- There are very few places in this game where you can drown without doing so on purpose. Accessible water that goes over the characters' heads is relatively scarce, and the water you do find that meets this criterion can usually be escaped with a single jump. However, if you do find yourself in a tight underwater situation (usually with Big the Cat), all your childhood nightmares will come to life as the infamous drowning music from the Genesis games plays, this time embellished with an entire orchestra.
- Red Mountain, a Norfair-like U-rated hell, with the addition of gravestones, and walls with cells containing ghosts dressed in prison uniforms and scary spiders. A mission card in Director's Cut hits the Surprise Creepy home:Mission: A fugitive have escaped from the jail of burning hell! Find the fugitive!
- Perfect Chaos, pictured above. A gigantic snake-like beast made of water materializing out of a building.
- The Lost World has creepy music, a spooky underground city, and dark areas. Kinda unsettling. And at the end, a mural of Perfect Chaos destroying Knuckles' entire tribe◊; Sonic, not knowing what it is, is flummoxed.
- Falling off the snake can be traumatizing; as Sonic raises the water level, it eventually becomes impossible to make his way back up, leaving him to either drown or jump off into the endless abyss. And the snake is glitchy; it's all too possible to simply fall right through it as it's moving.
- The flashbacks to the past that Tikal takes all of the playable characters on reveal the dark backstory to the reason Chaos exists, and why Knuckles is the last of his tribe. In his tribe, a girl named Tikal befriends the Chao. Her militaristic father, Pachacamac, wants to take the Chaos Emeralds for himself and has no problems with slaughtering all of the Chao along the way; he doesn't even hesitate to throw back his own daughter. This naturally triggers Chaos' Berserk Button and he destroys the entire tribe, and to stop him from destroying the entire world, Tikal has to seal Chaos and her own soul inside the Master Emerald.
- This game's Eggman is portrayed in a considerably darker light than he was in earlier games. His plan is to team up with an ancient, civilization-destroying Eldritch Abomination to destroy a city so that he can build his own on its ruins.
- What's Eggman's Plan "B" after Chaos is apparently defeated? Blow up Station Square with a missile! Oh, and it's suggested it might be a nuclear missile. The threat of annihilation by a weapon of mass destruction that actually exists only makes this game's version of Eggman scarier.
- The frantic music that plays during the first half of this scene coupled with the red light from the sunset makes the whole thing even scarier.
- Eggman's "You fool. Away, before I make mincemeat out of you..." line. It's supported by the exhausted way in which he realizes that Tails beat him to the missile, and then he threatens to make them all pay for this before he summons the Egg Walker — this is one of those few times the Eggman makes a genuinely threatening line.
- Amy's entire story, involving her being endlessly chased by a persistent robot called ZERO. It never stops following her. The worst part is that certain times, ZERO seems to disappear, only to crash through a wall and continue chasing you. As Tikal puts it in her calm, emotionless voice, "The robot that was following you is closing in on you. It'll be over if that robot catches you."
- Amy's Twinkle Park. It starts out just fine, outside in Pleasure Castle's amusement park with the cheerful ride music playing. Then, unlike any other character who visits the level, Amy unlocks the castle's main doors and gets to go inside. It quickly becomes clear that something is very wrong with the rooms inside. And the best part? ZERO. Still following you.
- In Hot Shelter, one part involves Amy collecting colored cubes to fit in slots that will supposedly do something. The area has video monitors all around it that all display static. Once the last cube is placed, the screens go silent, then cut to shots of ZERO threatening you... cue the real ZERO smashing through the screens and blasting you. You escape the room through the hole it made.
- The Limestone cave level has yet another example of spooky music. The area itself inspires some acrophobia, especially as slipping just a little off the precarious ledges can send Sonic plummeting all the way to the bottom.
- One NPC in the Mystic Ruins implies that his friend never found a way out of the maze-like jungle.
- The Continue music, aptly called "Will You Continue?". It's like you're in a between-life-and-death limbo.
- The depiction of Station Square after Perfect Chaos goes on a rampage in the Final Story is legitimately horrifying in a real sense, and it may even remind you of recent tsunamis and floods in various places, like New Orleans, New Jersey, and Tokyo.
- Perfect Chaos first appears by bursting out of a skyscraper. Fast forward to September 2001 in New York.
- Chaos, in general. Especially when Knuckles is alone on the soon-to-crash Egg Carrier with Chaos 6.
- If you exploit a glitch that allows Knuckles to reach Sky Deck through the Egg Carrier's swimming pool, you'll enter his flackback with Tikal as normal, but there will be no dialog whatsoever. Even when you reach the area where the emerald shrine is on fire and Tikal and the Chao are laying on the ground, no cutscene plays, making it seem as though they're all dead. The kicker? You're stuck here forever. If you quit the game and return to Knuckles' adventure, he'll still be there with nothing to do but watch the shrine burn endlessly. The only way to fix it is to start a completely new file.
- E-102 Gamma accidentally walking into the room with his "brother" E-101 Beta being rebuilt into his Mk II form. The scene is implied to be very traumatic and scarring for Gamma to see, especially since what is happening to Beta is implied to be the robot's equivalent of being horrifically mutilated and dissected as a science experiment. No wonder it plays a role in Gamma's eventual HeelFace Turn against his master.
Nightmare Fuel / Sonic Adventure