- The episode when Evil Jimmy tricks Jimmy into thinking he's good, and creates a new world that's sapping reality from earth. Jimmy proceeds to reverse the process, killing every one of the billions of evil humans.
- Many of the evil duplicates of Jimmy's friends, family, and acquaintances are shown to be highly disturbing. Evil Jimmy's parents are shown to be the most deranged as Evil Judy is shown gleefully dirtying her house while Evil Hugh laughs sadistically after recounting how he killed and mounted ducks on his wall after they begged for mercy.
- "One of Us" can get surprisingly scary at times, especially when Jimmy finds himself alone among his friends-turned-mindless zombies. The ending's rather intimidating as well: as the grandmother boards the mothership, it seems like the episode will only end on a peculiar "WTF" note. Instead, she turns around, lifts her glasses to reveal completely black eyes, and says "WE'LL BE BACK." in a terrifyingly deep voice. And to matters worse she returned in a later episode.
- The Nanobots proceeding to delete everyone from existence due to them being "flawed", thinking they're doing their jobs correctly.
- "Sheen's Brain" where Sheen's head eventually gets so big it takes over his body. And then his voice turns demonic when he starts speaking. Worse, his IQ would keep on growing infinitely until his head explodes. Sheen also becomes a sociopath and Knight of Cerebus — to the point where he declares himself a God and nearly kills "Ultra Lord" (actually a disguised Jimmy and Carl), his lifelong idol, for trying to revert him to normal.
- Win, Lose, or Kaboom has the race between Jimmy's team and the team of brainy aliens. When it seems like they have made it to the finish line, they return to Retroville and are greeted by their parents with a celebration of their supposed victory. When they find some things off (like the ice cream tasting like sheet rock), the "parents" urged them to "Eat and Forget" repeatedly in an increasingly unsettling manner like zombies. It was all a dream implemented by the brainy aliens to distract them; the only way they could wake up is to fall into the void outside where they find out they are in the middle of nowhere. It could be worse to think about what would happen if the "parents" have captured the kids.
- Flippy. Hugh purchases a puppet named Flippy to practice ventriloquism, but his comedy routine is lacking, so Jimmy puts a computer chip in Flippy's head to enhance Hugh's brain. Instead, Flippy uses the chip to draw consciousness from Hugh to give himself sentience and become a real person who happens to be malevolent and pretty sociopathic, while Hugh loses his mind and becomes a lifeless empty shell. When Jimmy caught on, Flippy threatened to destroy Hugh's brain, since he controlled Hugh's body. When he gained full sentience, Flippy planned to kill Hugh by chucking his body off a cliff so Hugh couldn't get his brain back. Worse off, even though Jimmy manages to destroy the chip, it's implied in the end Flippy is still alive and still has some control over Hugh's mind.
- In Who's Your Mommy, Carl gets impregnated by a single alien egg Alien facehugger-style. Jimmy is terrified by the situation and describes how the alien is a glowing mass of energy that could kill Carl via electrocuting him, growing till it splits him in half, or eating his insides once it's born, but everyone else including Carl's parents react with utter joy at Carl's pregnancy. Then the alien, that looks like a giant lightning spewing jellyfish, that laid the egg comes all the way to Earth to look for its baby!
- The animation in this show. Growing up in the early 2000s back when most cartoons used 2d animation, the style seemed creepy and off-putting to some children. Especially the Jimmy-Timmy Power Hours, where characters who had always lived in a 2d world suddenly became computer-generated big-headed kids.
- "Sleepless in Retroville", where Jimmy, Sheen and Carl have a sleepover with a machine that cranks out scary stories, pillows, and pizzas. The climax is when Carl accidentally creates a flesh-eating pizza that chases them around the house, and a pack of flesh eating pillow go after the parents. At the end after disaster seems to be averted, the pizza monster strikes back - "Haven't you ever heard of sequels?" Then it spirals into a series of nightmares from each of the characters. While most of them are funny, one ends when Carl tries to hide under the parents' bed, but gets stuck and is eaten by the pizzas. Yikes.
- "The Evil Beneath" has Dr. Sidney Moist, one of Jimmy's scientist role models and leading researcher in phyto-chemicals compounds thought long dead. He ends up revealing that he's been kidnapping people who come to the Quadrangle to turn them into Algae-based manservants because of his own psychotic paranoia that newcomers were sent to spy on him. He's done this many times and would have successfully done it to Jimmy and his friends if not for Jimmy finding a way to overload the Algae Men and destroy Dr. Moist's lab. Afterward, a dense fog appears out of nowhere with multiple pairs glowing red eyes inside the fog, and Jimmy and flee away in terror.
- "Nightmare in Retroville": Jimmy's monster machine that he created in an attempt to make his friends look like monsters for Halloween actually turned them into monsters, complete with bloodlust, by mutating their molecular structure on a subatomic level and altering their DNA. As such, both Carl and Sheen become bloodthirsty monsters, hell bent on killing or turning others into monsters themselves, with Carl turning into a bloodsucking vampire and Sheen a hungry werewolf stalking Libby.
- At one moment in "Monster Hunt," something both cryptic and very unsettling is revealed:Betty: Gadgets go in the water! You go in with the gadgets! Monster in the water. Our monster.
Jimmy: Wait. Who goes in the water?
Betty: YOU do!
Carl: Why does the monster go in with the gadgets?
Sheen: No no, the monster goes in with the water.
Carl: Our monster?
- For anyone who's still confused... Betty intends on using Jimmy as bait to lure out the Lake Monster. A crazy old man was willing to kill a child to catch something that for all anyone could know doesn't even exist.
- Captain Betty's backstory is pretty creepy too, despite the Bathos surrounding it. He was harvesting sea monkeys (here depicted as actual monkeys) for a mail order company when suddenly his ship was attacked by the monster. Not only did the monster eat his hand, as shown earlier, but it also devoured every last one of the sea monkeys he caught. The ominous way he tells the story, right down to describing the sea monkeys' screams, implies that the incident traumatized him (possibly explaining why he's so loony now) and it haunts him even to this day. And THAT'S why they call him Betty!
Nightmare Fuel / The Adventures of Jimmy Neutron: Boy Genius