How to Write Mystery Villain?

I’m not very good at writing mysteries either, but maybe you could make it like the main character’s idol, somebody who isn’t directly involved in the story till later, but held a grudge on the main character’s sister because they damaged their reputation or maybe the sister attacked the idol’s country because they were being threatened, and in doing so the sister indirectly killed the idol’s parent. OR it could be like a maid or friend of the sister who helps the main character find her sister, then really captures the main character because they were like the original heir to the throne, but something happened, like they were overlooked and now they want to take backs what’s ‘rightfully theirs’. Just some ideas. Hope that helped!

You could make several people seem like the guilty party. Give multiple characters motives for killing the MC's sister. It's easier to write than making everyone seem innocent, and it also creates an atmosphere of suspicion and distrust, which is what you want in a mystery novel.

Although I don’t have too much experience with the mystery genre, I find that creating these types of secret or plot twist villains is often easier when you make them caring, kind hearted, or able to fit into a hero archetype. For example, the “gruff, washed off mentor who imparts wisdom on the hero” could be secretly manipulating them to get back at someone or to gain power. Or the “goofy sickick who always seems to screw up” is purposely doing so to hinder your protagonist.

Thought I'd give a bit of insight. This is really for villains in general. The story has to make sense from their point of view. For example, would a person really just kill another person because they're "evil?" Genuine malice is very rare in people and usually occurs because of some sort of corruption. A tip is to flip the story and look at it as if you were your villain. Does what they're doing make sense? If you do this, you might find you love your villain instead of totally hating them. Even a cliche villain from an anime or something can be hilarious. Anyway, thats all I had to say. Hope it helped! Good luck!