The puppet-master villain, unseen yet seemingly omnipresent, is a trope designed to keep us guessing.
The best hidden villains often strike fear with just their faceless name, manage to outsmart the team, staying a step or three ahead of their efforts.
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When they turn out to be hiding in plain sight as part of the team itself -- moles, double agents, sometimes even sleeper agents -- it's simultaneously shocking and devastating.
Sometimes it's a case of plotted betrayal. Sometimes they don't even know. Always, it's a reveal that melts our brains a bit.
Lenny Busker/Amahl Farouk - Legion
David Haller doesn't have a lot of people he trusts. Being simultaneously psychic and schizophrenic, he can't even be sure about the reliability of his own thoughts and senses. With so few options, he puts a lot of faith into the figment of his imagination he assumes is looking out for him, a post-mortem hallucinatory figure of his IRL friend Lenny Busker. So when it turns out that Lenny's image is been used by a disembodied mutant psychic named Amahl Farouk who has been feeding off of David's powers and tormenting him since infancy, it's no wonder that he feels pretty put out by the whole situation.
Harrison Wells/Reverse Flash - The Flash
When Barry Allen gains his metahuman abilities, his first mentor is the brilliant and wheelchair-bound scientist, Harrison Wells. Harrison's team of Cisco Ramon and Caitlin Snow soon become Barry's best friends and, with Harrison directing them, they soon train and equip Barry to be a superhero. As it turns out, Wells' intentions are not at all altruistic, grooming Barry's connection to the Speed Force so that he can return to his own time in the future. When he reveals that he is actually Eobard Thawne, aka the Reverse-Flash, Barry's mother's murderer and the reason Barry's father goes to prison for much of Barry's life, he doesn't only destroy Barry's world but Cisco and Caitlin are destroyed as well.
Kathryn Nemec/Mr. Kaplan - The Blacklist
One of Raymond Reddington's closest associates for over twenty years, Kate Nemec, operating under the professional moniker "Mr. Kaplan" knew almost all his secrets and (quite literally) where the bodies were buried. Despite her up-front warning that she would always put "Masha's" interests above his (and him agreeing to this), he was completely unprepared for her attempt to destroy his empire in order to free Elizabeth from his influence. Always the epitome of efficiency, her suicide by jumping from a bridge guaranteed an easy clean-up.
Eli "Rowan" Pope/Command - Scandal
Oh, daddy dearest! Not. Under his cover as a mild-mannered curator at the Smithsonian, he raises Olivia to be a force to be reckoned with, although apparently oblivious to the true nature of her father (and mother too). When he is revealed to be the director, known simply as Command, of B613, a covert branch of the C.I.A., it soon becomes clear that he is capable of petty and deadly attacks in his megalomaniac power frenzy and his own daughter barely gets a pass when she stands in his way.
Ash Tyler/Voq - Star Trek: Discovery
In possibly the DUMBEST sleeper agent plot ever concocted, sussed out by Internet fans well ahead of the reveal (but I tried REALLY hard to believe it wasn't going to happen), rescued prisoner-of-war, Ash Tyler, turns out to be a physically-reconstructed, psychologically-groomed, passcode-enabled Klingon spy. Allowing for the fact the Federation was desperate for officers, it was still highly improbable that he would have passed the PTSD screeners quickly enough to end up on the away missions he was assigned to. (It's even more unlikely is that the medical scans missed that half his Klingon organs had been removed AND that the remaining ones WERE STILL KLINGON.) Anyhow, his fake human psyche apparently derailed some of his real Klingon programming so his activation didn't go exactly as planned.
Petyr Baelish/Littlefinger - Games of Thrones
So many hidden villains to choose from here but Lord Littlefinger was our first and definitely one of the most unrepentantly self-serving. Even as he betrays Ned Stark to Joffrey's "justice," he's pretty clear that he doesn't see himself as much of a liar. "I did warn you not to trust me," he comments almost cheerfully. And yet somehow, for season after season, alliance after alliance, people continue to strike deals with him, confide in him, and trust his word. Thank goodness the Stark girls eventually caught him out at his own game.