The greatest mastermind of all villains is none other than Xehanort of Kingdom Hearts. SKIP THE NEXT THREE PARAGRAPHS IF YOU DON'T WANT BIRTH BY SLEEP SPOILERS!
In KH:BbS, Master Xehanort tried bringing out Ventus's darkness so that he could fight against the light hearts of Master Eraqus's students Aqua and Terra to create the X-blade. When that didn't work, Xehanort ripped out Ven's darkness by force creating Vanitas. He then sent Ven to Master Eraqus so that Ven's light could get stronger. That way, Ven and Vanitas could fight to create the X-blade.
While Xehanort was at Eraqus's castle, he noticed that his student Terra had a bit of darkness in him. Realizing he was getting old, Xehanort decided to use Terra's darkness as an arc to steal the boy's body. A few years later when it was time for the Mark of Mastery Exam, Xehanort sabotaged Terra from becoming a Master by telling Eraqus that he was uncomfortable with someone possessing darkness obtaining such a prestigious rank. As a result, Aqua passed but Terra failed.
At the same time, Xehanort had Vanitas unleash a horde of Unversed across the worlds forcing the students to leave home to fight them. Over the course of their separate journeys, Xehanort fed Terra's darkness and Ven's light in preparation for his Keyblade War. By the time anyone figured out Xehanort was up to, it was too late to stop him. The X-blade was forged and Terra's body was stolen successfully. If it weren't for Aqua destroying the X-blade and defeating Xehanort, he would have been victorious.
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Fast forward ten years to KH1, his Heartless Ansem is trying to create Kingdom Hearts, the Heart of all Worlds. Part 1, use the Disney Villains to find the seven Princesses of Heart to open the Door to Darkness. Part 2, find another boy with a strong affiliation for darkness so he can steal this boy's body to gain a physical presence. Part 3, obtain supreme darkness. Again, Ansem was almost successful having opened the DtD and stolen Riku's body. His only miscalculation was that Kingdom Hearts is light, not darkness.
In 358/2Days and KH2, his Nobody Xemnas is attempting to make Kingdom Hearts out of the hearts of men. When Sora's Nobody Roxas is born, Xemnas brings him into the Organization as its thirteenth member. Problem is, Roxas is a bit catatonic the first week so Xemnas goes to Hollow Bastion to battle Sora as a test, but also collects data on the Keyblade wielder so that Vexen can make a replica. Thus brings about Xion, the fourteenth member though she is slightly imperfect.
When Sora gets put to sleep, it doesn't matter because Xemnas has two Keyblade wielders at his beck and call. Thing is though, Xion is a bit rebellious and after awhile she starts unconsciously feeding off of Roxas's power weakening him. No matter, Xemnas has them fight each other and plans to keep which ever one lives. Xion is destroyed and Roxas is kidnapped and merges with Sora. That doesn't faze Xemnas at all, he just uses Sora. Sora wises up that he's being used by the Organization, but Xemnas has an Ace up his sleeve. Sora's girlfriend Kairi was recently kidnapped so he uses her as bait to lure Sora in.
Of course as soon as Kingdom Hearts is ready, DiZ blows it up with a machine that he was originally going to use to turn it into data. Even then, Xemnas is still an evil genius so he uses the remnants of Kingdom Hearts to become the most powerful being in the universe. He was even strong enough to almost beat both Sora and Riku working together. Too bad for Xemnas though, he ended up losing.
All of this just goes to show why Xehanort makes the greatest evil plans ever. Every time they nearly come to completion, and he can make multiple contingency plans on the spot for any failures. It almost makes you wonder what he has in store for KH3.