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  • Alternate Character Interpretation:
    • The SA-X. The computer proposes the X parasites as mindless organisms that gradually adapt with the more they devour, and the multiple SA-X markedly makes a target out of Samus since she's their biggest threat. But when it narrowly saves Samus at the end from the Omega Metroid and then promptly dies as a result yet grants Samus the Ice Beam needed to win, can it be construed as a pragmatic assault leading to its demise or a mix of Enemy Mine and a sort of villainous Heroic Sacrifice? Or perhaps it saw that it was being faced with two possiblilities of losing and decided it would rather be absorbed by Samus than killed by the Omega Metroid?
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    • Some fans have theorized that Nightmare, during his first appearance in the background of his level, isn't actually stalking Samus, but running away from the X parasites before being killed off and taken over by them.
  • Anti-Climax Boss:
    • The SA-X's monster form. Despite looking horrifying, it dies to 2-3 charge shots and its only attack is to Goomba Stomp Samus. The eye Core X it turns into afterwards is actually more threatening.
    • B.O.X. Round 2. The first time, you fight him on a completely flat surface, and he tosses bombs that spit fire waves that go up and down, requiring you to maneuver around to avoid the tall waves. The second time, he is fought in a depression in the ground that he cannot move out of, but that the monkey bars you have to clutch to extend past, allowing you to stay harmlessly out of his reach. To counter this, he uses missiles instead of the fire bombs this time, and those missiles home in on you, but those missiles are easily shot down with the Plasma Beam. Also, he will come to a resting position in perfect position for a diagonal missile attack. The only part of the battle where hanging in one spot cannot prevent harm is the Core-X fight.
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  • Broken Base: Aside from the split opinions on how a Metroid game should handle storytelling, Samus's radically altered suit really divided fans. To this day, people still argue over whether the Fusion Suit looks so alien it becomes cool, or is just a really terrible design.
  • Demonic Spiders: The X infected Ki-hunters do massive amounts of damage even by this game's standards and are faced during a section where you've likely taken tons of damage from an SA-X chase. They're also reasonably durable without using Power Bombs until you get the Plasma Beam. In fact, the first room after you obtain the Plasma Beam, you encounter rows of Ki-hunters, specifically designed to show off the new weaponry.
  • Ensemble Dark Horse: The Nightmare boss is extremely memorable due to the sheer horror of all the things that surround it. That's probably why it was brought back for Other M.
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  • Epileptic Trees: Given that the only scientists who were in any meaningful contact with the baby Metroid before it was stolen by the space pirates were the ones at the Ceres Space Colony, the fact that BSL and the Federation have Metroid DNA to create a serum to cure Samus with and enact a restricted Metroid breeding program makes their collaboration with them look pretty suspect. Even if one factors in the Other M Bottle Ship, it all points back to Ceres Space Colony in the end.
  • Franchise Original Sin: After eight years in rest since Super Metroid, the franchise exited hibernation with two well-received games in 2002, one of them being Metroid Fusion. Despite the positive reception, a point of criticism from fans was its stronger focus on a story, more linear level design and game progression, and it was even the first time Samus interacted with another character in-game. Since the generally poor reception of Other M, (particularly that game's choices in characterizing Samus Aran and making the game very linear), many have tried to lay the blame for that direction at the feet of Fusion.
  • Harsher in Hindsight: Because of the base breaking Other M has caused, some fans don't look toward Fusion favorably as they once did thanks to Fusion's Franchise Original Sin toward linear gameplay and plot-driven story.
    • Either this or Hilarious in Hindsight, but the computer's theoretical questions "Did this Adam care for you? Would he sit in a safe Command Room and order you to die?" after his controversial behaviour in Other M. Not to mention that this is also the part where the computer ends up remembering that it's actually Adam's Brain Uploading, so depending on how quickly he realized this, he may have deliberately insulted himself for said behaviour.
    • A story perspective, destroying all but one Metroid is this. Samus had been given a mission to exterminate all Metroids because of how dangerous they were (and an extended version, undergoing mutations due to Phazon). Doing so allowed all the X-Parasites to resurge after going into hiding. Now that all the Metroids are gone, they are able to multiply and conquer every living thing on SR388 (as seen in the Stinger in Samus Returns).
  • Hilarious in Hindsight:
    • A female protagonist stranded on a space station gone completely off the rails and fighting her way through it while being constantly stalked by an enemy that is impossible to kill, with a government-based agenda behind the whole thing, and a part where said enemy is seemingly killed off, only to be revealed that there's many more of it on the station? Are we talking about Metroid: Fusion or Alien: Isolation?
    • During the early days of the franchise (and even partially now), people thought Samus' name was Metroid because of the title. Come this game, and Samus technically is a Metroid now, if only partially.
    • One of the more contentious moments in Other M, a section where Samus runs through a heated area taking damage because despite having it, she hasn't been authorized by Adam to activate her heat shielding, makes a couple of the ship's computer's lines unintentionally hilarious. Especially since these come out of the mouth of the same character that didn't authorize Samus to turn on her heat shielding in Other M.
      Ship's Computer: And avoid the ultra-heated areas: your suit can't take such high temperatures yet, but we're working on it.
      Ship's Computer: There are no ultra-heated areas on this route, so turn back if you enter one.
    • Late in the game, the Computer CO uses the phrase "please understand".
  • It's Short, So It Sucks!: The game drew some criticism for its short length.
  • Memetic Mutation: If someone streams the game on Twitch, expect to see "EMERGENCY IN FrankerZ", due to the popular dog emote rhyming with "Sector 3".
  • Most Annoying Sound:
    • Neo-Ridley has ear-splitting screams that he will drop when you hit him, when he grabs you, and generally when he feels like it.
    • The noise Samus makes when she gets hurt. Too much of that and you'll be praying for a game over.
    • The Broken Record "WARNING! NO ENTRY WITHOUT AUTHORIZATION!" alarm that plays from when you try to enter the Restricted Zone for the first time to when you actually succeed in entering. It only stops during the boss fight against the Security Robot B.O.X., and even plays if you have the game paused.
      • Another Broken Record is "EMERGENCY IN SECTOR 3" that plays from when you are leaving Sector 5 until you reach the Navigation Room.
    • Not long after the Restricted Zone, this song, called The Final Command, plays as the background BGM. Get used to it; once it starts it never ever stops until the final boss fight. Woe be those who decided now would be a good time to explore all around the station and see what they can get into now that you have Samus' full ability loadout.
    • After killing the mutated SA-X, if you go off-screen from it after defeating it, it will start making a noise that continuously repeats until you return to the same screen as it.
    • The Power Bombs make an extremely painful tearing noise when they go off, especially when playing the game in headphone mode. So much so that they toned down their sound effect in Zero Mission.
  • Rescued from the Scrappy Heap: Retroactively. Many find Computer-Adam in this game to be a far more pleasant character than his living counterpart in Other M. His line of "Would he sit in a safe Command Room and order you to die?" could even be interpreted as a Take That! to an incredibly stupid move the original Adam made.
  • Special Effect Failure: Whenever the Omega Metroid slashes with its claw, something about the animation looks wrong even when played at normal speed, as though the Omega Metroid is reaching too far considering the length of its arm. Viewing the animation frame-by-frame reveals the problem: its whole right arm briefly disconnects from the rest of its body. There are a couple frames where the disembodied arm is clearly just awkwardly floating in the air a good distance away from the Omega Metroid itself.
  • That One Boss:
    • The well-named Nightmare is a Gravity Master where you must understand its three phases. During phase 2, missiles drop like rocks, so you must rely on a charge beam. Its final phase has it fly erratically around the arena inflicting tons of Collision Damage along the way. There is a way to manipulate Nightmare into stopping early so you can shoot its face some more, but it's very hard to pick up on.
    • Yakuza, the giant spider that knows kung fu and suplexes you into the ground. Once you destroy its body, though, the head will Space Jump erratically, occasionally throwing debris at odd angles. You have to learn how to juggle it properly. That its hitboxes in the second phase allow it to hurt you without touching you is fuel in the fire. And if you lose, you have to come back all the way from Samus's gunship, due to a power outage preventing all save rooms from working. There's also an SA-X chase not very long after this that requires great speed and reflexes as there's no way to avoid being seen.
    • B.O.X. the security robot, which requires Samus to hang from monkeybars, is invulnerable while attacking, and is frequently jumping to make its weak point harder to reach. And the worst part: the battle is fought twice! However, the second fight can be cheesed, as there's one spot where he cannot hit you by jumping, can be hit from a diagonal angle, and his rockets are easily dispatched as ever, making the second fight become an Anticlimax Boss.
    • Serris enjoys Super Speed in an Underwater Boss Battle (hint: Fight it on one of the three tiny platforms.) Every time you hit it, it Turns Red and gains a speed boost, flying all over the arena. Lord help you if it knocks you into the water, as it will hit you again on the way out. However, there is a spot underwater near the door you came in from where if you crouch, Serris will NEVER hit you, even if you leave the game on overnight.
    • The Omega Metroid has a slash attack which does ludicrous amounts of damage, will stun you for some time, and makes you unable to move. Oh, and there's a timer.
    • The Plant Core X, due to there being 3 annoying phases. In the first, there are Spores that can not only harm you,but can also knock you into the "Venus Samus Traps" between the platforms.In the second, the boss will start firing its Plasma beam, which hurts a good amount, can also knock you into the flowers, and have a surprising large hitbox. Finally, once you get it into its core X, it still fires its beam, both on its own and Everytime you hit it with a missile.
  • They Wasted a Perfectly Good Plot: Adam informs Samus late into the game, that there are now no fewer than ten SA-Xs running around the station, and they are hunting her. This would be a terrifying prospect gameplay-wise. Even when Samus is recovering strength, technology, and energy tanks... she'd be more outclassed and outnumbered than ever before. The player would be fighting to survive to the story's conclusion. However, we never see or battle more than one SA-X, at any one time.
  • Vindicated by History:
    • Zig-zagged. While considered as a good game at release, there was some controversy about the game's increased linearity and occasional use of dialogue and monologue. Then Metroid Prime Pinball and Metroid Prime: Hunters became the new black sheep of the franchise, and Fusion was seen as a worthy installment... for a while. After Other M, opinions were split between those who blamed this game for Other M's faults and those who continued to feel vindicated by Other M's plot being a rehashed and inferior version of Fusion's. Additionally, a lot of Fusion's fans were grumpy with the choices made in Other M regarding the characters introduced in Fusion, particularly Adam.
    • In the lead-up to the release of Metroid: Samus Returns and the time afterwards, many YouTubers have started to speak highly of the game. It is commonly argued that for what it lacks in exploration, it makes up with an overwhelming sense of dread, possibly exceeding that of Super Metroid. Fusion is now considered to contain some of the best examples of video game horror outside of actual Survival Horror games. What's more, fans have even expressed interest in a remake due to the appearance of X-Parasites in Samus Returns.
  • Unwinnable by Insanity: The TRO Trap glitch, which messes up the game's scripting and makes it impossible to finish if you Sequence Break past Yakuza and fight Nettori first. Thing is, it requires a hard to execute shinespark maneuver to execute it, so you'd have to be doing it on purpose in order to trigger the glitch.
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