Other M just seems like a random subtitle until you notice as an acronym it reads "MOM". Also if you place the M before Other it reads "Mother" signifying Samus's "relationship" with the baby Metroid and [[spoiler:MB's relationship with Madeline Bergman]].
** In fact, the "Other M" in the title probably refers to [[spoiler: MB, since she is an alternate Mother Brain.]]
*** Take a look at [[spoiler:the fake]] Madeleine Bergman's hairclip. Remind you of anything? [[spoiler:It looks like the red nuclei in the core of a Metroid.]]
** Also, Madeline Bergman warns us about MB. For a while, some could think that it was just the initials for ''Mother Brain''. [[spoiler:It's in fact a little more complicated, since they played with those initials: MB are the initials for Mother Brain, but also the initials of the director of the project, Madeline Bergman. We are lead to think that MB and Madeline Bergman are in fact one and the same person, but it's a RedHerring: MB stands for Melissa Bergman, who impersonated her own ''mother''.]]
** [[spoiler:Phantoon is the extra boss. Anyone remember what section he was the boss of in Super Metroid? The Ghost Ship. At the end of the game, Samus is all alone on the BOTTLE SHIP, making it a ghost ship]].
** A possible explanation about why [[spoiler:the baby Metroid in Super Metroid got so dang BIG: It was destined to be a Queen; how else do you think the scientists got a Queen's DNA patterns if their only source of said DNA was the remains on Samus's suit?]]
** Ever wonder how [[spoiler:Nightmare]] and [[spoiler:Ridley's remains]] end up on the Biologic Space Labs in ''Fusion''? Ever enter the rooms those two bosses' remains are left in during ''Other M's'' postgame portion only to notice that their remains are now missing?
*** Also, ever wonder why Ridley's body collapses so easily in Metroid Fusion when you encounter it in the freezer? That's not the sort of thing you usually see frozen corpses do. Unless, of course, [[spoiler: that frozen corpse was drained of all its energy by a Queen Metroid and turned into a dry, gray husk]].
** Samus' reaction to seeing Ridley seems incredibly out of character, until you realize that, at least according to some sources, Ridley never actually ''died'' until Super Metroid, the game before this one. It's not that she's scared of Ridley, it's that she's freaking out because he's ''supposed to be dead''.
*** Alternatively, Ridley's previous deaths took place between large spans of time. Other M is right after Super. He's not only supposed to be dead, he came back in record time!
Other M could be called Fridge Logic: The Game. F'rinstance consider things from Adam's perspective
* Metroids were officially destroyed according to whose report
* He opposes bio-weapons research but Samus broke protocol (an explicit extermination order) to turn over a living sample of a creature deemed too dangerous to exist to outpost science station
* He knows there is a faction in the GF out there trying to run around his recommendation and the standing "no bioweapons" ruling. So much so his XO and him are trying desperately to gather evidence
* Samus left to effectively become a one woman Blackwater after sympathetic but still less than stellar behavior and likely chasing a crusade to "rid the universe of suffering" or something akin to that or save everyone.
* Uh-oh, on a rush mission to uncover an illegal research conspiracy guess who just shows up and, oh yeah, could be the only source/expert for all this
In short played from Adam's side Samus's presence and overall participation and involvement is suspicious and possibly dangerous. Moreso when factoring in rumors of a possible assassin in his own ranks (that he observes over her comms but her presence like that could be...well a performance) This more than anything may help ease you into understanding his often overly stiff and reactionary attitude; though his trust and belief in her comes through in the end Samus, from his view, was looking as suspicious as he could be from our own
* At first, Adam's decision to [[spoiler: shoot Samus in the back]] seemed inexplicably horrible, many have even likened it to abuse and wondered why Adam didn't just [[spoiler: shoot the metroid larva]] instead but it makes sense if you think about it. [[spoiler: The metroid larva]] was acting calmly until after Adam already [[spoiler: shot Samus]] so he might have thought that [[spoiler: the larva wouldn't have attacked if left alone]] and, as far as he knew, [[spoiler: Samus was about to shoot at an unkillable metroid and get it angry at her]]. Granted, in retrospect, it was a stupid idea but it probably made sense to him at the time, especially in the heat of the moment.

Did Adam [[spoiler:die quickly and painlessly in Sector Zero's self-destruction]]? Or did he [[spoiler:suffer an incredibly painful and horrific death having the life sucked out of him by innumerable ice-proof Metroids]]?
** Invoked in-universe by Samus when she wonders whether or not [[spoiler: Anthony]] was conscious as he burned up in lava.
* Adam locks the doors behind you to keep you on the linear path. Due to a GameBreakingBug, a door becomes locked making progress impossible. Or in other words, Adam locks you in the Pyrosphere with no way out ForTheEvulz.

* The authorization system falls apart as an excuse to withold upgrades the moment Samus collects the only two new abilities in this game and immediately activates both upon acquiring them ''without waiting for Adam's permission''.
* The Power Suit working like a HenshinHero's completely breaks Fusion's ''entire plot''. Being in a coma implies a lack of concentration. Hell, it even breaks other parts of Other M's plot: how the hell did the Feds scrape Metroid goo off the Suit without her knowledge?
** To add to those examples: How did the Feds retrieve genetic material off of her suit while she was unconscious?
*** Perhaps the armor does exist out of a concentration, but can be summoned/activated by it?
**** If she merely uses concentration to summon the suit and it can be maintained when she isn't concentrating, then that breaks a fair chunk of both the Ridley scene and the Adam sacrifice scene, and we're right back where we started. Either way, it's a plothole.
** A proper explanation is as follows: During PTSD, her mind enters an unstable state which the suit interprets as her mind being about to shut down, thus it starts to shut down by itself. When she entered the coma in Fusion, it was too late for her suit to revert, because large portions of her Power Suit were corrupted by the X parasites. Accounting the fact her mind shut down too fast, the suit could never revert to its natural state.
*** That's stretching it extremely far.
** As for how they scraped off the Metroid DNA from her suit? What if there was a purification chamber she had to go through, which would wash off anyone's suit in seconds? Considering what we have seen of several Sci-fi games, this is the most suitable explanation.
* Although withholding weapons can be justified as not wanting to cause unnecessary damage, there's never a good reason for withholding defensive gear like the Varia Suit.
** Well, one can figure that Adam didn't want Samus to have full run of the ship, if she could potentially be the Deleter, so he wouldn't want to authorize the Varia Suit unless necessary, but its sorta hard to figure out the reason from Samus's end. Unless perhaps she was playing everything by the book (taking the outsider comment from Adam a bit harshly) to the point of saying "Fine I won't even use 10% of what I can do without authorization 'Sir'." Of course, this explanation seems rather stretched to this troper, but it is possible.