It may look like another innocent series made by Nintendo...but it's far worse than the outside implies, which delving deep into its subconscious may end up driving you mad. Case in point and putting it short, it may as well be the darkest Nintendo series to date. And that's saying a lot
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Mother 2/Earthbound
The final battle against Giygas in EarthBound. You spend the entire game fighting cartoonish monsters with baseball bats and frying pans, and end up battling an Eldritch Abomination with a terrifying, amorphous visage that looks like a screaming face, a demonic ghost, and a fetus. The creepy, atonal, jarring background music (and the dialogue inspired by the creator's trauma of seeing a glimpse of a murder scene, which he thought was a rape scene, in a movie as a young child) only adds to this. Then when you finally defeat Giygas, the visual and audio distortions get worse and louder until they peak, then instantly blip out like a TV set turned off. The fact that most of the rest of the game is so childlike and cartoonish only makes this more terrifying.
The music for that battle is not truly atonal. It's more like Prokofiev in style. There is a clear tonal center unlike in true atonality. However, it is still terrifying, especially since Earthbound is cartoonish normally.
It eats prayer. Also,
Giygas: It hurts. It feels... G O O D.
And just before Paula prays for the last time (which is when you come in), she gets no response from anybody.
Paula's call was absorbed by the darkness.
Poo's Mu Training in Earthbound. You're controlling an unfamiliar character who is told to go attend to a training session. The training initiates a battle, where an outline of a stylized Chinese-ancestor head appears. It then proceeds to (all in text, mind you) break your legs, tear off your arms, cut off your ears, and take away your eyes. Worst of all, before each step, it asks for confirmation. After each step, your health drops. The final step reminds the player that all they have remaining to them is their mind—which they are then asked to give up as well.
The Japanese version is even scarier; where in English the spirit informs you that he will "take your eyes," in Japanese he says he will "crush your eyeballs." See here for the comparison between the Japanese and English versions.
Wait through the logos for Nintendo, Ape (now Creatures), and Halken. Eerie red static flashes on the screen, with an quiet, high-pitched noise, and as the flashing slows down, we see a scene of UFOs shooting lightning at a city. Does This Remind You of Anything? Cue Scare Chord.
Really, besides the infamous Giygas battle theme, there are some pretty unnerving tunes in this game. Most of it has to do with creating an otherwordly-effect on the atmosphere of certain parts; a good example would be Alien Invasion.
Threed, anyone? Up until this point, the game has been pretty cheery, and then it drops you into a dark, zombie-infested nightmare where the undead can occasionally even be found walking around near the usually "safe" areas of town. Sure, it's all Played for Laughs, but try telling that to a kid.
Don't forget when Giygas says "...It hurts, ...it hurts... Ness, Ness, Ness, Ness, Ness..." You know that horrific Eldritch Abomination, the one that is so powerful that it's mind has collapsed and it's basically a mindless force of insane, chaotic destruction? Well, it knows Ness' name.
Mother 3/Earthbound 2
Mother 3 would have a terrifying scene at the final boss fight, but it is cut off. You still can see the unused scenes by special code (or by this link) if you dare...
Note that some people think they are unused bosses, but Itoi has said in an interview that they are just unused backgrounds.
The Ultimate Chimera. After the duel with the Almost-Mecha Lion in the Chimera Laboratory, your fellow Pigmask co-worker alerts you to pretty much get the hell out of a room if you see it, and for good reason: running into it kills you, no ifs, ands, or battles. If that warning doesn't scare you, the next part will: the creepy music will cut out, replaced with background sounds of other Pigmasks fleeing for their lives only to get devoured by that thing. Can you confidently traverse from one room to another knowing that such a powerful creature is loose inside the lab?
Perhaps even more horrifying, if you DO run into it, you get to witness the Ultimate Chimera chomping and crunching on Lucas while the screen turns red.
In Bathroom Dungeon, get near one of the doors to the women's restroom and hear an all-too-familiar Ba-DEET! noise. Go inside the room and see the Chimera, inches away from you, on a toilet.
The horrible change that occurs to your hometown. In the beginning, no one locked their doors, there was no crime, and everyone helped one another if the need arose... there was no concept of 'money'.
By Chapter 7, everyone is gone. All the doors are locked, and the only people left behind are complaining about their lot. The town is still there, but its soul is sucked away bit... by bit... by bit until everyone's gone. Shudder.
Tanetane Island. Oh God. The trip went bad, the trip went bad, the trip went bad...
To clarify if you haven't played: You have to eat the funky-looking mushrooms, which send you into a trippy world of pink trees and creepy music, plus the occasional mailbox (see page quote). Oh yes, and all the enemies look like people you know, most notably your father and your dead brother. They spout insane dialogue ranging from funny, "I'm going to lick you all up, ice cream!" to threatening, "I'm gonna beat you, boy. Daddy's gonna beat you." to batshit insane. "Touch my heart. See how it beats in and out? Lucas! There's noooothing to worry about now."
"Everyone's waiting for you, Lucas. Waiting to throw rocks at you, and spit on you, and make your life Hell. Who's everyone? Everyone you love."
More specifically your father and your allegedly dead brother.
After waking up from the mushroom-induced trip, you can backtrack to an area where a healing hot spring is located. It's essentially a toxic waste dump.
The People Jars in the Empire Porky Building. Made all the more disturbing by the fact that you can talk to them, and they're all quite 'happy' being there. There's even a cow, who will say he's going to become a wonderful steak. Yeesh.
If you've seen the unused sprites you can pretty much tell what happened between the prologue and chapter 1. As seen in this vid here To make matters worse this happens BEFORE the twins were found in the river WHILE they were still with Hinawa.
There is also Porky/Pokey Minch's original (or unused) death scene. While some people like to see what's coming to him for all he's done, others might find it disturbing when they see him in a sympathetic light. his machine crashes into the ground after his supposed defeat, breaking the glass on it. Pokey tries to reach out to get out of it, but he starts to go limp and he dies. What a way to go.
Porky/Pokey's situation provokes chilling thoughts: a little boy, yet trapped in the body of an old man and, by this point, is already the series' equivalent to Dr. Weil.
The final battle with him is rather horrifying itself.
