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Metroid: Other M
Mortrialus: Samus's Heroic BSOD upon seeing Ridley is still alive, a character she has already killed at least four other times at this point in the story line.
Crazyrabbits: Agreed, but this example needs some elaboration. Other M more or less legitimizes the Metroid manga series that was produced in the late 90's. In that story, Samus is the sole survivor of a massacre on her home colony by the Space Pirates and Ridley (who eats her parents), just like in the game. However, in the manga, Samus at one point experiences post-traumatic stress disorder during a battle with Ridley, where he goads her by mentioning how he murdered her parents. Samus shuts down for a period of time (and even contemplates suicide) before overcoming her demons and facing Ridley in an epic confrontation, monologuing that she's not afraid of him anymore.
Why is this relevant, you ask? It's because by the time she encounters Ridley on the Bottle Ship, she's already fought him several times in several different forms. She should be at a point where the appearance of Ridley shouldn't even phase her (and has left several different versions of him in circumstances that shouldn't have been normally possible to come back from). In short, Sakamoto reintroduced a character flaw Samus already overcame in a prior story for the sole purpose of overcoming it again.
Mightymoose101 The absolute worse part of the scene? From a storytelling and overall narrative standpoint, it's completely pointless. The incident itself is never referred to again, Samus doesn't grow as a character from it and Adam doesn't seem even slightly upset that she got one of his men killed, Ridley is killed offscreen, denying Samus both the chance at avenging Anthony or facing her demons, the most Samus seems to think of Anthony afterwards is a brief musing on whether or not he was awake as he horribly burned alive in lava, and Anthony himself comes back to life through a sequence of events so contrived they had to have added it only to make Samus seem less incompetent. In short, Sakamoto reintroduced a character flaw Samus already overcame in a prior story for the sole purpose of overcoming it again, and then doesn't bother seeing it through.
Mr W: By far the moment where I lost all hope it was gonna get better was the Sector Zero scene. I could ramble on about it, but I will sum it up in a few words: Adam shoots Samus. Without any provocation. ...What the hell, Nintendo?
Korval: While the Sector Zero scene is the worst entire scene, the worst part of that entire scene isn't where Adam shoots Samus. No, it's the Ian Call Back. Because it says everything the game wants to say about Samus Aran. Samus never gets to avenge her mistake with Ian. She was wrong when she was a girl, and she's still wrong now. Even though the entire point of My Greatest Failure is to give the protagonist the opportunity to overcome their greatest failure, to redeem themselves. But not here; in this case, it exists solely to show that Samus is still childish, she still needs a man to tell her what to do. It shows that the true protagonist of Metroid: Other M is Adam Malkovich.
Abodos: In contrast with about half the people who played the game, I generally liked the gameplay but found the story to be passable, neither great nor abysmal. The part that really left a bad taste in my mouth, however, was the whole sequence between the awesome battle with the Queen Metroid and the end credits. The whole introduction of Melissa and her backstory felt very rushed and contrived, and the "boss battle," which consists of you merely aiming (not shooting) at Melissa, was very poorly done, especially in contrast to the previous battle. I hope that next time, Nintendo will look back at this game when making the next entry in the series and preserve the good parts while avoiding mistakes such as these.
Peteroak96: While the whole authorization to get new power ups was already stupid, the worst offender is entering Sector 3, the hot area of the game where you take damage because of the heat, without the Varia Suit activated, and taking damage for quite a few rooms until Adam authorizes it. Why even de-activate something that is supposed to help Samus and causes to problems to the ship is beyond me, but Adam should had authorized it beforehand.
Indirect Active Transport: The flashback explaining the origin of Adam's catchphrase. It can be argued there are worse scenes, individually, but the grand scope is more important. It directly contradicts Fusion, where Samus states anyone else saying "lady" would sound sarcastic but Adam made it sound respectful. Yet Other M shows him saying it with sarcasm and disdain. More, it shows Samus in the military under Adam's command even though the manga already showed this could never have happened the way Other M tells it. Samus was a police officer engaged in inter service rivalry with the military and one of the few people who was not glad-handing Adam every time he showed up, unafraid to tell him off. Then Samus needlessly beats herself up, it is not her fault her commanding officer is unprofessional. It should not be overlooked that Samus is portrayed as a twerp when she's supposed to be huge and shrouded in myth either. This scene is the preview for most of Other M's plotting. First, it contradicts what was already established with reckless abandon. While the very concept of Metroid sequels lend themselves to plot holes, this is the first time a game so blindly dug such holes in ways so hard to wave over. Secondly it starts an annoying trend of Samus beating herself up for small slights, which makes even Fusion and Zero Mission's monologs harder to read afterwards. Self deprecation was forgettable before, now it's a wonder if this folk hero has any self esteem at all. Not that you would know Samus is a living legend if you only played Other M. Which brings us to strike three, Samus is puny and easily bullied when she has been consistently shown to be tall and awe inspiring up until now, even in the manga. This is the bounty hunter widely believed to be a male cyborg? She spends so much time unarmored, has such a faint frame and a visor that exposes her face down to the mouth! That could never happen. This is the warrior people thought could destroy planets? Yet now that she has actually done so she gets less respect than when it was an unfounded rumor? Metroid has other narrative flaws, Other M in particular, but this is where they all became highlighted, where it became impossible to look at the same way again.
Scar Doll: The reintroduction of fan-favorite boss Nightmare in Metroid Other M was my most disappointing moment. The Nightmare from Metroid Fusion was a popular boss among fans for its difficulty and mechanics, but also for its imposing appearance and bizarrely serene Leitmotif. One particularly memorable moment was when Samus blasted off its mask, revealing a hideous roaring face that began to melt as the battle continued. In contrast, Other M's Nightmare has only generic action music without any reference to the old theme and its face looks like a pouting baby's with no melting whatsoever. To add insult to injury, its roar was replaced with an infant's wailing.
Tuckerscreator: The Metroid Manga is full of plenty of mind-boggling moments that make me glad it was never imported to the US. Samus gets a cute sidekick pet that inexplicably grows ginormous, the alien designs look like Star Trek ripoffs, unneeded annoying characters from the Super Metroid comic are reintroduced, and there are narmy scenes like the Space Pirates equipping teddy bear-butterflies with laser blasters. But the biggest one has to be the manga's explanation for why the Chozo don't appear in the games: they were suicidally pacifistic, not only completely lacking planetary defense weapons (minus one easily evaporated energy shield) but genetically rewiring themselves to be unable to perform violence. As such, the Space Pirates invade Zebes once and completely slaughter them.
...what?!? The most advanced civilization in the galaxy, and they don't have a single weapon? On a planet full of dangerous predators, they thought being unable to fight even in self-defense was a good idea? And if they're so crazily pacifistic, then why did they train Samus as a warrior, arm her with an cybernetic suit of Powered Armor, and build bioweapons like the Metroids or combat robots like Torizos and Elysia's drones? And it gets worse. This is on top of the Chozo already all being old and infertile, even though they are masters of bioengineering who can create new lifeforms, organic supercomputers, and hybrids like Samus. Why didn't the Chozo use the time spent on wiring themselves against violence to instead make themselves fertile again or clone themselves and rebuild their species? It's a horrible excuse for the Chozo's absence that makes one wonder if they wanted to all go extinct.