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How to hint at an antagonist's identity?
A significant antagonist in my trilogy is an omnicidal alien by the name of Loki, whose characterisation borrows from Griffith, Keizer Ghidorah, Randall Flagg, Saruman and Hastur. Throughout the series, Loki takes forms called “Masks” to interact with disciples or masquerade as various species, per his epithet “the Billion-Faced Beast”. One “Mask” he uses is that of an priest named Father Nguyen to provide false emotional and spiritual support to the deuteragonist implied to be Jeanne d’Arc. Loki later tells the deuteragonist that he killed the real Nguyen to destroy her sanity (who suffers from Major Depressive Disorder, thanks to struggling to conform to modern society, everyone she knows being dead and having no human contact for over six centuries).
Another Mask used by Loki is a person who leads an anarcho-communist and anti-fascist group. Loki uses this Mask to have his sociopathic, authority-hating followers commit political violence against and kidnap innocent civilians to give the Degenerates (humans parasitised by prehistoric pentastomids styling themselves after nomadic Indo-Iranian cultures and resembling a certain endoparasitic extraterrestrial) with hosts.
I have scattered several hints throughout the series about Loki’s identity by having him only assume Masks between 10 (his true form’s height) or 5 feet tall and makes heavy footfalls when walking. Another major clue is that he always retains his scarred lips, venom burns, falconic eyes and high body temperature in every Mask. However, I still don’t think this enough, and it all comes across as very heavy-handed.
How, then, can I hint Loki’s identity without being unsubtle?
Why this is difficult: dramatic conventions
If a description of something is unique and also can't be observed incidentally by the reader, as with a character's highly unusual physical features, you can bet the reader will flag it as a notable detail. As soon as they encounter it again they will draw a connection, and they will quickly map all of the other hints and uncertainties onto that connection to see if their theory works. Those kinds of details work better in crafting a reveal or twist than in laying the trail of breadcrumbs because, as you noted, they're just too obvious.
The reason this is always a giveaway is because writing follows dramatic conventions, and readers are attuned to them and work consciously or subconsciously to identify them, especially when they are trying to resolve a mystery. To keep up the pacing and thrust of a story with suspense you can't have a bunch of irrelevant details gumming up the works, and so unnecessary information often gets chucked. Therefore if it is in the story, it must be relevant (see Chekhov's gun).
The weakness of using physical attributes as clues in writing
All of your tells are physical attributes, some of which are unambiguously unique. Therefore they are 1) too memorable, and 2) too difficult to shoehorn in as not-obviously-planted information.
I'm reminded of the books by Edward Rutherford in which we trace the history of a city through the eyes of certain characters and their family lines. He has to keep reinforcing the family connection by describing shared physical features, and it feels rather contrived because it doesn't fit naturally into the story. So you start to get multiple characters whose faces are described as "shaped like a spoon", and you know to expect it, and it becomes a weird sort of symbolism.
Some better approaches
- Don't be too heavy-handed with any clues. Not every Mask must exhibit all of the clues, and therefore they are better if they aren't right there on his face.
- On that note, it would be better to lose the permanent, difficult-to-disguise, and utterly unique features. Having your clues be more generic introduces a new element of uncertainty because your readers have more possible interpretations for them. Even if you want to keep some of them, don't keep all of them. Multiple characters/Masks have venom burns but not necessarily in the same arrangement? Perhaps they were all soldiers together in a battle against an alien enemy species with venom. Multiple characters have the same brand on their forehead? Maybe they're members of a cult. But if they all have the same splatter pattern of burn marks and also have a knife scar on the left side of their face and the same weird eyes, and shake the ground when they walk, it's pretty clear that this is a unique individual. You can easily lose the falcon eyes in transformation, even if the scars are important to the plot.
- At the very least give Loki the means to hide those tell-tale traits. If the scars are immutable as part of the plot, fine-- you can give him beards, hats, balaclavas, whatever, and make them more subtle. Have him wear contact lenses or sunglasses. Have him walk deliberately and softly until a moment of high emotion or distraction, when his heavy tread emerges.
- Even better, use other details as clues, particularly those that will fit naturally into the plot or the dialogue. Loki could have a specific philosophy or certain turns of phrase that he favors, and (if there is enough dialogue to dilute the effect) those could work their way into the conversations of the Masks. (Again, not every Mask every time.) He could react to a situation in a way that betrays an earlier experience, such as jumping to the wrong conclusion, panicking when he encounters venomous animals, etc.
- You can also subvert the reader's clue-seeking strategy by hiding the clues in plain sight, or disguising them as something unrelated. Don't make your Masks shadowy, mysterious characters whose identity and purpose are unknown. Instead, describe them fully, give them a benign surface agenda, make them seem unthreatening and well-meaning. That this blind monk with the warm smile happens to wear dark glasses doesn't mean anything, right?
Pick one thing that all the characters have in common, and I'd make it subtle. In dialogue, Loki has a favorite word, perhaps a curse, that no other character in the book uses. You might also give him a grammatical quirk, that no other character uses, and if any imitate him, he punishes them for mocking him.
Find something you can use fairly often, the equivalent in American English of "fuck" or "shit", a generic all-purpose curse, and in moments of anger or frustration he lets slip his ten-thousand year old version of it.
Don't be heavy-handed, with visual cues like eyes and lip scars, there is no need. The audience will pick up on this one thing.
Now you might think, this could be a family thing or cult thing, all these people might be a related group. But that is easily defeated with standard prose; whichever mask Loki is wearing, he has the same unique memories and experiences, and you can find opportunity for him to reference something he did in Mask A, while he is in Mask B, in a setting where we are inclined to believe he is telling the truth. For example As B, Loki casually explains to a collaborator what he personally saw in Chicago, but the reader knows it was Mask A that saw that.
Don't try to be so explicit, leave clues and the reader will figure it out, and it will be more fun for them than if you are heavy-handed about making sure they get it.
You must make the rules of your world clear
As your antagonist is disguising his identity through the use of these magic masks the first step should be showing the reader that such magic is possible. Once a reader knows that it is possible for such masterful illusions to be created they will try to link less obvious clues, such as speech patterns (if a character has a lisp or habitually uses certain phrases), movement patterns (if a character has a limp or surprising strength) and thought patterns (if a character has a specific goal).
For example in your question you give a couple examples of the masks Loki will wear, those masks seem to have a shared disdain for humans, from trying to break a person's sanity or convincing followers to kidnap, if all Loki's masks have a similar underlying disdain for humans a careful reader may start to link these characters together and begin to suspect an illusion.
You question prompts a wider question: the expected base knowledge of your target audience. "Loki" is a mischievous Norse god who who has the ability to shape-shift. I'm not in your target demographic but made the link on reading his name. If you continue to hint you'll be insulting the intelligence of readers like me.
You run in to other issues. The Norse god Loki is nothing more than prankster. However, Marvel's Loki in a villain who can also shape-shift. Marvel will claim you're infringing on their copyright.