* 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.]]
* 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.
* 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.
* [[MindManipulation "ALL HAIL PLANKTON!]] [[MadnessMantra ALL HAIL PLANKTON!]] [[AndIMustScream ALL HAIL PLANKTON!"]]