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Source: https://writers.stackexchange.com/a/35086
License name: CC BY-SA 3.0
License URL: https://creativecommons.org/licenses/by-sa/3.0/

Leave clues that make it possible to see at least the gist of his reasoning and line of thought for the observant and determined reader. Make it so that it's always possible, albeit very difficult, for the reader to predict his actions and to outsmart him.

For instance, let the villain disguise himself as some other character that interacts with (or is close to) the protagonist as a means of gathering information, but never tell the reader that outright. Leave breadcrumbs, instead. [Here's another, much better and lengthier example.](http://kingkiller.wikia.com/wiki/Master_Ash#Speculation) It should be noted that I loved this book and breezed through it, so I noticed exactly none of these clues; that's what I mean when I say that it should be possible, but difficult, for the reader to see the breadcrumbs.

Good luck!

P.S.: Consider giving the villain a power that grants the super-intelligence you speak of, rather than just ascribing it to his genius mind (and it doesn't have to be simply super-intelligence; for instance, Contessa, a character from _Worm_, has a power that tells her every step needed to achieve a desired goal and how to execute these steps). That would make it far easier for you to, as Amadeus said, demonstrate the villain's planning.

Original score: 4