The Dark Phoenix 4-parter is kicked off when the Inner Circle attempt to take control of Jean Grey while she is possessed by the Phoenix Force (which is slowly becoming corrupt). Despite Professor X's best efforts against Emma Frost, Jean is successfully converted into the Dark Queen... but not for long as she prefers to be called "Phoenix". Not even Mastermind's psionic powers are able to overcome Jeans love for Wolverine and Cyclops... or Phoenix's growing murderous intent.
Wyngarde wanted to introduce Jean and the Phoenix Force to evil... and unfortunately, it works a little too well as the Phoenix soon goes completely out of control, fully transforming into the Dark Phoenix.
Dark Phoenix: You had me do evil to gain you power... But through this body, I felt the thrill of that evil, now... I thirst... for more!
The Shadow King is a demonic-looking being who can control people's bodies, so it goes without saying that any scene involving him is disturbing or horrifying to the extreme.
That... thing that was imprisoned in a Shi'ar starship that crashed on Earth. It eats souls.
The animated adaption of the post-apocalyptic Days Of Future Past storyline. Everything about Bishop's Bad Future. The worst part about it? No matter how many times Bishop (and later Shard) travel to the past and set right what went wrong, nothing changes. Plus, that time era's Forge has Wolverine's bare skeleton suspended in a tube. Also the telepathic vision Xavier receives from Bishop of the nightmarish future.
Xavier: We have FAILED...
The shot of the X-Men's graves, each and every one of them having died in the prison camps save Logan. And the worst detail is who died first: Jubilee, the kid-appeal character.
A bit of YMMV, but it's possible that multiverse theory is in play here. Basically, Bishop's interfering in the past did technically save the future, but doing so created an alternate timeline split off from his. So while "our" timeline is safe, Bishop's is still the same, and nothing he does will fix it.
On the topic of the Bad Future, the first season finale "The Final Decision" has the very disturbing plot of Master Mold, the main Sentinel, gaining sentience and planning to remove Senator Kelly's brain, replacing it with a computer. And it's not just him: he plans to do the same to all world senators. While he talks about this, we see an Imagine Spot montage of the Sentinels abducting world leaders, one of whom is unfortunate enough to be abducted in the middle of the night. What's particularly scary is the flat and robotic voice he delivers the line in. All this in a kids' show.
The ultimate fate of Graydon Creed in the series, being left at his father's doorstep. Said father? Sabretooth. Sure enough, Graydon might have deserved it for being a bigotedmonster, but still, and the line Sabretooth delivers is simply chilling.
Sabretooth: Come to papa...
Wikipedia's article on Graydon Creed says that it's likely Sabretooth tortures Graydon...which isn't better at all.
All about Omega Red. A mad and sadistic communist who massacres an entire city, possibly killing many innocents in the process, and tries to restore the Soviet Union in order to dominate the entire world. And let's not forget, all this in a children's program.
The sadistic smile he puts on as he drains the life force of Illiana, a mere child. Creepy everywhere.
Oh, and let's not forget that later he tries to use nuclear missiles to destroy the 15 largest cities in the world in order to rule over the ashes.
A montage was put together of what would happen if Phoenix/Dark Phoenix were allowed to run amok. The results were fire covering the entire Earth. Sleep tight, kiddies.
The first episode of the Phoenix Saga ends with Jean Grey essentially being burned alive; the scene cuts out on her agonized screaming, and then the screen fills with a particularly scary-looking version of the Phoenix...
The end of the first part of Time Fugitives has Apocalypse straight-up murder the X-Men, on-screen. Even worse is how sudden it is. He grows to fifty feet tall, snarls at the X-Men, and in a flash they're incinerated.
There's a part during the X-Men's fight with Apocalypse where, instead of his usual ham, his voice goes incredibly low. And compared to that ham, it's very unsettling.
Watch me, and TREMBLE, for I bring the purity of oblivion to your world.
“A Rogue’s Tale”, where Rogue is haunted by an unknown woman in her head, which is later revealed to be Ms. Marvel, trapped in Rogue’s head for years after a run in when Rogue was a teenager in Mystique’s employ. And she wants out: so much so that she attempts to kill Rogue despite knowing that this will destroy both of them. The only way to stop her is to seal her up again, which Jean does.
Carol’s body was found and taken to the hospital as Jane Doe, where she lay for years in a coma.
The power absorption itself, with the tense music, Ms. Marvel’s pained screams, Rogue sensing something is going horribly wrong, and Mystique cheerfully telling her to keep going.
Related, the fact that Mystique willfully manipulated the teenage Rogue into essentially committing a murder in everything but name... and got away with it.
Gyrich's unhinged Villainous Breakdown after trying to assassinate Xavier in "Graduation Day". As he's dragged away by police officers, he raves about mutants infiltrating society and accuses any humans sympathetic to mutants of being mutant spies.
Gyrich: You see? THEY'RE EVERYWHERE! TRUST NO ONE!
