command devices." (Much like if you invite someone into your home, it isn't illegal for them to sit in your chair, but if you tell them they aren't allowed to and they do it anyway, you might kick them out and not invite them back.) In Other M (and Fusion), Samus IS under Federation Jurisdiction and was made a temporary member of 07th Platoon. She HAS to...