A rather large portion of Metroid II: Return of Samus is nothing butNightmare Fuel. After you leave the main tunnel with its heroic-sounding theme song, the side areas are completely silent other than a few random, tense, ambient sound effects...until the Jump Scare of an evolved Metroid heading straight for you, completely with a frightening Scare Chord. And, unlike most Metroid games, the Metroids themselves are everywhere...
The Metroid Queen's area is pretty spooky, too, especially when you've worked your Metroid counter down to 1 and are rolling through a random tunnel...when suddenly it jumps back up to 9. Cue the classic Metroids attacking you en masse, and like the first game your beams don't stack, so if you didn't go back and get the ice beam, you're in trouble.
The whole sequence with Crocomire in Super Metroid. Forcing the creature into a pit of lava and watching its skin dissolve. Creepy. Oh, and then its skeleton pops back out for a moment only to crumble before you. Harmless but still freaky.
Draygon is arguably worse. His battle starts off with a surprisingly effective Jump Scare, and when you see that he looks like a Gigeresque horror, you'll see why. His body pulsates in a disgusting manner, his eye looks mucus-coated and cancerous, his mouth looks like something out that wouldn't be out of place on a Yautja, and if you look closely, there are at least three parts on his body that resemble human faces. After you've killed him, you are subject to seeing his own children starting to eat his corpse. What the hell, Nintendo?
The music for Spore Spawn, miniboss of the Brinstar area. The boss itself is kind of creepy, but it's this strange medley of piano music and tribal drumming that's really spine-tingling.
Worse, it reappears for Botwoon, the miniboss of Maridia.
"Item Room Ambience" is an ambiguously disturbing remix made entirely out of mysteriously telephone-ish beeps with an extremely dark and ominous silence note in the background. Imagine waking up to that in a dark room in the middle of the night. Who needs sleep anyway?
Mother Brain's theme is effectively Oh Crap in musical form. Mother Brain herself is quite intimidating as well, seeing as it fakes you out into thinking the battle will just be a copy of the original's final boss. Nope. Instead, we're treated to a grotesque, snarling, drooling monstrosity that towers over you, who then proceeds to kick your ass. The music conveys the feeling of hopelessness quite well.
Despite being marketed as a Sci-Fi First Person Shooter, the entire Metroid Prime trilogy has so much Nightmare Fuel that they might as well add "Horror" to the list of genres it lies within.
The Chozo Ruins are pretty scary, all things considered. At first, they seem peaceful enough, then you get to the actual Chozo Temple, where the ghosts of the race that raised you attempt to kill you! And your only option if you want to get out alive is to kill what might essentially qualify as your surrogate family.
The in-game Chozo Lore scan-files contain a fair amount of Nightmare Fuel too. Especially if you read them all in a row. Essentially, the Chozo lived peacefully until a meteor carrying the sentient toxin, Phazon, hit Tallon IV, killing off anything unable to adapt. And while they were slowly dying (or worse), they waited for their prophetic saviour, Samus, to arrive and save them all. In other words, the only civilized, sentient species on the planet went extinct because Samus, AKA you, were too slow.
The Game Over screens of Metroid Prime and Echoes. Oops, you died. For your failure, you must watch poor Samus breathe her last.
Not to mention the first metroid itself, if you hadn't played any of the games in the franchise before and only had a vague idea of what they did (from in-game scans).
That scene is, by far, the absolute worst the first time around for fans of the original series. Why? Because you quickly realize you're in the worst possible situation: locked in a room. With a metroid. AND NO ICE BEAM.
And then there were the Phazon Metroids in the third game. They can let Ice Missiles phase through them. YEEAARRGGHH!
The way the metroids grip your face in first-person.
Phazon Mines! WHY, RETRO?! WHY?! Even with the Phazon Suit, it's scary to step in phazon. IT CRACKLES! CRACKLES! AND IT'S NOT JUST THE GEIGER COUNTER GOING OFF!
"Phazon Radiation" from the Prime sub-trilogy can make anything creepy.
In Metroid Prime, scaning data in the Elite Control Room in the Phazon Mines reveals that the Space Pirates actually tried to reverse engineer Samus' morph ball. The R&D team then decided to cancel the project after several test subjects came out HORRIBLY DISFIGURED. To give you a rough idea, imagine being thrown into a car compactor...
In general, most of the Pirate Data is this. Their utterly flippant attitude towards testing Phazon on live test subjects, some of their own race, gives you an idea of just how utterly ruthless they are. Then, of course is the fact that they still want to weaponize metroids, and even begin infusing them with Phazon.
The injuries many of the Space Pirates have suffered in the beginning of Metroid Prime are downright gruesome, and scans even show images of their injuries. Two of the worst ones happen to be one whose exoskeleton's joints were fused together by acid, leaving him unable to move, and another pirate who died by having his internal organs eaten while still alive.
Metroid Prime 2 Echoes:
The Dark Troopers. Right at the beginning, seeing the troopers you've been sent to rescue being turned into freakish automatons and turn their weapons against you. What makes it worse is finding the log books of marines who have either been ambushed or driven insane. One of the freakiest ones was the trooper who got away from the enemies, and as he was heading for the central building sees something in a hole, "Hello... Who's there?.."
Scanning the dead troopers at the very beginning of the game, one of whom was confirmed to have "at least thirty" attackers involved in his death, or the one who died of cardiac arrest.
"Chemical levels in the body suggest a state of extreme fear at time of death."
And it's...just...the horrible way they move. The jerky, "puppet with too few strings" motion, more zombie-like than a lot of actual game zombies. Especially when you're just starting out, and this music starts playing...
Seeing dead marine corpses all over the floors and walls with almost no sign that could confirm how they died is creepy in itself. Such as the ones in the "hive" that drop from the ceiling when you enter this one room!Suspended from their necks like they were HANGED!
Emperor Ing. What's not to be terrified of? An immensely powerful, mutated Reality Warper far stronger than any other Ing. He's powered by about a quarter of the planet's energy, can regenerate by leeching off said energy, and can take many different forms. Some of his attacks are almost impossible to dodge, and he's only capable of being hurt under specific circumstances.
The Grenchlers from Echoes. The roars and appearance, they can swim AND jump really high and far which means there is pretty much no way to avoid them...
Quite possibly the scariest part of the game: The Dark Grenchler.
Dark Aether, a nightmarish version of the planet Aether in which you quickly lose energy when not standing in a light-provided safe zone. The enemies in Dark Aether are even tougher versions of their normal world counterparts.
Quadraxis is a killer robot whose every step shakes the ground armed with a laser guided annihilation reaction gun, a force field generator and is capable of grinding apart targets by spinning fast enough to create a tornado to draw them to it and letting its frame to the rest. To Samus it is just another monster on a hellish death world but all the same it was most likely using all those abilities for the purpose of exterminating all life, without any discrimination whatsoever. Even she did encounter the last one still active, the parts to make more of them have already been forged and put into the possession of less killer robots with the same mass extinction goals. In short, Quadraxis is probably the only enemy that's more comforting with the knowledge it is under Ing control, though interaction with the Ing is what drove the machines to hate all life so keeping it locked away in their hive was the least they could do. One can only imagine what they did to make the Luminoth even consider building such a thing in the first place place.
The new weapons made available to Samus certainly qualify. First off, the beams are pretty insane. There's the Dark Beam and the Light Beam, both of which are obtained relatively early, and both of which are potentially devastating weapons. The Dark Beam has the power to freeze a target in a chunk of solid darkness. As in the stuff the ING consist of. When charged, it sends off a massive chunk of solid darkness that has a better chance of freezing stuff. The Light Beam has the power to set anything on fire. When charged, the Light Beam essentially becomes a shot-gun that fires tiny suns. One person should not be allowed to have both weapons. Oh yeah, and don't forget that the Dark Beam potentially can turn anything it doesn't kill into Dark-whatevers, essentially letting you turn everything into zombies.
The fourth beam-weapon you get, the Annihilator Beam is Exactly What It Says on the Tin. The in-game description states that its shots consist of a mix of matter and antimatter, essentially making it controlled chaos in a gun!
The Missile Combos are even more disturbing. The Sunburst is the Super Missile for the Light Beam, that fires a single slightly bigger orb of light that explodes and damages everything within range. The Darkburst is the exact opposite, in that it fires a single huge chunk of darkness that explodes and either kills the enemies or turns them into Dark zombie-versions of whatever they were. And then there's the Missile Combo for the Annihilator Beam... It is so powerful that it breaks the universe itself. And you can just get away with using it against the planet's native wild-life.
And don't think Nintendo didn't anticipate that you would set stuff on fire with the Light Beam. Unlike the Plasma Beam in Prime, you actually get to hear the enemy scream in pain as they burn to death.
Then there's the part where you open a door, everything's fine everything's good. Then the second you open the door a dead pirate's corpse greets you and instantly decomposes!
The fun doesn't stop there if you've played to the end of Super Metroid before, as you'll probably recognize exactly what caused the space pirate to decompose: having its life sucked out by at least one metroid.
Particularly freaky is when, in the Valhalla, you see a Metroid floating lazily down a hall...and then you notice that it's dragging a corpse behind it.
You can use the scan visor on corpses to determine how they died. While you can do that in multiple places, the death messages are creepiest in the Valhalla. One of them saying that the trooper was trying to crawl towards the exit before being attacked from behind, but there are probably far worse "gems".
Some deaths include getting impaled with a scythe before being tossed into exploding canisters, a PED malfunction eating a Trooper alive, phazon grenades, explosive decompression due to broken visor, friendly fire while trying to remove Metroids, self inflicted wounds while trying to remove Metroids, and getting attacked through walls by phase shifting Metroids.
Whatever you do, don't look out the window of Valhalla; that entire nebula out there? Metroids as far as the eye can see, some of them MASSIVE.
In Corruption, you're going to go get the Seeker Missile. As you do, you pass by several trapped metroids, but they do nothing, as they are properly contained. Then you acquire the Seeker Missile, the lights go out, and you KNOW what's waiting for you on the way back. And if it's your first run, PRAY!
After Gandrayda is defeated, she goes through a Shape Shifter Swan Song, finally settling on Samus' form. As Dark Samus appears to absorb her the way she did the last two bounty hunters, Samus knows there's nothing she can do to help Gandrayda, and essentially goes through the epic mindfuck of watching herself die horribly. Even worse is that Samus herself is pretty corrupted by this point, the dying Gandrayda takes on the form of a healthy Samus.
There's a reason the Aazelion, a creature found in Corruption on Phaaze, is this page's picture.
Corruption also features a sort of Fridge Nightmare Fuel. In the first one, Phazon damaged you until you had the Phazon suit. Even then, the stuff in the impact crater still damaged you. In Echoes there was no protection against it, it would always damage you. But after you get the PED suit, Phazon can heal you. It is some of the most toxic and corrosive stuff in the history of the series, and it's healing you. That's how corrupted you are.
Phaaze is pretty much a planet made out of Nightmare Fuel. Before going there, you are only 75% corrupted, and your ship can still sense that it's Samus that tries to use its facilities. Once you land on Phaaze, there is a quick cut-scene in which Samus becomes fully corrupted. As a result, her own ship can't even sense that it's her anymore, and to make matters worse, you're stuck in infinite Hyper Mode. On the bright side, you can't die due to lack of Energy. On the not so bright side, your 100% Phazon-Corruption-rate means you're only one step away from dying every second, meaning the atmosphere and any hostile attacks can actually kill you if you're not careful. And since your ship doesn't recognize you, you're stuck on that planet until you slay Metroid Prime/Dark Samus for good. Playing this part of the game right before sleeping is not a good idea if you actually want to sleep.
After killing the Infant Leviathan in the Genesis Chamber and before jumping down the final shaft, take a look around with the Scan Visor. You'll see some weird looking growths along the wall and, naturally, will want to scan it. Those aren't growths. They're husks. METROID PRIME HUSKS.
Omega Ridley is pretty horrifying in concept; he's a sadistic cyborg space pirate dragon-like alien pirate/terrorist, and you can clearly tell that Ridley himself is pretty much just a living corpse under the cybernetic enhancements. Even as a cybernetically-enhanced corpse, he still takes a large amount of effort to put down, and even after Samus defeats him again, the zombie cyborg Ridley manages to escape the destruction of Phaaze.
One of the cooler features of the game is the ability to sometimes see Samus's eyes inside her visor while playing. As you become corrupted, her eyes go from Green( non-ped suit), to blue, to blue with some strained blood vessels, blue with glowing eyes, and finally deep blue glowing eyes, with tendrils made of pure phazon crawling up her face!
Metroid Other M:
Metroid: Other M has some good scares, but the best one is retroactive. Throughout the game, you've been encountering distinctive Power Bomb doors; you've probably been looking forward to coming back and opening them all. Then the cinema before the final fight reveals that those aren't doors — they're dormant insectoid cyborgs strong enough to kick your ass. Next time you play, good luck passing one without shuddering...
Another one from Other M: At one point, you're running through a big glass tube thing. Suddenly midway through, the game goes all Matrix-y and a giant worm monster attacks, shattering the section of tube you're in. You're supposed to dodge the thing to survive, but on the first run through, it scared the crap out of me.
What about Other M's reshowing of Mother Brain's One-Winged Angel form? She was scary enough in 2D!
The SA-X from Metroid: Fusion. Not only are you powerless to defeat it throughout 95% or the game, but it relentlessly pursues you when you're in its sight. Heck, just the sound of its footsteps as it approaches—and the leitmotif that accompanies it—is scary enough.
The worst is when you're cowering in a corridor somewhere, listening to TAP TAP TAP and praying that it doesn't turn into that loud, fast paced track, because that means it sees you. The SA-X encounters are some of the most terrifying things in the entire Metroid series.
At one point, as you enter a long corridor, you hear the footsteps coming towards you from the right. The only way to survive this encounter is to dive behind a wall at the opposite end and wait. After ten or so agonizing seconds of TAP TAP TAP, SA-X will reach the wall and look around for a while, then turn back to look for an exit. If you make a noise (for example, shooting or jumping), it will turn around and stare at the wall for some time, before deciding it was probably nothing. Do it again before it leaves the screen and it realizes you're there, and suddenly jumps over the wall to get at you.
After finally getting rid of the damned thing in Sector Zero, you finally breathe a sigh of relief... just before Adam tells you there are more of them now hunting you. It doesn't factor into the game much at all, but the very idea of it is scary.
Just the X-Parasites in general. A normal human being would have no protection against them at all, and you wouldn't even know if anyone or anything was infected until it was too late.
Metroid Fusion is a lesson in Nightmare Fuel, and the scares don't stop at the SA-X encounters. Some enemies or events will catch you completely by surprise. After getting the Ice Missile in Sector 5 (ARC), on the last two rooms before the Navigation Room, alarms start screaming, the screen flashes red and the intercom announces "Emergency in Sector 3."
And a few rooms before that there's the shadow of a large creature flying around in the background. Later on, when you meet the creature (appropriately named Nightmare), it becomes scary fora different reason... more on him in a moment.
ARC is also where you first end up fleeing the SA-X. Apparently the reason you shiver in Sector 5 isn't because it's cold in there but because it's a Nightmare Fuel Station (attended by a gravity altering robot-zombie named The Nightmare).
Though that chase is due to a Schmuck Bait: You just received Power Bomb, find yourself between a solid wall and a thin wall that is the only thing preventing SA-X from finding you, what do you do? Most people think "Durr, just use the Power Bomb! The thin wall will be there to cover for you!", but oh how wrong they are...
When Samus's computer C.O. requests her to head back to her ship after saving Sector 3, there's a sudden power failure while on the Main Elevator. Everything that happened between the power failure and the power restoration will keep you on your toes.
How about the first time you see Ridley? You fall into his section of the sub-zero containment unit, his eye lights up...and then a Core-X breaks free from the husk and flies off, while the husk crumbles.
The music from Fusion. It's like the soundtracks from Super Metroid and Silent Hill got thrown into a blender. A good two-thirds of it is very subdued, tense, and ominous. Especially the arranged version.
As we were saying, there's a boss actually called Nightmare. He's big, has personal space issues, has some creepy ambiance instead of battle music, but most of all you kill him by melting hisface off!
As if Metroids weren't scary enough already, this picture makes them look like halfway realistic animals... and the accompanying description of death by Metroid will make your skin crawl.
Not to mention Ridley's cruel description of how he devoured the flesh of all of Samus's loved ones. Just merely saying that is horrifying enough, but Ridley goes further by taunting her of where her mother's cells could be. It's no wonder that Samus only fears him.
Hell, Ridley in general's pretty scary; he's a freakin' near-unkillable draconic space terrorist (hell, it takes an planet-scale bomb to actually kill him), and also murdered Samus' parents in front of her makes him an extremely frightening foe, and he's certainly one of Nintendo's most sadistic villains (he takes a cruel delight in describing the exact way he killed the parents of his archnemesis, after all).