* Unlike the rest of the series, this movie is considerably a lot darker and has plenty of horror elements. There's [[KnightOfCerebus Dennis]], the seriously threatening thugs, the brainwashing bucket helmets, the skull infested area, [[BodyHorror the horrible looking monsters]], the trench, the diver, and the climax involving drying up and turning into non-anthropomorphic animals in a gift shop. Worse than all of that, [[ArsonMurderAndJaywalking ALL HAIL PLANKTON!!!]]
* The activation of the bucket helmets.
** [[IneffectualSympatheticVillain Plankton]] going NotSoHarmlessVillain (to the point of [[KickTheDog pretty much crossing]] the MoralEventHorizon) is terrifying [[BewareTheSillyOnes as well]] [[VillainousBreakdown considering]] how [[HarmlessVillain he usually is]].
** The sequence when Plankton begins his takeover is sepia-toned to resemble ''Film/TriumphOfTheWill.'' [[ANaziByAnyOtherName Let that sink in for a second.]]
** Then he does it to [[spoiler:King Neptune.]]
** The first fish whose helmet is destroyed happily declares "I'm free!" which implies that [[AndIMustScream the bucket helmets keep the victim perfectly aware.]]
* The old lady at the ice cream stand, who turns out to be some kind of giant monstrous [[AlluringAnglerfish frogfish]].
* The GIGANTIC deep-sea eel that swallows the anglerfish and the Patty Wagon. It's so monstrous and quite spooky-looking that it surprises Spongebob and Patrick.
* [[HumanPopsicle Frozen Mr. Krabs.]] The worst part is that he is ''[[AndIMustScream still completely conscious]]''. The whole reason why he is frozen in the first place is for committing a crime he didn't even do and has only six days before he's put to [[KillItWithFire death by fire.]]
** His face is frozen in a permanent scream, too.
* [[PsychoForHire Dennis.]] Enough said. He's a pretty terrifying villain for a kids movie.
--> '''Plankton:''' ''HE'S A VICIOUS, COLD-BLOODED PREDATOR!''
** One of his creepier moments is when he [[DisproportionateRetribution rips the lips off of the hillbilly brothers]] after they laughed at him over a [[MoodWhiplash stupid joke they made up on the spot]] and later on punching a thug to his death. These scenes really [[EstablishingCharacterMoment establish]] how Dennis is [[NoNonsenseVillain not one to take nonsense of any kind]] unlike the rest of the [[KnightOfCerebus funny characters.]]
** He gets even scarier in his last moment when he is having his VillainousBreakdown and yelling at Spongebob and Patrick about how he is "through messing around" with them. It doesn't help that his eyes are all [[RedEyesTakeWarning red]], [[EyeScream swollen and watering from irritation]] as he glares down at them.
** (SlasherSmile) "Did you ''miss'' me?"
* Shell City, once you see it from SpongeBob's perspective. Just imagine being trapped inside a room with no way out with hundreds of dead people surrounding you.
** Not just dead people, [[WaxMuseumMorgue dead people dressed up to be sold like gifts]].
* King Neptune's facial expressions can get really freaky at times when he gets real pissed.
* The close-up on Plankton's face as he gives his third and final "YES!" when Neptune is about to immolate Krabs. His eye is crazed and widened and he's got a huge SlasherSmile on his face, complete with fangs for whatever reason.
* [[MindManipulation "ALL HAIL PLANKTON!]] [[MadnessMantra ALL HAIL PLANKTON!]] [[AndIMustScream ALL HAIL PLANKTON!"]]
* '''[[KnightOfCerebus The Cyclops]]'''. Mindy specifically warns the heroes about a giant cyclops guarding Shell City, and that if he catches them, they will never be seen again. Then they finally encounter the dreaded Cyclops, which turns out to be a [[UncannyValley realistic deep sea diver]] [[SicklyGreenGlow with a glowing green viewpoint]]. From Spongebob and Patrick's perspective, the Cyclops looks [[HumansAreCthulhu downright unnatural]] compared to what they have seen so far, and it is ''[[EvilIsBigger utterly massive]]'', accidentally crushing the nightmarish hitman Dennis with his boot. As the Cyclops quickly captures Spongebob and Patrick, he brings them up close to his glowing, expressionless "eye," silently watching them scream in terror, before taking them away to Shell City. Unlike most monsters in the sea, the Cyclops seems to enjoy watching sea creatures get scared, laughing maniacally before [[CruelAndUnusualDeath slowly killing them and turning them into gifts]]. And then he leaves Spongebob and Patrick to dry up under a hot lamp...
** The fact that Mindy knows about the Cyclops guarding Shell City is probably the reason why no one has returned, it makes King Neptune's utter despair that the crown is stuck in Shell City seem much worse; its possible that King Neptune is afraid of the Cyclops, or at least unwilling to challenge him, even to get back his crown.
* The main thug trying to weed out the "Bubble-blowin' baby". It starts off rather silly, but as Patrick and Spongebob actively try not to sing along to the "Goofy Goober" song, they start to melt, foam at the mouth and to top it off, [[NightmareFace they have pain-contorted faces.]]