- The plot itself is scary, as it definitely becomes a lot darker. Mario's been sent to prison for a crime he didn't commit, instead being committed by Bowser Jr. He's forced to then face off against Shadow Mario, a criminal mastermind, to not only save the princess, but the entire island, and his good name. Making it worse, he has no power-ups this time, only F.L.U.D.D.; the Flash Liquidizing Ultra Dousing Device as his partner and weapon worn on his back.
- A few of the music and sound effects in Sunshine can be terrifying. For example, Hotel Delfino, a Hell Hotel-type ghost house stage, is frightening enough on its own, but its background music is a fairly standard-sounding tune... with bones rattling in the background.
- Getting sucked into another dimension. You lose FLUDD, have only your jumps, are trapped in cheery, happy puzzle-worlds and the levels are Nintendo Hard.
- The Blooper Surfing course can be pretty spooky when you realize that there's no roof to the area. Instead, past a certain height, there is just blackness. It doesn't help that there are a lack of bright colours in the area, in contrast to most of the game, making the area feel unnatural as a result.
- Use a camera editor (like that included with Dolphin) and get the camera out of bounds, and it's revealed that the stage actually hides the background to the special levels. You're not supposed to see it normally, but it's exceptionally creepy to realize that a room that's supposedly under a building is actually floating in psychedelic space.
- The Boos in Hotel Delfino look rather demented, with glazed over eyes and tongues hanging out more than usual. They even look outright stoned.
- The boss theme in general. The battles feel quite frantic with this piece playing, and it practically keeps you on your toes the whole way through, which only serves to make the below bosses that much more threatening to deal with.
- Shadow Mario and his scary red eyes.
- In the Gooper Blooper battles, Mario is fighting a giant squid who uses his tentacles and ink that summons slimy enemies to attack. The method of defeating him is to jump on each of his tentacles and graphically pull them off one by one; after doing so, the pulled tentacle will wriggle wildly before disappearing.
- Phantamanta. It's a large, paper-thin orange shadow in the shape of a manta. Wherever it goes, it leaves a trail of goop and emits a really creepy shriek when you try to spray it. The worst part is that it's an Asteroids Monster and divides into smaller faster shadows as it is destroyed. When you've finally destroyed half of the original manta, the remaining 64 mantas stop fooling around and all converge on your position at once with incredible speed at a time when you're probably almost out of health. You may think that going in the lake would protect you from it, but it just hovers over any water, so nowhere is safe.
- What makes it worse is that it's referencing a passage from The Shining.
- Phantamanta has a remixed version of the Goopy Piranha Plant/Plungelo battle theme that is pretty unnerving.
- While King Boo was already frightening in Luigi's Mansion, this game has him look just as bad, if not worse, for the same reasons as the other Boos.
- The game features a stage in Noki Bay where you have to go underwater (thus, making it a Timed Mission), and clean the teeth of a giant eel (pictured above); complete with poisonous bubbles and a whirlpool that threatens to suck you in. Doesn't help that the eel lunges up out of its cave at you and you have to get close to its mouth to clean its teeth. It's huge and you have to fight it in a dark, underwater trench, it attacks by trying to eat you, and you have to get close to its open mouth to attacknote , especially bad if you're not good with water.
- Even worse is that looking at it in a model viewer reveals that it's hollow with a highly detailed esophagus and stomach area◊. It's unviewable in normal gameplay but it's still unnerving that they made those.
- The game uses bitmap images for generating goop on maps. The bitmap for an older version of Bianco Hill's goop shows what looks like "Kug" (a Dummied Out enemy), a Piranha Plant, and... a Nightmare Face with what looks like hexigonal teeth, big eyes, and a weird-looking wisp-hand sticking out. See it for yourself: here,
- Hacking will grant access to test rooms... one of which contains a Pianta, a soccer ball, and a huge yellow abomination (called "HinoKuri," meaning "Fire Chestnut", and nicknamed "Tramplin' Stu" by English-speaking fans) with long legs, big feet, torso and head that look like P-body from Portal 2, and no arms, not to mention its walking animation and the fact that it was originally supposed to wander around Delfino Plaza.
- It gets worse: There's another version of this unused enemy that has a giant creepy-looking skull over its head. You find it in Delfino Airstrip, the first location in the game.