When you’re developing a villain it doesn’t mean you can’t do a little narrative sleight of hand and have a hero become a villain and villain become a hero. Crime fiction is full of examples where writers use red-herrings misleading readers with who characters are.
Often they do this by presenting a list of possible suspects and leading the reader towards one then revealing it was in fact another character having, hopefully, dropped a few clues along the way to support this. Such a plot would be frustrating for a reader if there were no breadcrumbs to trace backwards, think of Agatha Christie’s Poirot and how he would list and dismiss each character before reaching the true murderer. To do this each potential murderer needs a logical reason and a hint or two dropped as the story progresses otherwise Poirot’s method would fall apart. However, the clues don’t need to be conspicuous otherwise the murderer would be obvious too soon. A way of doing this may be off-hand observations or things that are mentioned but overshadowed by a more conspicuous ‘clue’.
Another method that Agatha Christie used at least once, I haven’t read all of her books yet, was once having one of the investigating characters turn out to be the murderer. This trick works on the principle that the character is above suspicion in the reader’s mind because they are investigating the case and the detective, amateur or otherwise, would presumably not have done it. In the big reveal our hero/protagonist becomes the villain. I’m dubious about mentioning this book because I know people really don’t like having Agatha Christie books spoilt for them.
Another crime plot line is one where there is an obvious suspect with motive galore, and sometimes they’re even covered in the victim’s blood, and through the story they are presented as the obvious, perhaps even the only, suspect, until the reveal where it turns out they were set up. Sometimes these characters even think that they did it because it is so obviously them then they must’ve and they imagine they blacked out and can’t remember it. However, these stories usually have a hint that they were set up a small clue that might appear inconsequential to everyone but the extraordinary detective, perhaps a piece of cloth, a comment from a character or, in the case of a story like Gosford Park, they were beaten to it. In Gosford Park there are two murderers but, as it turns out, the second murderer stabbed a corpse. The second murderer believed they had killed the victim because they didn’t realise that they’d stabbed the corpse of a man who’d already been poisoned.
Perhaps at this point it should be noted that during the golden age of crime, of which Agatha Christie was considered the queen, the butler never actually did it unless it was someone pretending to be the butler. The reason for this is a classist one because it was assumed that the ‘lower classes’ simply weren’t clever enough to commit such an ingenious murder. So, if you’re reading an Agatha Christie you can be fairly certain it wasn’t one of the servants. However, secretaries were exempt from this rule because they were usually lower middle class women who were educated.
Ultimately a villain doesn’t have to be loud and conspicuous, they can be quiet and conniving and surprise the reader as long as there is a logical path and not a sudden inexplicable appearance. A villain that the reader had no chance of spotting is a frustration, but villain where they had a chance is a delight.