In the Medabots anime, the Big Bad turns out to be a (cybernetic) house cat using the body of a mad scientist as its puppet.
The Big Bad in Naruto is neither Pain nor Orochimaru but the Plucky Comic Relief Tobi. It later turned out though that it is a little more complicated than that. Tobi is one of multiple assumed identities he uses. He turns out to be (this one's for real) Obito.
Used in Hayate the Combat Butler, Santa in Hayate's 'imaginations' from the first chapter is revealed to be Mikado. Although the reveal doesn't really unnerve Hayate, since he's already been unnerved by this point in the plot.
Hardly anyone could have expected Aji Tae, the Big Bad of Shin Angyo Onshi, Diabolical Mastermind who had already brought down an entire country before the series began and is stated to be an Evil Sorcerer of the highest order to be that Adorkable prettyboy healer with a pet goose who shows up to save one of the main characters and clearly plays into the role of not-so-covert sage mentor later. All exactly as planned by him, of course. The fact that he completely changes his appearance between flashbacks and actual story helps to mislead readers.
In Higurashi no Naku Koro ni, this is done so well that even if the Big Bad had a creepy moment or two, you wouldn't have known who it was until The Reveal. The Big Bad has been shown in every single arc, and as far as the viewer was concerned, had no chance of being the villain. After all, it is extremely difficult to suspect a character that looked like she was promptly killed off every single arc. Even with the very few creepy moments before The Reveal, who would suspect that it was the dead nurse faking her death every time?
In Eden of the East, the mastermind behind the Selecao organization, Mr. Outside, is really an old taxi driver. You may remembering seeing him in the earlier episodes, long before his reveal near the end of the story.
In Code Geass no one could have possibly guessed that the co-Big Bad of the story was actually Anya, the fairly emotionless girl. Even less likely is anyone figuring out that the dear old Mommy everyone loves could be one of the biggest evil bitches in anime history.
In Domu, the psychic menace terrorizing the apartment block turns out to be the mentally-deficient little old man.
In Steins;Gate, it turns out that the SERN spy is none other than Okarin's landlord, the completely unsuspicious Mr. Braun, who had never spoken a single line about anything plot-worthy until then.
The lesser-known Lily C.A.T.. takes all of the tropes from the movie Alien and puts them in a blender. There's even a cat on board the ship, and a secret android working to bring back the murderous alien at the expense of the crew. The catch...is that the cat is the android.
In Rosario + Vampire, the leader of the terrorist organization Fairy Tale and most powerful character in the series is eventually revealed to be Miyabi Fujisaki, the guy who was almost married off to Mizore back at the start of Part II. This character was important when first introduced, but was never mentioned again afterwards, and certainly showed no signs of being Alucard himself.
In the Doom Patrol comic, the would-be cosmos-destroyers in the Cult of the Unwritten book are led by the Archons of Nurnheim—i.e. a couple of Punch and Judy puppets. Why yes, as a matter of fact this was written by Grant Morrison.
In a two-part story in Detective Comics (circa 1989), Batman tries to stop the anti-establishment villain (or anti-hero depending on individual viewpoint) Anarky. Over the course of the two issues, the reader is shown scenes of a family man and his son, both together and apart. These scenes slowly imply that Anarky is the father, and he even tries to take responsibility when Batman catches him with Anarky's cape. Turns out he was just covering for his son, who was the real Anarky. Keep in mind that the son was a middle schooler at the time.
Nick Fury, Agent of SHIELD, threw the readers a curve when the identy of HYDRA's leader, Don Antonio Caballero, proved to be an alias. Ripping off his life-like mask, the true Supreme Hydra stood revealed as Fury's long missing WW2 arch enemy Baron Wolfgang von Strucker. It was a moment so jarring, artist Jim Steranko made it a two page panel for the occasion.
In the Darkwing Duck comic book series, a recurring villain is a genetically engineered house cat who fakes his own kidnapping from a research laboratory. Yes, in the Darkwing Duck universe ducks can keep cats as pets.
In the original Silver AgeSpider-Man comic book, The Big Man — a New York crimelord and leader of the Enforcers — was revealed to be Frederick Foswell, a browbeatened reporter at The Daily Bugle.
This is something of a reoccurring theme among Spider-Man villains. The original Green Goblin was eventually revealed to be Norman Osborn, the father of his best friend (this being long before Norman established himself as the Lex Luthor of the Marvel Universe). The Jackal, better known as the villain who set up The Clone Saga, was Peter's nerdy science professor. The Hobgoblin, a villain modeled after the Green Goblin, had a two-for-one deal. He was originally revealed to be a Daily Bugle reporter and longtime minor supporting cast member Ned Leeds until a Retcon explained that he was yet another minor supporting character who had since faded into near-obscurity.
One particularly jarring example involves Spider-Man searching for the murderer of a scientist who had created a crime cataloging supercomputer. The culprit is none of the three suspects, but the computer itself.
In the third ever Justice Society of America story in All Star Comics #5, the JSA bust up a series of rackets headed by a mysterious figure known as Mr X. At the end of the story, an innocuous milquetoast who had appeared in each of the individual chapters turns up the police station. It turns out he is really Mr X and now, with all of his rackets smashed, he intends to turn himself in and live off the state in prison.
Rat-Man: one story has the eponymous "hero" meeting Graziello, a stick figure who annoys him by telling corny jokes and laughing in a monotonous way, and Rat-Man can't get rid of him. In the end we discover that everything that happened in the issue was Graziello's plan: as a failed comic book character who never got the chance to be published, he lured Rat-Man to the comic book school and in doing that he had appeared in a Rat-Man issue, thus finally being published and read by many people!
An Anti-Hero version of this trope happened in Watchmen. Rorschach's identity was mostly a secret until it is revealed he was that random homeless guy that was always hanging out in the background.
This happens twice in 52. The first time is a huge early reveal that the time issues going on are the work of Skeets, Booster Gold's sidekick. Oh, and he kills Booster. In the very last issues after Booster is revealed to be alive due to time travel tricks, it's discovered that Skeets is possessed by Mister Mind. Said villain had only appeared in a few panels without ever saying a word in the early issues.
Homaged in Bongo Comics' Radioactive Man series which generally parodied most of the major cliches in comics, superhero especially, and had the final issue reveal that Radioactive Man's deadliest foe was Radioactive Worm, an Expy of Mister Mind, who reveals it was caught in the same explosion that created RM. Indeed, as pointed out in a footnote, if you look back at the first issue's splash page of Claude caught in the atomic explosion, you can see a tiny earthworm crawling up from the ground right below him and being in it as well, thus planting the reveal as this rather than one of the Stranger Behind the Mask variety
Similarly, in their short-lived Bartman comic, the true villain behind the crime wave that's taken siege of Springfield? Lenny, thanks to the fact that a faulty leak had dropped minor radioactive waste on his head resulting in him going temporarily insane, a moment that's briefly seen early on in the first chapter as a Funny Background Event while Mr. Burns and Smithers were talking.
A variation in Jonathan Hickman's Avengers comic book. The Starbrand has come to our Earth, and we're shown several scenes at a college focusing on different characters we believe are potential hosts. At the end of the issue, the Starbrand chooses an inconspicuous background character that had meaningless interactions with each of the candidates.
In the Firefly fanfic Forward, it turns out that the mastermind behind the events of the "Charity" episode was Katie, the little girl following Zoe around, who was actually a powerful psychic.
In the Legend of the Five Rings fanfic "Rokugan 2000," the champion of the Realm of Evil turns out to be Hoshi Jack, the motivational speaker who stars in a cheesy TV talk show.
A Harry Potter fanfic called The Ones You Never Expect starts off with Colin Creevey being revealed to have faked his death in the final battle. He then meets up with his brother to report to Dedalus Diggle. All three report to Crookshanks. Who reports to "The Queen": Hedwig. As it turns out: The war wasn't between Voldemort and Dumbledore; it was between Nagini and Fawkes. And Hedwig as been waiting on the sidelines, faking her death, until the two sides butchered each other so that she could take over the world in the aftermath.
The Adventures of the American Rabbit has the eponymous hero getting a big surprise when he tackles the Big Bad, only to have him suddenly deflate. It turns out that the human like figure was a decoy and the pet vulture who is usually perched on him is the real villain all along.
Films — Live-Action
In the Japanese film Suicide Club, the real culprit turned out to be the 14-year-old singers of the band named Dessert, who are often shown singing songs on the television at regular intervals but not actually playing any role in the plot - until The Reveal.
In Blood Work, the serial killer turns out to be the protagonist's drunkard fisherman friend from the same marina.
In The Bone Collector, the killer is Richard, the technician from the beginning of the movie.
An early cut of House of 1000 Corpses had the relatively harmless Grampa Hugo Firefly turn out to be Dr. Satan. Rob Zombie decided this would have been anti-climactic and changed it.
Parodied in the "Scooby-Doo Ending" of Wayne's World, where it's revealed that Ben is really Old Man Withers, the amusement park owner who Wayne spoke to for five seconds near the beginning of the film.
And talking about Scooby-Doo, the first live-action movie has a literal example, as it turns out that the mastermind is Scrappy-Doo, who, up until that point had only appeared in a short flashback.
The first Saw movie (see page quote). The "guy on the floor" (John Kramer) is also seen in a flashback, where he's equally inconspicuous as a patient at the cancer ward.
There is a hint, though. When someone starts loading the revolver the guy on the floor supposedly committed suicide with, it's empty. Revolvers don't eject spent cartridges. You can't kill yourself with an empty revolver...
All of the movies in The Thin Man series operated this way. Start with a murder, present a colorful parade of suspects, end by revealing the killer to be someone the audience had no reason to suspect.
In the Hungarian film Kontroll, the masked killer is a welder who appears briefly in one scene. (Although that's not revealed in context; you can only find it out from behind-the-scenes information about the same actor playing both parts.)
Subverted in Phone Booth. At first, it looks as though the Caller was the pizza guy who only had a very brief appearance at the start of the film. However, it turned out the real Caller had the pizza guy hostage until he got caught, when he slashed his throat and left him as a decoy to escape.
Played straight, and somewhat deconstructed, in the German Film "Net of Steel - The witness" (Stahlnetz - die Zeugin). The murderer is the eponymous witness, a 12-yr-old girl picked on mercilessly by her family and threatened by others because of their secrets. The deconstruction applies because the girl is not a "mastermind" - rather a desperate (but still aggressive) child - and before The Reveal she is seen just as a random girl who saw too much.
Played double in Takeshi Kitano's Zatoichi, when the leader of the Yakuza is revealed to be the tavern keeper. Then it's revealed that even he was a decoy for the elderly busboy, who was the real power behind it all.
In Cube 2: Hypercube, the supposed superhacker and mastermind Alex Trusk turns out to be... a blind girl?
The entirety of Identity's plot consists of a massive build up to who the murderer will be. Upon reaching the happy ending, it turns out it was the kid all along, and the viewer is treated to a hilarious montage that involves a grumpy looking kid walking away from an explosion and an obese maniac talking in a high voice.
Source Code: Major suspicion is cast on every person in the hero's immediate area (including The Hero himself!), and then in an interesting twist the Villain turns out to be a background character who at most appears for maybe about five seconds each time the protagonist goes back into the program, during which time he gets off the train when it stops- so he can plant phoney evidence of his death and detonate the bomb without killing himself in the process.
Similar to the Source Code example above, Dream House throws suspicion over nearly every character introduced. The actual killer? Someone who drove by the main character's house during one scene and did not become relevant again until The Reveal.
In Scary Movie, the Scream-esque serial killer is actually revealed to be the apparently retarded officer. Then again it is a parody.
Debbie Salt, the seemingly harmless journalist reporting the murders, is the killer in Scream 2. And mother to the previous film's killer.
In White Noise, a random construction worker seen for all of three seconds earlier in the film turns out to be behind the kidnapping repeatedly mentioned in the background and in league with the evil spirits.
Philosopher's Stone. Professor Quirrel, although he wasn't really behind the Man, but working for him. Of course, since the man was growing out of the back of his head, he technically was behind the man...
Prisoner of Azkaban Scabbers, Ron's pet rat. Of course, he's actually Peter Pettigrew in Animagus form.
These became so expected that Rowling ended up adding a page to her website's FAQ where she asked readers not to assume that EVERY named character in the series had a world-exploding secret. In particular, fans had fixated on a random muggle kid who appears at the beginning of book five, with many emailing Rowling and saying they had "figured out" that he was the true key to the entire storyline. In reality, he was just a random muggle kid who was never seen again who Rowling had (accidentally) made a Red Herring by giving him the same surname as Harry's mother.
In the Star Wars Expanded Universe series New Jedi Order, an evil alien race called the Yuuzhan Vong invades. Their leader is Supreme Overlord Shimrra, a God-King who truly looks the part. The last novel in the series reveals that he is actually being force controlled by his jester, Onimi, a being so far below Shimrra that he was considered as little more than a pet.
In the Star Trek: New Frontier novel "Stone and Anvil", the Excalibur crew needs to find the man who created Janos' intelligence to help him extend it. To bad he doesn't exactly know how to do that...the real mastermind is his pet Gribble, a small animal no larger than a rat. Before the Gribble can do anything, though, Janos eats him.
In Accelerando by Charles Stross, everything that happened turns out to have been masterminded by the Macx family's robotic cat.
Occurs in Zilpha Keatley Snyder's The Egypt Game — the murderer is not a suspect and is only mentioned once in passing.
Quentin Makepeace (a foppish playwright in the prime minister's company) turns out to be the mastermind of all the events in The Bartimaeus Trilogy.
In Murder In Pastiche, the killer turns out to be the ship's purser who was a detective fiction fan and thought it would be a waste if there were so many famous detectives on board and they didn't have a murder to solve.
In the first Norby book, Ing is Fussbudget 2 Gidlow.
This pattern is also repeated in other books of the Lincoln Rhyme series. The Coffin Danceris pretending to be a hobo taken into custody as a witness and The Ghostis masquerading as one of his own victims, as a chinese illegal immigrant.
In Isaac Asimov's Lucky Star and the Moons of Jupiter, while there is a human villain, it turns out the real bad guy is a robot dog who served as a Seeing-Eye dog for a scientist. Subverted in that the dog was just the tool of the Big Bads, revealed by doing something he shouldn't be able to do. There's an early brief clue concerning his reaction to a Venusian Frog.note The frogs are telepathic. A cat's feelings were conveyed to the heroes by the frog.
In Skulduggery Pleasant: The Faceless Ones, we find out early on that the elusive Batu is the man behind the Diablerie, but the mystery remains: Who the hell is Batu? It was a mortal Farmer who wanted to bring back the Faceless Ones as a means of getting his own magical powers.
In Bridge of Birds, the true identity of the tyrannical Duke of Ch'in turns out to be the meek, perpetually scared Key Rabbit. Oh, and his greedy peasant wife is a long-lost goddess. It actually makes perfect sense once Master Li explains it and there are many hints dropped throughout the novel, especially for the latter part, but it almost certainly stunned many first-time readers.
In The Dresden Files this is Molly's reaction when she is shown a photograph of the traitor on the White Council in Turn Coat.
...Huh. Who's that?
In Doorways in the Sand, there's a near-literal example: the mastermind is in nearly every scene, disguised as the cat. Also, the being who was influencing Fred to steal the artifact in the first place was the artifact itself.
In Harry Harrison's Star Smashers of the Galaxy Rangers, the race of Big Bads, who were mentioned throughout the book turn out to be tiny turtles with Psychic Powers kept as pets by another race.
In one of the Agaton Sax kids' detective books, someone who appears to be an average-looking member of the crew of crooks turns out to be the criminal mastermind boss himself.
In Hush, Hush, it turns out that the person trying to murder Nora was Jules. Given how he was virtually nonexistent in the story, it was rather...jarring.
Pretty Little Liars does this a few times with the reveal of each A. The first A turned out to be Mona, one of the main character's best friends who pretended to be an A victim herself. The second A was Alison — the real one. It's revealed that all along the girl they thought was Alison was actually Alison's twin sister, Courtney. The current and third A has yet to be revealed.
Inverted in the Robert Cormier novel We All Fall Down. One of the two main POV characters is an eleven year-old boy who calls himself The Avenger after killing a bully with his grandfather's gun and then killing his grandfather to cover it up. It turns out he actually committed the murders a couple of decades ago, and he is actually a seemingly insignificant middle-aged character who appeared briefly earlier in the novel. He's no mastermind, but rather a pitiful, profoundly mentally ill man who regularly retreats into the delusion that he is still a child.
The same idea was used by Kim Newman in Dracula Cha Cha Cha (aka Judgment of Tears). The book has some parallels to the James Bond series and the Bond character shoots the Blofeld character. However, Bond had misread the situation. The real villain was a vampire shapeshifter. He was the cat and the Blofeld character carrying him around was just one of his minions.
Often done by Fred Vargas : in quite a few of her novels, the murderer is a very inconspicuous and/or sympathetic character. Ariane Lagarde, in This Night's Foul Work, Lawrence in Seeking Who He May Devour and Louis Nicolas Emeri in The Ghost Riders of Ordebec are notable examples. The latter gets extra points for being the cop initially tasked with the investigation of the Ordebec murders.
In The Burglar in the Rye by Lawrence Block, Bernie Rhodenbarr has to find out who stole Gulliver Fairborn's letters and murdered Anthea Landau and Karen Kassenmeier so that he doesn't get sent to prison for the crimes. Karen, the second murder victim and absent owner of the hotel room in which Bernie hides from the police, was the thief with some help from the hotel clerk. Erica, Bernie's best friend's overly-controlling new girlfriend, is the murderer.
In The X-Files novel Goblins, the invisible killer turns out to be the dispatch of the local police, whose role in the story up that point has been saying few words over the radio. She is recognized by her Catch Phrase.
In Smallville, Roulette, Oliver is put through a series of life and death games. Whoever designed it has a really sick sense of humor. It is Chloe Sullivan.
Good guy version: In the Get Smart episode "The Mysterious Dr. T", it turned out the genius inventor Dr. T was a kid seen selling newspapers.
Sherlock has already pulled it twice. In "A Study in Pink", the serial killer turns out to be a cabbie, seen earlier when Holmes and Watson chased down his cab because they thought the passenger might be the killer. In "The Great Game", Moriarty is revealed to be Molly's boyfriend Jim, who showed up briefly earlier in the episode. (Though this last was guessable, considering "Jim" is a nickname for "James.")
The second example also incorporated a subversion—for a moment or two, before the real mastermind appeared, the audience is led to believe that Watson is Moriarty.
Many made for TV cop shows have this but it was especially noticeable in Murphy. The killer is the bloke who is in the background of scenes. If most of the suspects are interviewed in a club it's the barman - also expect him to be a long lost relative of victim or chief suspect.
Mr. Yang in Psych is revealed as this through flashbacks when Shawn meets her at the end.
In the Monk episode "Mr. Monk Makes the Playoffs", it is revealed that Monk met Bob Costas after helping him out with a matter of a cat salesman who sold demented cats. In particular, Monk proved that Costas's cat planned to kill him with a squeeze toy.
An episode of Community has the study group trying to discover who among them stole Annie's pen. It turns out it was Troy's pet monkey living in the vents, who we hadn't seen since his only episode one season ago. The study group doesn't find this out until much later in the season, though. At the time, they all decide that the most logical explanation is that a ghost stole Annie's pen.
In an episode of Pushing Daisies the killer was, of all people, a pig. It was an accident, so the characters promptly adopt him as a pet.
One episode of Bones has the killer turn out to be the father of a friend of the victim, who was seen once in the beginning of the episode and had no lines whatsoever.
Quite literally applied in an episode of Married... with Children when the Bundys are arrested for harboring fugitive Steve Rhoades. They all accuse each other of ratting Steve out to the police, but the true mastermind was Buck, the Bundys' family dog.
In "Aquiel," where the crew finds out that a shape-shifting organism is behind the Mystery of the Week. Two people, a Klingon and the eponymous Aquiel, are suspected of being the monster, but it's really Aquiel's dog, which served as a minor comedic subplot during the episode.
In "Future Imperect", Riker awakens sixteen years in the future with apparent amnesia. However, the details of his future life don't add up; when he question his surroundings, the Enterprise bridge reveals itself to be a holodeck, with the evil Romulans pulling Riker's strings. Seems plausible. Yet, even this reality doesn't jibe with what Riker knows to be true. The real mastermind is Riker's "son", who is present in both realities. The boy is actually an orphaned alien let behind on a desolate planet, with only a holodeck to amuse himself. When Riker came upon the cave, the boy was delighted to have a playmate and pieced together a false world from Riker's memories.
On the Angel episode "Harm's Way," Harmony wakes up after a one-night stand to find the guy dead, and though she doesn't quite remember what happened, she eventually realizes that she was set up for the murder. It turns out the real killer was...some random other vampire chick named Tamika working at Wolfram and Hart, whom Harmony had bumped into earlier. Tamika was upset that Harmony was on "the fast track" just from knowing Angel and his friends before they took over the company, and framed her so that she could take her job.
In The Sarah Jane Adventures: Mr. Smith is a supporting character who gives information on aliens that land on Earth. It turns out he's a Xylok (sentient crystal) who created the computer as a host - and the most important thing to a Xylok is their purpose. Mr. Smith's purpose is to destroy the Earth's crust to free his kind - they were trapped there after their ship crashed to Earth (wiping out the dinosaurs). Mr Smith escaped in the eruption of Krakatoa.
Merlin has an unusual inversion in that it's from the POV of the dog. Merlin is Arthur's manservant, and thus while the audience sees everything he does, Arthur has no idea. So when all is revealed, it's probably going to be shocking to a lot of people that the king's clumsy, cowardly manservant has been behind everything (or at least aware it was going to happen).
Particularly noticeable in the Series 4 finale, where Morgana takes over Camelot and Arthur loses his belief that he can be king. Merlin guides him to the Sword in the Stone, telling him that it belongs to the rightful king of Camelot (when in reality Merlin put it there specifically for him), thus restoring his faith. Then, when everyone falls asleep, he sneaks into Camelot and leaves a Voodoo Doll under Morgana's bed to disable her powers. So while it seems to Arthur that he was destined to retake Camelot, Merlin controls the entire situation.
In a third season episode of NCIS: Los Angeles, Sam and Callen gun down a group of arms dealers, including Callen shooting the leader's driver in the cheek when he made a run for it. In a later episode, "The Chameleon", the driver turned out to be the mastermind, and everyone else was just hired help for that one job. The team started calling him the Chameleon after this turned out to be his standard M.O.
The head of the Dirty Cop organization "HR" in Person of Interest turned out to be a guy who was onscreen for all of five minutes: a mayoral candidate's campaign manager.
Subverted in the conclusion of the Carver arc in Nip/Tuck. As Ryan Murphy said, "It's always a horrible cheat when it's someone like a neighbor who you met once, and they're the killer."
In The Prisoner, Number One turns out to be a previously un-hinted-at duplicate of the hero, Number Six. Some of the writers have also hinted that in some way, The Butler was behind everything.
In Criminal Minds the BAU are investigating the death of a child who was believed to have been killed by a captured pedophile, it turns out the pedophile was guilty of killing several children but not the one they found. The real killer was the boy's older brother who was a budding sociopath, and his parents were trying to cover it all up.
In a third season episode of Lost Girl, one of the therapists at a psychiatrist office is believed to be influencing the patients to commit suicide by attempting to enact dangerous childhood dreams. The main suspects are a regression therapist who practices hypnosis and the receptionist, who is a type of Fey that feeds on despair. However, it turns out to be the regression therapist's pet cat, "Dr. Bob", who is actually a shapeshifting rakshasa.
In Broadchurch, a boy is found dead and the main suspects are an old man with a sex crime record, a technologically savvy vicar who likes to volunteer at the school, and a woman who had hidden evidence from the police. In the end the killer is revealed to be Joe Miller, the husband of Detective Sergeant Ellie Miller who had been investigating the case.
In True Detective, the primary culprit of the murders, and the "Green-Eared Spaghetti Monster" ends up being the caretaker on the lawnmower from Episode 3.
Parodied in The Far Side when (what else?) a cow suddenly stands up in court and says, "All right, I confess! I did it! That's right! The cow! Ha ha! And I feel great!"
Played With and Subverted in Luann. In the arc where two of the teachers (acting as chaperones) ended up dancing with each other, and getting recorded by an anonymous student via cell phone and posted on the internet and getting in trouble with the principal, one of the teachers thinks Luann did it, while another felt it was more likely that Tiffany did it. The male teacher's reason was because of this trope, to which the female teacher pointed out that he would also qualify for that exact trope to prove that it shouldn't be used. It turns out Tiffany really did do it, after Luann tricked her into revealing to her deed by claiming credit as being between her and herself, although she ultimately wasn't able to reveal it after Tiffany recorded her changing and then used her old cell phone as a decoy in case Luann did attempt to tell her.
Almost parodied in at least two episodes of The Goon Show- The Spanish Suitcase and The Phantom Head-Shaver, where Greenslade is the villain, in much this style. For which reason it's also Narrator All Along
In the game Art of Murder: FBI Confidential, the killer turned out to be Raches, a character briefly mentioned in a newspaper article and supposed dead. Although this is minorly subverted due to the fact that Raches is- in fact- your boss, Leon Chaser. Actually pretty obvious when you compare the two names.
In Portal 2's co-op campaign, the robots are sent to kill what turns out to be the bird from Chapter 6 of the single-player game.
In this case its played both both metaphorically and literally. In Deadly Premonition the happy go lucky Forrest Kaysen turns out to be the Red Seed Killer the whole time- and his faithful companion Willie? He INTRODUCED Kaysen to the Red Seeds... yeah, chances are if you search his underbelly you'll see a 666 and a Willie + Cthulhu Forever tattoo.
The Dog ending from Silent Hill 2 is a literal example, although it's really a parody. Said dog (named Mira) makes cameos in future joke endings.
After spending the short four hours playing through the 12 other ranked bosses in MadWorld, you find out Rank 1 and a major accomplice in Deathwatch is none other than the man who hilariously gives tutorials for the bloody minigames. The Black Baron gets extra points for being the most challenging and epic fight in the game.
Sam & Max: Beyond the Alley of the Dolls plays this to excellent effect; the true mastermind turns out to be the ventriloquist's dummy Max has been carrying around for half the episode.
In the beginning of the series finale, The Narrator of the series so far shows you a wall of pictures showing characters from the series, and proclaims that "one of the characters you see before you will betray Sam and Max." This sounds like an unnecessarily leading Reveal, until it's shown that "one of the characters you see before you" includes The Narrator himself.
As well as the Season 2 finale What's New, Beelzebub?, where it turns out that the Soda Poppers have taken over Hell itself and have masterminded the events of the season in an attempt to make Hell more efficient (even going so far as to kick out Satan).
Subverted, though, in that Telltale thought they were playing this trope straight, because they thought the Poppers were quite popular little schlubs, when in fact much of the fandom considered them The Scrappy, and thus thought The Reveal that they were the villains behind the entire last season was only too appropriate.
Subverted in MARDEK Chapter 3, as the mastermind is a major villain that everyone suspects, but he's disguised as a "dog", Clavis, an enigmatic but inconspicuous character. The persona was actually made up by the villain in order to talk some sense into Rohoph, who was sprinting towards becoming a Knight Templar hard and fast.
In The Bastard Of Kosigan, the real mastermind behind the whole plot happens to be Alexandra de Velan, your childhood sweetheart, who also happens to appear to die near the end of the second module.
Persona 4 practically runs on this trope, in keeping with its theme of not letting first impressions or outward appearances deceive you. All three of the major players in the kidnappings and murders can be frequently found around Inaba doing absolutely nothing out of the ordinary.
The real kicker is that the true final boss, the one who set the events of the game into motion, turns out to be... the nameless, forgettable gas station attendant whom you met at the very beginning of the game, who turns out to be none other than the goddess Izanami in disguise.
The head of the evil organization, H.A.R.M., in No One Lives Forever turns out to be a recurring background character that shows up drunk in most levels as a Running Gag.
The player is given one hint: he sputters an alarmed "Uh-oh!!" when interacted with on the space station. He reverts to his usual drunken behaviour afterwards. This can also be taken as quite the compliment as most everyone else has been doubting Archer's abilities the Big Bad responds to her appearance with Oh Crap!
In endings of Vampire: The Masquerade – Bloodlines where the Ankaran Sarcophagus is opened, the whole affair is revealed to be a massive practical joke orchestrated by Jack and the cab driver (who may or may not be Caine).
In Heavenly Sword it's revealed that King Bohan's bird is actually The Raven Lord; a demonic warlord from the sword's backstory. The final battle is against a fused version of the two.
In Heavy Rain, the Origami Killer being Scott Shelby is a big surprise even to Lauren, who spent half the game in his company. The Player does especially not suspect Scott since he rescues cute widdle Babies, saves a man from a shoplifter and helps a prostitute against an aggressive customer. Not to mention the player can LISTEN TO HIS THOUGHTS.
In Taz: Wanted, TWEETY is the mastermind behind it all. This is especially mind-numbing when you consider that he's been your tutorial and hint provider for the ENTIRE GAME, including the final level.
In Baten Kaitos: Eternal Wings and the Lost Ocean, it turns out the traitor is the one person everyone suspected least: Kalas, the player character.
Until the reveal from a Drama CD revealing that Saya was brought forth to Relius shortly after her kidnapping and Relius made a cryptic comment that she's going to be a vessel for something, meaning Imperator Saya, for all means, could be a Puppet King manipulated by Relius and Hazama, therefore the mastermind may have been both of them since the very beginning.
In BlazBlue: Chronophantasma, this turns out to be triple subverted. In the end, Saya backstabbed them after their failures, and left them to their fates, claiming that they have played their parts, and seized Phantom for herself. But it was because the mastermind isn't exactly Saya herself, but the Goddess of Death Izanami who was possessing her. And it turns out that she is the aforementioned 'something' that Relius modified Saya as the vessel of. A Goddess of Death is no mere 'dog', my friend.
One that's really only known in Japan is the culprit in the old mystery game The Portopia Serial Murder Case (although some may have heard about its Shout-Out in Haruhi-chan). The culprit is quite literally the one you'd least suspect, because not only is he your assistant, he's also (since the main character is an unseen Heroic Mime) the guy executing the player's commands and speaking for the main character. The revelation was so out of left field that the phrase "Yasu is the culprit" is something of a minor Japanese meme for this sort of trope.
In Wild AR Ms 3, you'll occasionally notice a purple-haired little girl. She might just walk by for a second as you enter a town or dungeon, or show up standing near a plot-important character as he begins conspicuously talking to himself. She is, of course, the Big BadManipulative Bastard.
Played with in the "Killerman" event in Illbleed. Midway through, you're asked to finger a suspect for the role of Killerman (if you're right, you win more money). Besides the proper suspects you've encountered, the choices for who may be the murderous Killerman includes... Killerman, and the player. The latter is explained that playing Illbleeddrove you insane and made you go on a killing spree. (This being Illbleed, this is at least somewhat plausible.) As it so happens, Killerman is the correct answer. Turns out the ghosts of those who've died at the park possessed one of the Killerman suits and have started murdering the employees in order to get their revenge.
In Ghost Trick, it turns out that the course of the entire game was orchestrated by an alternate future version of seemingly-irrelevant-to-the-overall-plot character and literal dog Missile, trying to prevent the death of Lynne and Kamila that would have happened if he had not convinced Sissel to interfere — in the original version of events, The Bad Guy Wins. What makes this particularly memorable is that at this point, everything is wrapped up in a neat little package; what other game waits until the end to justify the tutorial?
Played very straight in Discworld Noir. The serial killer who has been ritually murdering the citizens of Ankh Morpork (including the main character Lewton) is revealed to be the god Anu-Anu. When his worshipers are all gathered in church praying to him, his power grows and he transforms into a large bestial monster... but the rest of the time, he's trapped in the form of a small dog, which Lewton sees outside the Guild of Tomb Evacuators shortly before he is killed.
This might count as a subversion, though, since Anu-Anu himself is manipulated by some members of his cult.
In Pokémon Colosseum the diabolical Evice is none other than the mayor of the town you saved at the very beginning. And he promised he'd help!
In the first Laura Bow game, Lilian turns out to be the Big Bad. You would have easily suspected anybody else but especially Rudy since they all had motive. However; it turns out that the inheritance was after all a Red Herring and the real motive was a psychological disorder on Lillian's behalf, thinking everyone was getting in between her and the Colonel.
In The Last Express, it turns out the thing that killed the main character's best friend, Tyler, was the very MacGuffin he was hiding: a gorgeous golden egg covered in gems. When a certain sequence is entered and a whistle is blown, it turns into a mechanical falcon that comes to life and kills everyone present.
The first case of Ace Attorney Investigations 2 involves the attempted assassination of a visiting president. It ultimately turns out to have been orchestrated by a clown at the local circus.
In the Stylistic Suck "movie" Dangeresque 3: The Criminal Projective, which is an episode of Strong Bad's Cool Game for Attractive People, after a plot involving Dangeresque's nemesis Perducci and Uzi Bazooka, the true identity of actually, impostor of Dangeresque Too, the Big Bad is Craig, a character played by The Cheat, who had been in multiple scenes, unnamed, and previously referred to with the in-game tooltips by "The Cheat" when everyone else was described using their characters' names in the tooltips.
On the Homicide Desk in L.A. Noire, you are tasked with solving a string of murders, all seeming connected to the real-life Black Dahlia case. At the end, you discover the killer...Garret Mason, a bartender you had interviewed as an incidental witness in the first case, and had likely forgotten about by the third.
DS Visual NovelTime Hollow posits the notion, in an optional extended ending, that Sox the cat was the being behind most if not all of the game's events, or at the least that he's a mightier being than he lets on.
The World Ends with You : Okay, on the one hand, something was seriously wrong with Joshua. On the other hand, nobody really was expecting him to be the Composer.
The InfocomText Adventure game Bureaucracy (written by Douglas Adams of The Hitchhiker's Guide to the Galaxy fame) eventually revealed that the bureaucratic troubles the player had to navigate through during the entire game were secretly masterminded by an annoying nerd character who kept appearing at random and nagging the player to buy useless junk (and asking female characters for dates).
In Hotline Miami, who is organizing hitmen in animal masks to murder the Russian mafia? It's the two janitors you see briefly in one of the first few missions in the game.
In Blue Dragon, the mastermind and final boss behind it all turns out to be the friggin' blue frog thingy the bad guy carried around all the time.
In Rayman Origins, it turns out the person behind the all mess is the magician who gave you advices in levels and collected your lums at the end of each one. Many players barely notice his appearance through the game leading to Shocking Swerve. This twist was a holdover back from a time in development when the game still had an actual story, namely that The Magician idolized Mr. Dark, the ever-mysterious Big Bad of the very first game, and the whole plan was an attempt to emulate him.
Appears often in the Professor Layton series. Many seemingly innocuous, or at least well-meaning, characters, including Chelmey in "The Curious Village," Flora in "The Diabolical Box," Doland the butler in "The Last Specter," and Angela in "The Miracle Mask," are revealed to really be villains wearing infinitely clever (and impossibly detailed and well-fitting) costumes.
It is especially prevalent in Professor Layton and the Unwound Future, which sees Dimitri Allen disguised as the bartender at the Thames Arms, and Clive disguised as Future Luke. The latter plays it particularly straight because Clive has been parading around, as Future Luke, with Layton and his friends for most of the game, and had deceived his partner-in-crime, Dimitri, into believing he was building a time machine, when in reality, he was creating an enormous robotic weapon with which he intended to destroy London.
The inverse also occurs in Unwound Future, when Don Paolo disguises himself as Layton as part of a plan Layton devised to foil Dimitri's attempts to trap him at the top of the Towering Pagoda.
In the indie game Pizza Delivery the real mastermind in the house was the doll.
In the When Gravity Fails licensed game Circuit's Edge the mastermind behind what is going on turns out to be the guy running the carpet shop who had no earlier involvement in the plot and you do not even have to meet at all when pursuing leads.
The Adventures of Dr. McNinja story has one such reveal in the story "There Is A Raptor In My Office". It turns out everything was engineered by the Fox News weatherman. Earlier in the story, he was all puffed up to do a story about three hurricanes in the Atlantic forming a Mickey Mouse shape only to be deflated by a lead in story about velociraptor riding banditos. The entire story sprung from his efforts to keep Dr. McNinja's latest adventure under the rug so that everyone will be interested in his story.
In RPG World, after Galgarion disguises himself to infiltrate the heroes, we get an extremely elaborate Red Herring Mole in the form of Eikre. Galgarion's actual disguise? A flower that Eikre had bought and attempted to give to Cherry.
One Electric Wonderland story detailed Trawn's attempts to report on the bombing of the Nettropolis Mall. Lululu helps her find the man she suspected of causing the explosion, but he turns out to be a decoy. Who really led the attack? The cat seen sitting on the suspect's table while Trawn searched his apartment for evidence. Anyone can take on any form in Cyberspace, after all.
Homestuck has Betty Crocker and Her Imperious Condescension. Both of them are little more than background references until it turns out that they're actually the same person and the (likely initial) Big Bad of Act 6.
Everybody figured that Lil' Cal was at minimum extremely creepy. It was a bit of a shock when he's revealed to be Doc Scratch's "father" of sorts. Then it's revealed that Cal himself isn't inherently evil. He's just a Soul Jar, and has most likely been one as long as we knew him. The being he contains? Caliborn, aka Lord English, aka the Man Behind Everything, Including Himself (Don't Think About That One Too Hard).
The Roommates special titled "Mystery" would be a pretty standard Fair Play Whodunnit, if the culprit wouldn't turn out to be (for everybody's surprise including the detective) a freaking Muppet. It was basically background color and didn't seem to have any life of its own (carried around by a puppeteer) until the reveal. It... she also gives a pretty awesome Motive Rant to explain why she did it (basically she was jealous of the Cult Classic status of some other muppets running around the comic).
In Greek Ninja, the one behind the attacks at Ariadnio and the danger unlike any the world had ever faced before, turned out to be none other than a weak and bitter man from Sasha Hunter's past. Really really past life....
The identity of the butcher in There Will Be Brawl turns out to be a duo: Ness and Lucas, who were seen briefly in an early episode. This was so effective that nobody in Wild Mass Guessing correctly guessed it. Word of God near-explicitly denied the possibility beforehand, claiming that Ness or Lucas wouldn't play a large part in the series, since child actors were too hard to work with. While not technically false, since they only appeared in those two scenes and had no speaking parts, this was a highly misleading statement that helped to divert suspicion from the culprit(s).
In episode 86 of Bonus Stage it was revealed the second version of Evil was MALCOLM, a very minor character who only appeared in one episode prior and never showed any signs of being evil.
Occasionally happens in Shadow Unit—due to the nature of the anomaly, the gamma could be anybody, including the sweet little old lady, the shy teenager, a member of the team...
In OH GOD THE RAPTURE IS BURNING, Cockroach Jesus was meant to be a throwaway creature, the warmup to all the silly crazy creatures in the serial novel. However, by about Act III, it is discovered he is the Big Bad of the entire thing, and is the emissary to the universe-destroying Rapture.
Used/Parodied by Linkara in a "previously" that had nothing to do with the comic.
Linkara: You! You're the secret manipulator behind everything! *pulls out a stuffed bear* BEARRRRRRRRRRRRRRRRRRR!
The "DNA Evidence" arc of Homestar Runner. After being Arc Words in a number of otherwise unrelated shorts, we get a story about a vial of green DNA Evidence that keeps changing hands and getting stolen. Turns out that it was from Strong Sad, who doesn't want anyone to find out if he's part elephant.
In Becoming Human, it turns out the killer is Mr. Roe, the mild-mannered teacher, helpful teacher who was the only character to never be a suspect. A second more minor example is the janitor, who spent a lot of time in the background before being believed to be an accomplice, but eventually turned out to be a Red Herring... or was he?
Phelous has some fun with trope while reviewing The Amityville Horror 4. Why? The big villain is a demon possessed lamp. No, really.
Lamp: NO ONE EVER SUSPECTS THE LAAAAMP!
The genocide arc of Gaia Online's storyline started in 2010 with vampire assassin Zhivago taking out a hit on Johnny K. Gambino, then reporting back to someone. Since Zhivago's previous boss was Killed Off for Real in 2007, the forums were abuzz with speculation on who the new boss would be, with guesses ranging from a resurrected Vlad Von Helson to the de-powered demigods to Gambino himself. Finally, an update revealed Zhivago talking to his new boss... Don Luca Kuro, a side character from a half-canceled forum event the year before.
Similarly, the main villain in Gaia's MMO game, zOMG!? Labtech X, a character who hadn't been heard from since his apparent death in 2005. Most of the players didn't know who that was, unless they'd been very thorough in reading the plot events and comics.
Le Visiteur du Futur: When confronted to the Big Bad, who so far only had been shown in the shadow, the Visitor asks him who he might be, successively suggesting a future or past version of himself, a future version of Raph or even a future version of their idiotic henchmen. Turns out they were... a future version of two of Raph's friends who had only appeared briefly in the first episode of the season at this point.
In one Global Guardians PBEM Universe story, the mastermind behind the assault on a bank was the ten-year old boy the bank robbers released as a "good faith" gesture to the police.
Mel Gibson: You want me to replace the villain with a dog? I mean nobody will know what's going on. Homer: They will if you set up that the dog is evil. All you do is have to show him doing this. [lowers eyelids and glances around in shifty-eyed fashion] The people will suspect the dog.
The two-part episode Who Shot Mr. Burns?. The culprit was Maggie.
Funnily enough, there's a "shifty-eyed" moment that lets you know it: in Part 1, Mr. Burns asks the angry mob who's actually brave enough to stop him. Watch that scene and notice the one person who just keeps glaring without looking away.
This twist ending gets a call-back a few seasons down the line, when a Mob gang that has come to punish Homer are all taken down with precise, non-life-threatening shots from an unseen sniper. Who shot Fat Tony? Who do you think?
In "About Last Night...", Kyle's toddler brother Ike was the key player in Obama and McCain's Ocean's Eleven-style heist.
A variation occurs in the Mysterion Trilogy (Coon 2: Coon and Friends, Mysterion Rises, and Coon vs. Coon and Friends) when Kenny as Mysterion tries to find out the origin of his immortality, learning it has something to do with the Cult of C'tulu. When a Jor-El typeman in a glowing ball appears to explain everything completely out of nowhere, it turns out he was actually talking to Bradley Biggle AKA Mintberry Crunch, a character introduced pretty much entirely for these episodes, who learns he really is a super hero who combines the powers of mint and berry. Kenny never really learns the truth about himself and is as confused by the entire encounter as the audience.
In The Powerpuff Girls episode "Cat Man Do", the girls defeat a villain and adopt his Right-Hand Cat — only the cat was the real criminal, using hypnosis to make his "master" do his bidding.
In Ed, Edd n Eddy, one episode has the Eds track down someone who went to great lengths to frame them for various crimes. It ultimately turned out to be Jimmy, who was angry at Eddy for casually giving him a wedgie.
Scooby-Doo! Mystery Incorporated uses this a fair bit - usually, of the named characters, the culprit is the one who seems secondary, is introduced completely outside the course of the mystery, and doesn't seem to have anything to do with it at all.
Appears in an episode of What's New, Scooby-Doo? that took place in Greece involving a series of centaur attacks. At the end of the episode, Velma explains all the evidence that suggested that the criminal was the archaeologist, then unmasks it to reveal... a woman that she doesn't know. The mastermind was the archaeologist's partner, who appeared in the teaser before the gang showed up. The trope is even Lampshaded when Velma complains that this should not count as her being wrong because she'd never seen the woman before and begins to sulk.
The biggest examples from Mystery Inc. are probably the Trickel's Triquids mascot from "Revenge of the Man Crab", who only appeared for 10 seconds, and the Minner brothers from "Battle of the Humongonauts", who didn't appear at all before the unmasking and were only mentioned in radio ads and one scene on a billboard.
And one-upped in "Wrestle Maniacs" where the monster was really an unidentified man, who was really "The Coolsville Comet", who looked different because he wrestled with a different mask on that made his face look completely different!
The three-parter "Brainwashed" of Pinky and the Brain has several false leads behind the mastermind heading the plot to dumb down the world. Turns out it's the cat belonging to the scientist responsible for genetically modifying the eponymous mice.
The climax of the Futurama movie, Into the Wild Green Yonder, involved Fry trying to figure out the identity of the Dark One, who was the only individual whose mind Fry wouldn't be able to read. After he's able to read the mind of seemingly everyone else there, he comes to the conclusion that he himself has to be the Dark One. He isn't. The Dark One is the leech that Leela saved at the beginning of the movie, and which has been attached to her neck more-or-less ever since.
In "That Darn Katz!" Amy finds out the professor who failed her doctoral presentation was an elaborate marionette worked by his cat, who sabotaged her so he could steal her idea to use it to sacrifice Earth to save the cat home planet.
The villain from the Justice League mini-arc taking place in a parody of Silver Age comics was actually the Jimmy Olson Expy that had only appeared a few times before that and had actually created the false reality with his mind.
Simon Trent: What did you find? Batman: Fingerprints on the toy car. And they belong to you, Simon Trent. Simon Trent: That's not possible. Batman: Your prints are on this car. You had the only copy of the show. The Mad Bomber followed the show step by step. Simon Trent: But I'm not the Mad Bomber, Batman. I'm not. I sold my Gray Ghost cars months ago to pay for my... No, it can't be him.
Spoofed in an episode of Invader Zim:Zim is plotting in his lab, and we get several establishing shots of his surroundings, including an inexplicable cooked turkey with flies buzzing around it. A few minutes later is suddenly bursts open to reveal his robotic servant, GIR.
GIR: It was MEEEE! I was the turkey all along! Zim: (Beat) I was wondering what that turkey was doing there.
In the murder mystery episode of Family Guy. James Woods invites the core cast, "Family, friends and neighbours" to his mansion during a storm and people start getting killed off one by one. Turns out its Diane Simmons, Tom Tucker wanted to replace her with a younger sexier co-star which would cost her her job so she started murdering people in order to frame him Another twist, is that Lois is the only one who knew she did it, so she was going to kill Lois. But Stewie from the mansion roof kills her first, saying no-one kills Lois but him. The twist about this is that several seasons back he gave up trying to kill her and turned from the psychotic murdering child, into a giddy cheerful (possibly) homosexual, so it was unexpected to see Stewie acting like his old evil self.
A throwaway scene in the third Robot ChickenStar Wars Special reveals that Jar-Jar engineered the events of both trilogies, as he was a powerful Sith Lord.
Steven Universe has an In-Universe example: Steven and the Gems are watching a kung-fu movie, and the bad guy turns out to be the janitor. Pearl says it was obvious, since he had been in the background of every previous fight and was also on the DVD cover.
An early Hey Arnold! episode has the Twelve Angry Men Plot, as Arnold tries to defend Eugene from the accusation of having pulled the school fire alarm. The evidence for his innocence piles up and eventually Curly, one of the other jurors, confesses. This was pretty much the first time the culprit had any sort of characterization, but sure enough s/he can be seen several times in the background when the crime was committed.