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The reason Barry takes hostages in the first place is because he is so terrified of being abducted by aliens again. The abductions themselves are scary, and the episode acts as a reminder that alien abduction tropes that are regularly laughed at on film and television are really very frightening if taken seriously, involving major trauma and abuse. When Barry’s fear leads him to put others in danger, culminating in him taking Scully off so that she can suffer instead of him, the genuinely scary aspect of the whole set-up of the show is driven home in a really effective way.
9. Tithonus (Season 6, Episode 10)

If you’re looking for scary, how about an episode about Death himself? Like the earlier highly acclaimed ‘Clyde Bruckman’s Final Repose’, ‘Tithonus’ follows a character who sees that other people are about to die. However, unlike Clyde Bruckman, who only told us about his premonitions, in ‘Tithonus’ we see events from Alfred Fellig’s point of view. And so we get the sight of everyone in an elevator turning grey before Alfred steps out and the elevator car crashes, and of course, towards the end, we see Scully greyed out and apparently about to die as well (Scully being in danger is going to be a recurring theme of this list).
The idea of a man following around people who are about to die, not to help them or offer them comfort but to take their photograph, is also quite creepy. Fellig is basically a really sinister paparazzo, following people around in order to exploit them for his own gain. And in the end, it seems like Fellig’s “condition” may even have been passed to Scully, who was, after all, told by Bruckman that she wouldn’t die – and according to Fellig, that’s not a good thing…
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8. Folie á Deux (Season 5, Episode 19)

It’s Mulder who is in danger in this one and needs to be saved by Scully. This is also another episode featuring a hostage situation with an active shooter, but that’s not the scariest aspect of this story.
There’s the doubting of one’s own senses, which happens a lot in The X-Files, but is particularly extreme here. The monster design is also really effective. While the suit by itself didn’t work out all that well, extensive re-editing including adding a speed blurring effect and a buzzing sound created something properly unnerving, and the fact that only two people can see it at a time makes it even scarier – Skinner’s complete obliviousness is almost as alarming as the monster. Those who have been attacked take on a corpse-like appearance that isn’t exactly reassuring either.
But most of all, the scare factor builds to a height in the climax; Mulder is strapped to a hospital bed, being menaced by a terrifying insect-like monster, with a nurse who is one of the monster’s minions, screaming and screaming but no one believes him. It is the stuff of nightmares. Luckily for him, Scully is the shoot first, deny everything you’ve seen later type.