It can be the hero, antihero, villain, antivillain, or side character... but regardless of their overall role in the story, in the time they do have, these characters have demonstrated a huge capacity for strategy, backup plants, organization, and tactics. Generally starting with just a handful of tools and assets, characters like this can grow their power into entire cults or nations; or otherwise can bring down said entities like they're nothing. To be clear, I'm not looking for the best leader in anime - often times the masterminds will remain behind the scenes and anonymous even to their closest allies.
I'd like to see who you guys think deserves the title of "Best Mastermind in Anime."
Some candidates I can think of (which you might like to make cases for) are as follows:
Lelouch vi Britannia (AKA Lelouch Lamperouge, Zero, Julian Kingsley) from the anime Code Geass.
Born into Britannia, the greatest empire the Earth as ever seen, Lelouch's destiny as a royal was forever changed when his mother was assassinated and his sister left crippled by the same bullets. Seeking revenge against his father and the royal family (whom he blamed for the assassination attempt), Lelouch accepted the power of Geass - the ability to have anyone he made eye contact with follow his commands. Using this power, as well as strategy and diplomacy, Lelouch assembled a terrorist group known as the Black Knights and proceeded to match the military might of Britannia time after time. He serves as the hero of Season 1, the villain of the midquel, and the antihero of Season 2.
Yagami Light (AKA Kira) from the manga and anime Death Note.
The son of a police chief and the antihero of the manga, Light was initially just another student in the Japanese education system when he one day discovered the Death Note - a magical notebook that would kill whoever's name was written within. Armed with this weapon, Light sought to purify the world of all criminals, regularly purging those he felt did not meet his standards. Though he withheld his identity, some of the public came to worship him under the identity Kira and formed cults, television shows, and riots in support of their savior. Guided by a delusional messiah complex and the belief that he could construct a new, pure world free of crime, Light would meet his equal in the form of the genius international detective L.
L (AKA Lawliet, Ryuuzaki) from the manga and anime Death Note.
A famous adversary of Kira/Yagami, L is an anonymous international detective who takes interest in the Kira case. Perhaps less because he believes it is right and more to entertain himself, L undertakes the dangerous task of hunting down the seemingly omnipotent killer; as such, he becomes the series antivillain. In just the first two episodes, L manages to narrow down his suspects from any of the 7.1 billion people on Earth to a likely urbanite from the Kanto region of Japan. If this incredible feat is not enough, L is also repudiated to be the best detective in the world, having solved many other cases before.
Makishima Shogo from the anime Psycho-Pass.
A psychopath (or "criminally asymptomatic" person, as it is known in the Psycho-Pass universe) born into a postmodern Japanese society, Shogo Makishima becomes disgusted with the present nature of human living. Under the organization of the algorithms of Sibyl, a functional role in society is secured by a person's submission to the system and their ability to keep their stress level down. Makishima serves as the antivillain of the series: while his goal of freeing people from this submissive, cowed way of living is admirable; his means are grisly and horrific. He assembles a team of murderers and powerful individuals to destabilize society from the inside, but does not shy away from dirtying his own hands with innocent blood to realize his goals.