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The game takes Samus Aran, a mostly silent, but strong character and not only gives her a personality that's completely off from what every other game displays, but also effectively makes Adam the actual main protagonist and reduces her to his much more active cheerleader. They made a character-driven Metroid game and practically shelved the most important character. The game tries to say that, with Samus wanting to rescue Ian and fight the Metroids, both probable suicide missions, that she's some sort of Wide-Eyed Idealist, something no game even hints at before this. Truthfully, if Adam really were the main protagonist, as in playable, Samus would likely be considered a boring Satellite Character for doing nothing but hanging on what he says and nearly always quoting him instead of giving her own opinion of things.
Adam asks you to go to a lava-filled area without the Varia Suit. Which in this series, is the only thing that can protect Samus from the heat and convection of an area full of lava. Hoo boy. To clarify - Samus already has the Varia Suit at the beginning of the game, but she's not allowed to turn it on, and she never asks why. It's not justifiable as upholding the series tradition of gaining powerups over time, either; unless you count the Dark Aether runs in Echoes (and even those had healing beacons and life pickups), there is no prior instance in the Metroid series where Samus needs to go through painfully hot or cold rooms before she can get the Varia Suit. Fusion even specifically told her not to, and that's the game that inspired Adam's role in this game.
Why Samus respects Adam so much. He never directly shows her any real respect until toward the end of the game, long after she's already completely devoted to him. The first time we ever see him show any true respect for her was his very last cutscene before he's killed off, where he tells Samus that, in essence, he's going to die with the pod the Metroid population is on and let Samus fight Ridley since she can handle him and he can't. But even then, we always see Adam treat Samus with a mixture of condescending rudeness and cold indifference, in this case rising just slightly above that to compliment how valuable a weapon she is, not as a person. Adam generally still treats Samus as just another member of his crew, despite the fact that she's not part of his crew and therefore, he has no actual authority over her, and that she's known and feared throughout the galaxy and quite possibly more skilled and qualified for the mission at hand than Adam and his entire crew combined, something more or less proven considering the fact that they were all wiped out by a combination of incompetence and treachery. In fact, Adam only has authority over Samus because she's actively deferring to him. And aside from that, Adam generally displays at least some level of the sexism that seems inherently present in the Galactic Federation. One could say that what Samus liked about him was that he treated her as an ordinary soldier, as opposed to the other soldiers who possibly treated her as just some tag-along lady, but we never really see them do that. Even then, we have Anthony, who openly teases Samus with a gender-based, semi-deriding name, "Princess," and throughout the game, even he treats Samus better than Adam does.
No authority part needs elaboration. This is not just an instance where a state legal bounty hunter, a branch of public service, should technically have jurisdiction over military since it is a non military vessel and no government order stating otherwise was brought up. It is not just that Samus is a bounty hunter so trusted by this state it regularly gives her mercenary work and had her lead their soldiers to war once. It is that Adam asks for her help. Even if Adam did have some technical authority over her she is free to back out and leave. Adam could not have have gotten two doors inside without Samus. In Fusion and Corruption Samus was actually paid to follow orders, something she actually does not like doing as she said herself in Fusion. Furthermore her superiors in Corruption were a lot less demanding and willing to apologize for their mistakes despite the fact they did not have to be since they were paying her. Where is this from Adam, who is getting charity?
Samus' weapon restrictions are justified by Adam because he wants to avoid accidental damage to innocents (Power Bombs being the main example), which is within the realms of logic. The problem is that there's no reason why Samus can't use defensive gear (like the aforementioned Varia Suit) or non-offensive powers like the Grappling Beam (which Samus authorizes herself in one cutscene).
The Power Bombs. You can play with it in the tutorial, but you are forbidden to use it for the rest of the game due to how dangerous they are to other people. You never get to use them except in the fight against the Metroid Queen, but the banger is you are never told by the game that you can use them and it only tells you after you beat the game! The worst part is that Samus at one point authorizes a power up on her own and the game displays the same unlocking screen that happens with every other power up... but no such thing happens with the power bombs. So it doesn't matter how much you pay attention to the game, the ONLY way to know you have power bombs active at that one moment is trial and error after exhausting every other possibility.
Samus' suit is inexplicably revealed to be controlled by her concentration, despite nothing in the earlier games hinting this was the case, and several others (Metroid Fusion, Metroid Prime, the Super Metroid Nintendo comic) showing that Samus' suit is made up of pieces that can be taken off, like her helmet.
Samus, despite being a one-woman wrecking crew who outright destroyed the Metroids on Zebes and almost entirely purged them from SR 388, is treated with dismissal at best and utter contempt at worst by Adam Malkovich. The events of the game, Adam's standoffish actions, and this all point to one thing: the Federation didn't want Samus there. Even though she was the best person to call in, even if she would inevitably question the goings-on of the Bottle Ship. More ridiculous, however, is that the only reason Samus is even helping out is because she respects him. Except we see him do nothing to earn that respect. Some even compared their relationship to that of an abuser and his victim. Even if that's not true, the "Any objections, Lady?" bit seems a lot like sexual harassment, or at least gender-based harassment.
The subplot involving "The Deleter," a traitorous member of Adam's team, is brought up and then never truly resolved. The closest thing is that Mother Brain drops a bridge on the Deleter off screen, after which Samus finds his body, revealing his identity to be James. The Deleter's very presence seemed more like they needed a quick and convenient way to get rid of some of Adam's crew, who could be disposed of once the story didn't need them anymore.
Everything involving Ridley is a concentrated storm of these:
Samus, at first, doesn't recognize adolescent Ridley as being Ridley because he has patches of white fur growing on his back, despite the rest of his body being nearly identical to adult Ridley.
In the pre-boss battle cutscene, Anthony is supposedly killed (via Ridley swatting him off a platform), but is revealed at the end to have not only survived through a ridiculous set of contrivances, but only revealed himself after Melissa and the Metroid Queen were defeated. He doesn't bother to contact Samus at any point after his near-death experience (even when it was shown that both of them working together were a force to be reckoned with), but he takes his own sweet time showing up while knowing there's still a job to do (find the survivors and leave).
Samus gets a bout of post-traumatic stress disorder after seeing Ridley at his full-grown size, despite every other Metroid showing Samus facing him with resolve and determination (six times not counting the X parasite body in Fusion), even after games where he was left in situations he had no way of coming back from, like the ending of Metroid Prime or Metroid: Zero Mission and him not even coming back here (its just a clone and she should know that). No explanation is given for her freakout, and it even makes the semi-official Metroid manga series from Japan (where Samus faced a similar bout after Ridley mocks her parents' deaths, then overcomes it and beats Ridley soundly) pointless as a result.
Adam shoots Samus in the back. For no justifiable reason. The reason he gives is because she was about to shoot a Metroid and wanted to stop her in fear that the Metroids wouldn't be vulnerable to ice anymore (they still were). ''And he does this by shooting her, leaving her unconscious, disabling her suit, and with only Adam himself to defend her at that point. Adam himself admits that he wouldn't be able to take Ridley, so say in the event that Ridley or another boss had shown up, both of them probably would have been slaughtered.
From a writing standpoint, it would make a slight amount of sense. It's an attempt to create intrigue, since the Deleter is still walking around, it's an attempt to lead the player to believe that Samus has been attacked by him. The main problem is that they apparently didn't think for even a second how much of an asshole and idiot this would make Adam look like.
There is a rational reason for him to do it but that reason causes a much worse wallbanger. The real reason is that he needed Samus to be disabled so she wouldn't be able to stop him from sacrificing himself to destroy the Metroid section of the station. When Samus tries to stop him and take his place she's unable to move properly and Adam tells her that it has to be him since he wouldn't be able to fight Ridley so if she sacrificed herself instead the mission would probably fail. But the problem is that this scene mirrors the flashback where a young and brash Samus tried to sacrifice herself to save Adam's brother but it was already too late and staying any longer would have put everyone at risk. Writers tend to use mirrored events like this to show how a character has changed and grown from their younger and inexperienced pasts....only in this case Samus not only makes the SAME decision with the SAME result, but Adam KNOWS she is going to so he forcibly puts her out of commission first. So yes, the complete reason for why Adam shot her in the back is because the writing says that Samus has not grown or matured at all since leaving the Federation, and Adam knows this already.