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  • Accidental Aesop: Don't kill off an entire species of animal, as doing so will disrupt the ecosystem and may cause something worse to appear.
  • 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.
    • Just how true was the claim that Samus couldn't use the Ice Beam because of her Metroid DNA? Considering the fact the Federation was deliberately withholding upgrades from her so she couldn't kill the SA-X since they saw potential in it, it's highly likely they also lied about the Ice Beam so Samus couldn't use it against the SA-X; or, more likely, the Metroids they were breeding on the ship. Combine this with the fact that Samus gets and uses the Ice Beam with no ill effects at the end of the game, and it comes off as a Rewatch Bonus.
  • 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.
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    • 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.
    • The Omega Metroid at the end. There is no elaborate attack pattern to it, all it does is slowly walk forward and scratch you when you're close, and it'll keep backing off while being blasted with the Ice Beam. There is a time limit, but you'll kill it so fast that it shouldn't matter at all. Certainly a very disappointing final boss after all the incredible boss fights in the game.
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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.
  • Catharsis Factor: Finally being able to defeat the SA-X after having to run from it for a whole game is extremely satisfying.
  • Cheese Strategy:
    • In the room where Serris is fought, there is a spot underwater closest to the door you entered in. Crouch there, and Serris will never be able to hit you while you can blast away at him.
    • Similarly, for the second B.O.X. fight, if Samus hangs from the ladder above the raised underwater section, she cannot be hit by the security robot's jumping, and the missiles it fires are easy to take out with her plasma beam, and she is able to hit the robot's vulnerable section with a diagonal downward aim, making the boss trivially easy.
  • 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.
  • Difficulty Spike: Roughly halfway into the game the X try to blow up the station to kill Samus, in an attempt to protect the X on SR388. Up to that point most normal enemies, bosses and even the SA-X encounters were relatively not that aggressive or fast-paced. However, after the boss fight with The Scientist (which itself isn't that tough, though the time limit can make it nerve-wreaking), normal enemies tend to have more tricks up their sleeves such as flight or additional projectiles, all the following bosses are dramatically harder (with the exception of the B.O.X. refight), and the encounters with the SA-X offer Samus next to no hiding spots and are overwhelmingly more frantic and desperate.
  • 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.
  • 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.
  • Good Bad Bugs: The Gold Zebesians that appear near the end of the game have to be shot in the back to damage them. However, they can also be damaged by just having Samus shoot a charged Wave Beam shot at their front, then turning her to face away from the Zebesian before the attack reaches them.
  • Harsher in Hindsight:
    • 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".
    • Any mention of Ridley in the context of his appearance in this game is generally followed by hyperbolic terror of the ear-damaging power of his screeching, which is loud even by the standards of later games.
  • Signature Scene:
  • 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.
    • 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.
  • Unwinnable by Insanity: The TRO Trap, which is a very tricky Sequence Break that lets Samus fight Nettori (the root boss) before defeating Yakuza (the suplexing spider). It's unwinnable because the game breaks when bosses are defeated out of the scripted order, as Nettori will give you an error message saying Level 1 hatches are unlocked instead of the Plasma Beam, and Yakuza will be gone if you try to go and fight it afterwards; it's insane because executing it requires you to do a very tricky Shinespark to a path you shouldn't even know exists at that point in order to skip Yakuza, then navigate through several areas without the Space Jump that the boss gives.
  • 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.
    • Around the release of Metroid: Samus Returns, many 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; not a flaw, but a deliberate choice made to finely tune the game's pacing and enable its much acclaimed atmosphere. 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.
  • WTH, Costuming Department?: The Fusion Suit's Varia form, a bright yellow-green with magenta accents, is considered to be one of the worst suits in the series, if not the worst. Here it is, as seen in Prime. It's so infamous that the yellow-green was changed to a deeper forest green and the accents became pink instead of magenta when Samus Returns brought it in. That said, general consensus is that the purple and cyan Fusion Gravity Suit more than makes up for it.

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