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Nightmare Fuel: Ultimate Spider-Man
"Didn't anyone tell you smoking is bad for you?"
The pan view of the frozen Asgard in "Field Trip" shows a crying baby and her mother encased in ice.
Doctor Octopus. Even though he' not seen clearly in his first appearances, the few gaps we get of him reveal creepy, almost zombie-like features, as well as a Creepy Monotone voice.
When Peter considers telling Harry he's Spider-Man, the possible consequences of his secret getting out (even ones that aren't as bad as the others) flash by in a terrifying thought-sequence. No wonder Peter's protective of his identity if that's what he thinks might happen.
While Venom was no joke in his first appearance, it's in "Venomous" that he actually becomes scary as hell.
Venom: I will tear your soul into pieces!
Likewise, "Me Time" has Doc Ock finally decide to do things up close and personal, and he's terrifying. The sheer amount of close shaves Spidey goes through as a result is truly harrowing.
Sandman is surprisingly scary in his first appearance: the Creepy Child act, the way he controlled the whole island, the distortions of his body...
Norman Osborn as the Green Goblin is creepy as hell.
Carnage is nowhere near as terrifying as he could be, but that constant screaming plus all those SHIELD agents he pulled into the cloud who never came out won't be sweet dreams for the kids watching this.
Peter's transformation into Carnage could be considered scary.
Nightmare certainly lives up to his name. He even provides the image for this page.
Of special mention during the "discovering other people's nightmares" sequence of that episode is Ava's nightmare of getting chewed out for not studying by a nightmare version of Principal Coulson with deeply unsettling proportions. It's especially uncomfortable for any students with test anxiety who've had similar dreams, since it's not trivialized as such fears usually are.
Deadpool was pretty scary in "Ultimate Deadpool".
He wanted to buy Spider-Man's brain for his spider-sense. Think about that.
Deadpool only loses his playful personality once throughout the entire episode and his line is terrifying.
Spider-Man: Are you out of your mind?!
Deadpool: Totally! But I know that list is going to make some supervillain very happy and that's going to make me very ri-ch! (Suddenly serious) So hand it over and I'll only partially un-alive you.
Venom possessed Fury. We only see him with one eye, and it's not pretty.
And then, the Goblin gets infected by Venom.
Infected?Try willingly choose to become one with him.Which is arguably worse.
Scorpio's using an unstable formula that gave Luke Cage his powers on himself, transforming into a colossal mass of muscle and absolute power. His defeat at the end combined with his agonizing shriek is something to behold for a show of this nature.
The special Halloween crossover with Blade takes a turn into Darker and Edgier territory with the gripping threat of Dracula and his terrifying vampire army.
Blade himself is pretty scary. Fangs? Check. Deep sinister voice? Check. Decapitating a helpless vampire onscreen? You got it.
The Sinister Six Return; Doc Ock's Powered Armor looked much nastier and creepier than that of the others, but that paled in comparison to the return of the Goblin. Beating up Peter? We've seen him do that before. Getting away from the heroes? Small potato. Him abducting Peter's friends and intending to turn them into horrible monsters? Yeah, this just captures how horribly sick that monster is, with a nice side dish of Adult Fear.
Dormammu, he was able to use Cloak ability to move the mindless ones, capture Iron Fist, White Tiger and even doctor strange and give his mind control victim flame eyes and a evil aura like attack!
One of the dragons Loki summoned to conquer New York was still bonded to the Venom symbiote when it was thrown through the portal.
Spider-Man becoming Savage Spider-man (Aka, Man-Spider). Four arms grow from his waist, and his mouth becomes insect jaws. Eesh.
In the aftermath of Taskmaster and the Thunderbolts' attack on the Tri-Carrier, the Goblin has now has control of the Siege Perilous. The Goblin's true plan is to use Electro's power and goes to different parallel universe to steal the spiderman counterpart's DNA and INJECT HIM ONTO HIMSELF. Not only that it work, it transmute him into Spider-Goblin.