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  • Anti-Climax Boss: The final fight with Dark Samus. While no pushover, she's a Breather Boss compared to the Emperor Ing even with the time limit for the fight. Her death animation is also very long and drawn out.
  • Best Boss Ever:
    • The first two Dark Samus fights, which are by common consent the most fun fights in the game, particularly the Elevator Duel. Dark Samus is usually a good bit more powerful and significantly more agile than you and has a lot of tricks up her sleeve, but not so much that she's overly frustrating. Combine that with an amazing atmosphere, good opportunities to test your new powers out, and narrowly avoiding her blowing up everything around you, and top it off with excellent music.
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    • Quadraxis is also a fan-favorite battle due to the sheer scale of the fight combined with the act of tearing apart the boss's defenses little by little, and the awesome, pounding theme.
  • Best Level Ever: Excluding the portion with the Spider Guardian, the Sanctuary Fortress and Ing Hive are frequently cited as the best area of the game due to the Scenery Porn, the energetic music, the elaborate Morph Ball puzzles, and the aforementioned fights against Dark Samus on the elevator and Quadraxis.
  • Complete Monster: In the manga adaptation (Episode of Aether), "Boss", the unnamed Space Pirate leader, raids the space ship Crest and tries, alongside his crew, to hijack it, killing a civilian who happened to be there. When the Crest Captain begs "Boss" for mercy, the Space Pirate overhears a worried child calming his sister down, saying that help is on the way. "Boss" torments them as much as possible before trying to murder them, as well as everyone else on board the ship, laughing at the older child trying to protect his younger sibling. When Samus comes to the rescue, "Boss" holds one of the children and the Crest Captain hostage and when Samus aims at him, he throws the hostages, chasing after them with the intent to slice their heads off.
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  • Contested Sequel: Fun game with interesting new locales, different powerups, and increased challenge, or Mission-Pack Sequel loaded with Fake Difficulty and unnecessary key-hunting and ammo mechanics?
  • Demonic Spiders:
    • Grenchlers are basically the baby Sheegoth from the first Prime game, only smarter, faster, have more health, and are more shot happy. The only saving grace is that their shots no longer freeze.They will also pursue you if you try to avoid them,as they can swim and jump on platforms.
    • Hunter Ing can be difficult if you don't know how to deal with them. They can phase to avoid your shots, are hard to lock on to, and are generally creepy. Once you realize they can only attack you once they stop phasing, and can have all their attacks interrupted by a single light beam shot, they're cake. Even on hard mode just a handful of light beam shots will take them down, and better yet, if you're in a light-charged crystal or beacon, they have a tendency to just fly right into it and suicide when they get bored.
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    • Rezbits have a very crippling form of Interface Screw, as it completely crashes Samus's visor; you can't even see out the viewport without its aid, it crashes so hard.
    • Dark Pirate Commandoes are especially this before acquiring the Dark Visor. They only intermittently phase in and are vulnerable, their EMP bombs haze over Samus's visor with whitenoise static, they do lots of damage, the Light Beam does not nearly enough to kill them quickly, and you can't even duck out a door to escape them as the room gets locked down. Counter-intuitively, the best way to deal with them is to freeze them solid with a charged Dark Beam shot and then finish them off with a missile.
  • Disappointing Last Level: The Sky Temple. After backtracking through the entire game world to find those Sky Temple Keys, you are rewarded with the final, brand-new area... that has three rooms. These rooms are devoid of enemies and the only thing of note is the Final Boss. While its Aether equivalent didn't have much to it anyways, Sky Temple feels really shallow and empty compared to the rest of the dungeons, even more considering it's the last one in the game.
  • Ensemble Dark Horse: The Rezbits found in the Sanctuary Fortress. They're remembered for being a fun enemy with a cool design and a creative attack... although not fondly.
  • Fridge Brilliance
    • Space Pirate logs stated Metroids were freed by Dark Samus, but they don't attack her. Why? Because Dark Samus was formerly Metroid Prime. And Metroids are capable of attachment, meaning at her most evil, Dark Samus still has a place for her fellow Metroids in her Phazon corrupted heart.
    • Ing eyes are not visible in puddle form and they don't usually attack while in it. Even the Emperor Ing can't hit Samus with its eye closed, further suggesting it might be a vision problem. Why then does the Boost Guardian rely on it offensively so much? It has taken Morph Ball technology, it can "see" the same way you can!
  • Fridge Horror:
    • The Ing could have possessed Samus at any moment between her landing and her seizing the Energy Transfer Module. That, mixed in with Back from the Brink above, means that the Ing were defeated through sheer blind luck. Considering this, remember that Ing Possession generally makes the host more powerful. Imagine a horde of Ing overrunning the galaxy in a fleet of hijacked Luminoth, GF, Space Pirate, and (thanks to Samus' gunship) Chozo tech. With a possessed, even stronger than usual Samus leading the army. The galaxy wouldn't stand a ghost of a chance.
    • The threat the Ing pose, in terms of being able to possess/mimic organisms and use their abilities for their own ends, seems very similar to that posed by the X-Parasites from Metroid Fusion. But the Ing have one crucial and frightening advantage over the X: they can possess Metroids.
    • Before the second Dark Samus fight (taking place on a huge tower), you can look out the window and see two Phazon crates on a ledge. After the fight, a weakened Dark Samus falls off the tower. When you come back down, the crates are gone...
  • Goddamned Bats:
    • Dark Pirate Commandoes. They appear from nowhere in pairs, sometimes locking down the doors until they leave after a few minutes or are killed. They Flash Step all over the place, making it difficult to get a good shot at them once they vanish. They can pull up reflecting shields. They also shoot dark blasts that cause a damage-over-time effect and obscure your visor, and throw EMP grenades that turn your view into a mess of static. They would be perfect Demonic Spiders, but they aren't actually as powerful as they seem, are easily killed with a charged Dark Beam shot and a missile on any difficulty, and the Dark Visor sees right through their Flash Step invisibility. They still manage to be quite annoying.
    • Rezbits. They can put up a deflecting shield at will, become unable to be locked onto, and infect your suit with an annoying virus. Much like the Dark Pirate Commandoes, a charged Dark Beam shot and a missile takes them down in one hit, but good luck hitting them with it before they notice and put up the shield.
  • Goddamned Boss:
    • The Spider Guardian. It's a Puzzle Boss that must be done entirely in Morph Ball mode and all the wonky physics and controls associated with that. You have to bomb the boss to stun him 'then' do some creative bomb-jumping to actually hurt him before he becomes invincible again. Oh, and he does 30 damage a hit, you're going to get hit by him a lot while bombing him, and if you die you have to start all the way back before you got the last Translator package. The Trilogy release added the Spring Ball to the game, which at least removes the bomb-jumping requirement, but everything else is unchanged.
    • The Power Bomb Guardian is also this to a lesser extent; you have to navigate a network of Spider rails using your Boost, Bombs and timed drops while the boss and its Inglets lob stuff at you. Plus it's fought in Dark Aether so your health is draining the whole time!
    • The final battle with Dark Samus can also be rather aggravating- to finish her off you need to catch enough motes of her phazon shots on your charge beam to be able to unleash a blast of pure phazon back at her, but the positioning to catch the motes without getting hit can be unforgiving (you have to be directly in front of her) and if you get hit your drop your charge. If it happens enough times you can easily end up running out of time, causing an automatic loss even if you're not even CLOSE to running out of life. You can't save between the battles with the Emperor Ing and Dark Samus, but you do get some solace in that the game sets up a checkpoint just after the Emperor Ing's defeat, cutting down some of the tedium from fighting the Emperor all over again.
  • Good Bad Bugs: During the Chykka battle, standing in dark water and triggering a cutscene will cause Samus to be able to jump like she's underwater above the water once the cutscene concludes. Touching dark water again removes the effect. Just be careful, because you mess up your game if you leave the arena before killing Chykka.
  • Hilarious in Hindsight: Dark Samus debuting in Metroid Prime 2: Echoes is funny because she would one day be Promoted to Playable in Super Smash Bros. Ultimate as one of several Moveset Clones, or as they're known in that game, Echo Fighters.
  • Memetic Mutation: Science team has vapor for brains.Explanation 
  • Most Wonderful Sound: The screeches of dying Ing, especially the Ing Hunters and the various Guardians.
  • Nightmare Fuel: While all the Game Overs in the Prime trilogy are frightening, this one seems to be the one that gets to most people. Once you run out of health, you're treated to the lovely sight of Samus going into cardiac arrest as the camera zooms in on her failing heart. Complete with loud beeping and a flatline in the background. Not helping is the unnatural shape and positionnote of her heart. When Nintendo wants to go dark, they do not mess around.
  • Paranoia Fuel: The game is guilty several times over of letting you see the boss before you fight it, but it stands out in lower Torvus. Upon entering the Sacrifical Chamber, players are greeted with the sound of something huge stalking around up there and occasionally roaring. But because of the darkness and the grating, you can't see exactly what it is. There's no real danger until you actually fight it, though.
  • Scrappy Mechanic:
    • The entirety of Dark Aether can be very overwhelming: At the start of the game, Samus loses health incredibly quickly whenever she's outside a safezone, and the safezones need to be triggered manually to remain active. This causes the Dark Aether sequences to turn into a series of mad dashes from one safezone to the next, carefully waiting one run after the other so that Samus' health can regenerate between battles. Thankfully, the Dark Suit alleviates the speed at which Samus loses her health and the Light Suit stops Dark Aether from hurting her altogether, but the constant loss of health still contributes at least partially to the below-mentioned Boost Guardian's difficulty.
    • All beams except for the standard Power Beam require ammo. This makes it a little aggravating when enemies and boxes shot with the Dark Beam leave behind ammo for the Light Beam and vice versa. In areas like Dark Aether where pretty much every enemy is vulnerable to the Light Beam and the Dark Beam is almost useless, this can lead to huge frustration when you run out of ammo for it and can't pick up any more. The Annihilator Beam even uses up both kinds of ammo (though thankfully, enemies have a chance of dropping both kinds of ammo upon defeat with it). This mechanic was removed from Corruption and only missiles required ammunition.
    • Seeker Missiles sound good on paper, but held back by the fact that they have a tendency to not work if you stand a little too close to what you're shooting. It can be rather irritating to try opening a door with a Seeker Missile blast shield, only for the smoke to clear and realize that one of the missiles, for whatever reason, did not hit its target, forcing you to waste another six missiles trying again. Most of the time, when the Seeker Missiles aren't required, it's easier just to use normal missiles or Super Missiles. The Trilogy re-release makes Seeker Missiles slightly easier to use with motion controls, but it's not much better.
    • The controls of the Morph Ball in this game are oversensitive, the camera placement is often wonky, and several puzzles require precise bomb-jumping and movement. It's no coincidence that the game's three hardest bosses (Boost Guardian, Spider Guardian and Power Bomb Guardian) all require you to remain in ball form for the majority of their fights. The Trilogy edition retroactively added the Spring Ball mechanic to ease the reliance on bomb-jumping, but the other issues remain the same.
  • That One Boss:
    • The Boost Guardian is probably the most infamous boss, ending more games than all the others combined. Aside from the obvious issue of being the first Dark Aether boss fought without Safe Zones (meaning you constantly take damage from the atmosphere and U-Mos have mercy on your soul if you plan to do a No Dark Suit run), he is a Lightning Bruiser who either bounces randomly around the room or deals 50 Collision Damage in puddle form, when you have 5 energy tanks at most. While he's in puddle form, you must bomb him while in Morph Ball mode, further limiting your mobility. One of the game's developers even admitted that he was unable to beat the Boost Guardian without going into debug mode to make it easier. The Trilogy rerelease toned down the damage significantly.
    • The Alpha Blogg. He is fought at the end of a long and arduous water segment in which it's easy to lock yourself out of the save point, thus potentially requiring you to go through the whole segment again if you die. In battle, he is a Lightning Bruiser of a Bullfight Boss that hits hard, moves fast, takes a lot of punishment, has a tiny and risky window of vulnerability that shrinks even further as he takes damage, and gives up few health restoratives. Fortunately, the normally Awesome, but Impractical Darkburst allows you to take off 50% of its health if you fire it into its opened mouth when it tries to bite you. Unfortunately, the Darkburst is a Death-or-Glory Attack because you spend massive amounts of ammunition to fire one. If you miss, you are screwed because you now have significantly less dark ammunition which the Alpha Blogg is weak against.
    • The Emperor Ing is possibly the hardest final boss in Metroid history. You have to shoot his tentacles in his first form while they’re either (a) being swung at you for huge damage, unless you do some creative dodging and jumping; or (b) being held above his head, which means you’ve gotta aim above him and keep backing up to see all of him. Either way, the aiming system will inevitably force you to back up into the walls of his tiny room, which are covered in damaging Phazon. Even when you can nail all the tentacles, he can only be damaged via a quickly rotating slit in his core - good luck sidestepping to get one or two shots in before he rotates it away, or he shoots a stun-locking laser at you, or (you guessed it) you wind up in the Phazon. And after this difficult phase, the second one is an all morph-ball form... and there’s still another form after that.
  • That One Level:
    • Torvus Bog. It's filled with enemies that are much stronger and more annoying than those faced so far. Half of its bosses can be That One Boss, and it is home to the infamous Boost Guardian (one of said bosses). Then you travel into the water-filled depths, in which visibility is extremely limited, you have very little mobility while your enemies are highly mobile, there are long stretches of difficult puzzles, and completing the final puzzle blocks off access to the save point, meaning you might have to go through the entire sequence again if you die to the Alpha Blogg. At least both areas have amazing music.
    • The end-game scavenger hunt for the Sky Temple Keys is one of the main criticisms of the game. Only four of the nine keys can be obtained without the Light Suit. Although many hints are provided as to the locations of the Keys, they can be a little obtuse and it still involves a great amount of backtracking and exploring the both the light and dark worlds.
  • Uncanny Valley: Unlike the more realistic face used in Metroid Prime or the more stylized face used in later 3D games, Echoes tries to go for something in-between for Zero Suit Samus... and the result is rather off-putting. The overly saturated colors clash with the realistic shading, and her expression is just a blank stare as lifeless as a Barbie doll.
  • Unwinnable by Insanity: If you use Sequence Breaking to bypass the area where Samus loses her gear, that's fine and dandy, but do not go back to that area afterwards unless you can glitch out of it again. The scene will play, and any gear obtained since then will be lost. Already obtained that gear? Well, you can't get any more of it.
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