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.
Zack Addy/Apprentice to the Gormogon - Bones
This one was a heart-breaker. Zack was Brennan's protégé, Hodgins' best friend, and, IMHO, the sweetest Squint ever. So when, at the end of Season 3, it's revealed that he's been working for a cannibalistic serial killer called "The Gormogon," it stunned the audience just as it shocked the Jeffersonian team. In typical Zack fashion, he accepts the logical consequence of his crimes and is committed to a mental asylum. His later exoneration for murder never really canceled out his betrayal of the team, even to himself.
Alex Drake/A.D. - Pretty Little Liars
More of a secret "Single White Female" plot than anything, the End Game of "Pretty Little Liars" revealed that Spencer Hastings was being impersonated by her unhinged, long-lost identical twin sister, Alex Drake. After being discovered by Wren tending bar in London, England, Alex makes connections with Rosewood residents only to have one murdered and kill another herself when he won't buy into her delusion about becoming her twin sister. Secret bunkers, fire axes, and full-sized dollhouses all make for one trippy-crazy finale.
Klaus as Alaric - The Vampire Diaries
Not quite a sleeper agent situation since Klaus takes possession of Alaric's body to gain access to Elena. The plan works although no one's super happy about how it works out. It only takes a single episode for Klaus to reveal his true nature and another one for him to regain his own body. Things develop quickly in Mystic Falls.
Grant Ward - Agents of S.H.I.E.L.D.
This was an incredibly well-played bit of double-agenty shenanigans. Agents of S.H.I.E.L.D. pilot episode introduced Grant Ward as the newbie to Coulson's team, spotlighting him as the hot-shot agent with a lot to learn. In other words, he was our freakin' protagonist. The first season then proceeds to develop intense relationships between him and all members of the team, especially Skye and May, with everything indicating that he was exactly who he presented as. And then, with the season finale in sight, he turns out to be HYDRA. Seriously? Multiple casualties and Fitz's brain damage later, he persists as a thorn in their side even as he takes revenge on his own family.
Jay Garrick/Zoom - The Flash
So, how does the old saying go? "Fool me once..." Yeah, beyond the ongoing joke which is the S.T.A.R. Labs security system, Team Flash has a terrible track record with insanely evil speedsters embedding themselves in the team and missions. First, there was Harrison Wells, their fearless leader, who turned out to be Eobard Thawne, time-traveller and Nora Allen's murderer, grooming Barry for his speed so he can return to his time. Then, in the very next season, Jay Garrick appears, a dimensional traveler from Earth Two, who helps Barry improve his speed as well (again, with ulterior motives) and HE turns out to be a SERIAL killer (named Hunter Zolomon, aka Zoom) who then kills Barry's DAD. The Allens just cannot catch a break, it seems.
Adrian Chase/Prometheus - Arrow
Arrow's past catches up to him with the arrival of the villain Prometheus who is ALWAYS ahead of Team Arrow, causing Oliver to kill Felicity's new boyfriend, and ruining the Arrow's reputation in Star City. When the oh-so-helpful District Attorney, Adrian Chase, turns out to be a completely bonkers son of one of early Arrow's you-have-failed-this-city victims, things just get worse. He kills his wife when she realizes what sort of monster her husband is and pins it on the Green Arrow. Then, to get revenge for being forced to kill her (???), he kidnaps Oliver's son and taking him to Lian Yu. That island gets a LOT of traffic from Star City.
Bendik Halvorson - The Innocents
A good doctor is hard to find. Especially when you're a shapeshifter, it seems. Bendik Halvorson runs an off-the-books clinic (FIRST HINT) for those afflicted in hopes of healing Runa, his dying partner (SECOND HINT), and ostensibly to help the population in general. Of course, his methods turn out to be the far side of horrifying and his solution for saving Runa is to basically steal another shapeshifter's body to store Runa's memories and keep her as his lover while Runa's actual mind and body continue to degenerate.
The Final Five - Battlestar Galactica
No one seemed more surprised by the reveal of the Final Five Cylon sleepers than the Five themselves. In a series riddled with passing-for-human individuals, it was a shot in the dark who would turn out to be the big toasters on the block. It literally could've been anyone. As it turned out, they had been living as BSG officers (Tigh and Tyrol), a Caprican athlete (Anders), an administrative assistant (Foster), and a power-hungry socialite wife (Ellen Tigh). Although Cylons, it may be a bit far to paint them as villains.
Alex Krycek - The X-Files
The classic double agent although how the F.B.I. didn't peg him as one from the beginning with that last name, I'll never know. After gaining Mulder's trust (whatever happened to "trust no one" huh?) his cover is blown and he just goes full-blown baddie all over the next seven seasons -- killing Mulder's dad, helping kidnap Scully, bargaining for directions to alien ships. He's so persistant that his ghost even comes back for a final appearance.
Jim Moriarty - Sherlock
Oh, Moriarty is a smarty, don't we know? He doesn't try to insinuate himself directly into the Holmes-Watson duo. That would be too obvious. Instead, he takes a parallel access route and woos the vulnerable Molly Hooper. Sherlock quickly and callously outs him as gay, sending Molly off in a huff, and then summarily dismisses Jim as someone not worth notice. Of course, he certainly notices when Moriarty gift-wraps Watson in a vest loaded with explosives. And that marks the beginning of a highly stimulating relationship.
Nina Myers - 24
A day can last forever when you have no idea who you can trust. Jack Bauer's staunchest supporter at the start of Day 1 is Nina Myers, CTU's second-in-command and Jack's former lover. After Jamey Farrell is revealed as a mole (and then found dead by suicide) it should've been smooth sailing for the team but Nina's alternative allegiance made that somewhat problematic, what with telling Jack his daughter was dead and then actually killing his wife, Teri. Her villainy plays a long arc over three seasons, fittingly ending in the same room where she killed Teri.
Razor/The Master - Doctor Who
That The Master is a villain is no surprise but when you aren't looking for him, this "master" of disguise catches everyone off-guard. In Doctor Who Season 10 Episode 12, "The World Enough and Time" Bill is befriended by Razor, a hospital employee, when she awakens from being shot for being human. Separated from The Doctor and the rest of the team, she has no chance when Razor signs her up for an "upgrade" which eventually leads to her conversion to a Cyberman and her ultimate demise. It's an interesting way to try to derail Missy's rehabilitation but The Master really should know better than to trust himself.
Suzie Costello - Torchwood
As the second-in-command of the Torchwood team, Suzie Costello was a brilliant strategist, efficient commander, and effective agent. (In other words, the total opposite of her replacement, Gwen Cooper.) Unfortunately, she was also ruthless, violent, and without much conscience to speak of. Her unscrupulous use of Torchwood tech is found out early on but her planning serves her well and death is only temporary for Suzie. Until it isn't. My only regret is that she wasn't able to take Gwen down with her.
Angel/Angelus - Buffy the Vampire Slayer
Honestly, we should've known this one was coming. A vampire with a soul? Cursed with a soul? A curse safeguarded by a line of gypsies? All those flashbacks. All that exposition. Yeah, everything about this set-up was a sermon on abstinence. I still weep for Jenny.