I want to create a villain who is very smart and manipulative, capable of twisting other’s minds. A villain who seeds doubt and division, even between his allies. Someone who is always a step farther than anyone and able to analyze the situation and his enemies. For the moment I would say that he needs to know everyone's desires and internal conflicts.
What do you mean by "how to handle"? Do you mean as in how can your hero(es) defeat them, or more like how to write one well?
This right here can get very annoying if not done well. I'd say be careful with this. He'd have to do a lot of careful study, plotting it out. I'd say a good inspiration for you might be Xanatos from the Gargoyles animated show. He wasn't all-knowing, but he did know how to benefit from every possible outcome. That, IMO, is a lot more interesting than 'oh I know what you were gonna do and countered it already!'
Study, study, study. This villain would have to study his opponents and allies, possibly for years, to get to know them intimately. This, naturally, would mean that he has to be able to do so, which raises the question: Who is this villain to our protagonist? Is he someone the protagonist knows, or is it someone who has been lurking in the shadows and is just now striking? He'd also have to be a master at instilling doubt in the minds of our main players. This circles back to study. Once he knows his targets intimately, he'd know how to prey on their insecurities to plant that small seed of doubt. While he would undoubtedly have thought out many scenarios, none among us can predict exactly how someone is going to act. Therefore, his big plan, as well as he, would have to be flexible enough to adapt to the reactions of our protagonist(s). I absolutely despise the villain archetype that predicts everything someone will do, like, "Hah! I knew you would walk through that door at exactly 5:47 and 14 seconds, which is why I had peanut butter fall from the ceiling, an allergy even you didn't know you have!"
If this is a fantasy story, it would be good to play the character abilities/powers into this. In general, I agree with Zerotonin. Don't play this too strong like they are omnipotent. It's not very interesting or very believable- even in fantasy.
To write that kind of villain well you study narcissistic personality disorder. Study deep. Study wide. Study if from all angles. Focus on the dynamics of narcissistic behaviour + what patterns they victims repeat. Another focus on fractured self of narcissistic person and the way (s)he tries to earn value to himself by denying his negative features and how (s)he projects them to other peoples. After 10-20 good books about narcissistic personality disorder you villain will live. You will find good books connected to... - Criminal psychology - Intimate relasionships & family - Working life - Selfhelp & recovery - Some famous people - Business & politics...
