: When writing science fiction or horror, how to prevent the villain from becoming less scary as they are fleshed out? I'm trying to write a horror short story about a shape-shifter, but I have

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Different Trope: Hannibal Lecter and Dracula
I think that if you want to have your horror villain become more of a character and less of a stereotype, you need to look to a different kind of horror villain. As your audience moves from being scared of your villain to empathizing with them, the intrinsic horror needs to become less random and more intimate. In short, it needs to move from jumpscare (physical) horror like zombies, to a more mental (psychological) horror of a villain like hannibal Lecter.
No longer is your villain leaping out to eat your hero the emphasis. You come to understand the motives, and even sympathize, with the (serial killer/vampire/werewolf) and see yourself and your own reactions in the situation the villain is in. THAT is screwing with you head, since the villain very predictably is walking into the room to insert a mind control chip into your hero and make him betray everything he loves. Worse comes when he succeeds, and the hero kills his wife and children while aware he's doing it.
That's not to say that there isn't a very real physicality to psychological horror. It's just the scale is often smaller, more personal. Torture, for example, is a much more intimate horror than scenes where aliens keep dragging away people to an unseen but known fate. Knowing you're infested with zombie virus but are responsible for keeping your young child alive is a real mindf**k The scene where Hannibal Lecter (well, okay almost EVERYTHING he did) still screws with my head. The Ring is amazing not because you don't understand the villainess, but because she's utterly relatable as a vengeful ghost, angry at the world.

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I'm actually going to challenge the premise a little here...

I either have to have the main character run indefinitely, or explain why the shape-shifter is chasing them. Once I explain it, it doesn't seem scary no matter what I do.

Then don't explain it, not only is it unnecessary (particularly in short story form) it's actually often counter-productive to do so. While not universal fear of the unknown is a common one - think about how a unexpected noise in the night is often scary until you know what it is.
As for why certain implementations of the shape-shifter trope are scarier than others, some of that comes down to how the shape-shifting is used in the story, if we look at the examples you gave:
IT
"It" transforms with the express purpose of scaring the victim - on top of the scare-potential from the actual shapes we see It assume the basic premise of changing into the victims own personal worst fear leads the reader/viewer to start to wonder what It would appear as to them. The raison d'être of shape-shifting element of the story is to be scary, and as much of a motivation as we get for It's actions (which for a cosmic eldritch abomination is a surprising amount) is that it's eating people, and fear makes them tastier. Plus, I mean, c'mon.. clown (shudder).
The Thing
I was surprised to see you classify this as "Science Fiction" rather than "Horror" as the sci-fi elements are nominal. The themes here are paranoia and mistrust - and the shape-shifting is central to building that, the men turn on each other at points because they don't know who is still themselves. And of course neither does the audience, and that ambiguity is why the film works (and something that Carpenter fought hard to keep present even in the film's ending).
The actual motivations of the titular Thing are never actually explained, there's some conjecture from the characters but no definitive explanation - and this helps feed that paranoia, if they don't know what the creature's goal is they can't even judge another's actions against that goal.
T2
Unlike its predecessor (which arguably is a sci-fi take on a slasher movie with added explosions) T2 doesn't really make any attempt to be a horror film, it's a straight up sci-fi action flick (and a damned good one I might add) - and the shape-shifting element stays true to that. The T-1000 uses its ability to shift purely as camouflage - it’s just a more sophisticated version of the flesh covering T-800 models, the point is to let it get close enough to the intended target. It never sets out to scare the protagonists or by extension the audience with this - in fact from the point we the audience know about its existence there's only two instances where it isn't immediately apparent that a shifted T-1000 is said homicidal robot, and in both instances it's very quickly revealed.

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I have read It. I've watched Terminator 2. (Not familiar with The Thing.) I think I see the difference which makes one horror and the other sci fi.
Horror Is Inherently Arbitrary
The killer clown (ancient god-spider, whatever, etc...) in It is malevolent, delights in making victims miserable, and will go after anyone who is vulnerable and unfortunate enough to catch its attention. You could be next. For no good reason. And there's not really anything you can do about it.
The shapeshifting murder-robot from the future in Terminator 2 will incidentally kill bystanders for convenience, if they are in the way - but it will not go out of its way to harm anyone who is not directly connected with its mission. Sure, the ultimate outcome of its success will be the eventual extinction of humanity (or that's the plan). But it is neither fundamentally malevolent, nor unpredictable. Unless you're too slow to get out of the way, or unless you are personally the fated savior of mankind, there's no immediate threat to you.
Horror is very often supernatural, and this is not a coincidence. Part of horror is the unpredictable, the unknowable, which meshes well with supernatural themes. There is also the element of the irresistible - and if there was no fighting chance, no robot protector etc, then Terminator 2 would have been more of a horror film; desperately running, but merely delaying the inevitable, and not even being sure what face your doom will wear when it finally catches you. Incidentally, you talk about wanting to remove from your story the element of inevitability; not having to run forever, at least until the pursuing doom catches up. This just strips away another layer of the potential horror.
In general, if there is some sense to the source of the horror, if you can engage your reason and try to come to a solution or an understanding, if there is a way to understand or even overcome, then of course the horror dissipates. Now you've reduced your thing to a problem to be solved. When we know what is stalking us, out in the darkness, we can think, lay a trap, build a wall. Something. Horror is a feeling, not a thought at all. When our fear is tied up with the dark itself, something we cannot keep out, something we do not or cannot understand or reason about or anticipate and avoid... Only then it is truly horror.

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