I really like it when someone who seems harmless/incompetent is actually really dangerous and hiding in plain sight. It takes a high degree of manipulation and cleverness to work. 

Xigbar/Braig/Luxu - Kingdom Hearts - At first, Xigbar seems to be just another member of Organization XIII - then in Birth by Sleep we learn that when he was still a human named Braig, he actually was very heavily involved with Xehanort from the beginning. Even then he comes across as nothing more than an ambitious thug who likes to troll the good guys. At the end of III we learn that Xigbar was playing everybody - his true identity is Luxu, one of the Lost Masters, and his goal was to ensure the second Keyblade War took place. We need to wait for Kingdom Hearts 4 to learn more about his motives, but we now know he is a master manipulator. 

Tobi/Obito - Naruto - When he first appears, Tobi seems to be a new recruit for the Akatsuki - a goofball who enjoys messing with his partner Deidara and acts as comic relief for the increasingly dark and tense story. Then after Itachi dies, he drops the act and reveals he's been the leader of the Akatsuki all along. We eventually learn that his true identity is Obito Uchiha - Kakashi's best friend who was long believed dead but had turned evil. Black Zetsu could also be mentioned here but people were pretty mad about that reveal lol. 

Selim Bradley/Pride - Fullmetal Alchemist Brotherhood - When we first meet Selim, he seems like a friendly kid who looks up to his father, King Bradley. More than halfway into the series we learn that Selim is actually Pride, the strongest of the homunculi and Father's right hand. Fittingly, Pride's powers involve manipulation of shadows. I know that Pride isn't the mastermind in this case, but I feel this still fits. 

(Loved Trope) The mastermind is the last person you'd expect