* 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 ''TriumphOfTheWill.'' [[ANaziByAnyOtherName Let that sink in for a second.]]
** Then he does it to [[spoiler:King Neptune.]]
* 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 can ''still'' [[AndIMustScream move, see, and hear what's going on.]] 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 to stay frozen in place 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, 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.
* [[MindManipulation "ALL HAIL PLANKTON!]] [[MadnessMantra ALL HAIL PLANKTON!]] [[AndIMustScream ALL HAIL PLANKTON!"]]
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