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For some reason, organ music and villainy seem to go hand in hand. Perhaps it just sounds sinister and scary. But, in any case, if a character has organ music for his Leitmotif, it's a sure sign he isn't going to be petting any dogs.
Combine this with Ominous Latin Chanting and/or some For Doom the Bell Tolls, and he's got Big Bad written all over him.
Sometimes this analogy goes so far to show the villain sitting at a big spooky pipe organ, playing ominous tunes, as the heroes walk in on him. This iconic scene was probably inspired by The Phantom of the Opera, whose villain is often similarly shown with his sinister organ. The standard music for this scene is the Toccata and Fugue in D Minor by Johann Sebastian Bach. Bonus points, however, if they are playing their own Leitmotif. Even better if it contains lots of diminished seventh chords.
The exception to the organs = villainy rule is if you're in a church, but the existence of the Corrupt Church and God Is Evil help to blur that distinction. If the organ is accompanying a good religion, then the music is generally more subdued and ethereal rather than overtly "ominous".
See also Circus of Fear, which is another place you'll often hear a creepy organ.
Played straight during the first appearance of Isaak Fernand von Kämpfer in Trinity Blood: when Abel finds him, he plays Sagrada Familia's pipe organ which he equipped with the Silent Noise system that destroys half of Barcelona in a matter of minutes, along the way killing a major character for the first time in the series.
In the tenth Pokémon movie, Darkrai's Leitmotif contains organs and bells, befitting a Dark-type Pokemon that can literally cause nightmares. This could be considered a subversion as Darkrai is actually the hero of this movie.
In the first Pokémon movie (only the original Japanese version since the score was rewritten for the English speaking audiences) Mewtwo's theme is played on the organ. Lots of diminished chords and chromaticism; following the cliches to the letter. The opening leitmotif is D-E-F-C# (Dm -> Cdim7).
The theme for Nakazato's GT-R in Initial D is Toccata and Fugue.
Kiddy Grade: the last third of the series contains two closely-linked tunes, both with ominous pipe organs, that represent the main "antagonist" of the last arc.
In Sailor Moon, Eudial challenges Haruka and Michiru to a showdown at the Marine Cathedral. When they arrive, she's playing the Bach Toccata and Fugue on the organ to help them find her, which turns out to be a recording on a tape.
Slayers Next has a guitar tune used for exposition sequences. When it's not just "everyday" exposition but Lina learning that the Lord of Nightmares, the source of her strongest spell, is not a Mazoku but the primordial chaos itself we get the same tune, but upgraded to this trope.
In the Second Season of Space Battleship Yamato (a.k.a. "Star Blazers"), the theme of the antagonist White Comet Empire is a dark and imposing Pipe Organ track - as if the sound the comet produces while moving (the screeching of many souls crying out in terror) wasn't enough to clue you in.
The Read or Die OVA features an evil reincarnation of Ludwig van Beethoven playing a massive pipe organ on a rocket that will broadcast his lost Death Symphony worldwide, causing everyone who hears it to commit suicide.
The Professor Laytonand The Eternal Diva animated film tops the previous example by having a pipe organ that is also a giant clockwork orchestra, a memory storage and download machine, and a control device for a giant mecha. When the true Big Bad is revealed, he gets the Ominous Pipe Organ as background music.
Rozen Maiden has this as well. "Broken World" fits this trope to a T, plenty of destruction foretold.
Revolutionary Girl Utena uses the organ at certain ominous moments. Or just as elevator music for the Student Council for extra drama.
The TV version of the Demon Sisters' theme from Panty & Stocking with Garterbelt combines this with (of course) stripper music, no doubt to emphasize their Lawful Evil (and infernal) natures. (The version from the show's first OST replaces the organ with synth sounds.)
One of Yoko Tsuno's adventures involves an instrument called the Devil's Organ, whose sound can drive listeners to insanity or death. The Smug Snake uses it to brainwash his uncle and try framing him for his plans. He also kills the organist who built it and discovered his intentions... but his daughter Ingrid escapes from him and reaches for the titular Action Girl and her friends.
The Duke of Owls in Rock-A-Doodle played an organ for his Villain Song.
In The Brave Little Toaster, the phonograph in Elmo St.Peter's junk shop kicks off the song "It's a B-movie" with a pipe organ intro.
In Wreck-It Ralph, a few organ notes of Big BadKing Candy/Turbo's Leitmotif play twice during the film's climax: once before a final showdown with Ralph, and again when he's entranced by the light of a volcanic eruption and drawn towards it to his doom.
Professor Petrie in The Phantom of the Opera (1962) plays Bach's "Toccata and Fugue in D minor" with his pipe organ as his assistant kidnaps Christine and brings her to him.
Parodied at the beginning of Back to the Future Part III. After Doc faints in shock after seeing Marty at the end of Part II (having just sent the Marty from Part I back to 1985), Marty takes him back to Doc's house. When the latter wakes up, he recalls that event as having just been his imagination - until Marty also wakes up and Doc notices him. His response? Screaming his head off, tripping over Marty's hoverboard and backing into an organ's keyboard, which carries on wailing as Marty tries to explain what happened.
He also plays the organ in a somewhat unusual manner, using only the black keys (what today would be the white keys).
Parodied in the Discworld novel Carpe Jugulum, in which a traditionally-minded vampire has an organ ... but it's one of Bloody Stupid Johnson's Clock Punk synthesizers, with a wide variety of screams, wolf-howls and similar Hammer Horror sound effects.
The Unseen University's organ is another parody, especially when it's played by an ape or by a Professor of Post-Mortem Communications who would have wanted Ominous Pipe Organ music but can't get it quite right. That Ridcully won't stop calling it "our mighty organ" and pointing out "it's a Johnson" doesn't help.
Lawrence from Cryptonomicon began playing his local church's organ because the previous performer was kicked for being "too dramatic".
Live Action TV
Doctor Who, "Pyramids of Mars": Ibrahim Namin, a sinister worshiper of Sutekh (ancient Egyptian devil-like figure) plays the organ. He's not the Big Bad, though; he gets killed at the end of Episode 1.
Sutekh summons him by telekinetically playing the organ, and when Sutekh sends his Dragon to take command, Namin apparently activates the time corridor by playing the organ, thus giving the impression that Osiran technology is powered by organ music.
In "The Seeds of Doom" Chase plays an atonal electronic instrument instead, but that's mainly for his plants' benefit.
Toccata and Fugue is played in Boardwalk Empire after Richard Harrow does his first assassination, which is kind of a visual joke in that Harrow looks a lot like the (post-Lon Chaney) Phantom of the Opera. Then, there's sort of a Diegetic Switch and the music is shown to be playing at a silent movie elsewhere.
Supernatural. Spoofed in "Monster Movie". Sam enters an old movie theatre (currently showing Phantom of the Opera) and sees the sinister shadow of someone pounding away on a pipe organ. The man then presses a button and starts playing light music instead, as the 'organ' is just a digital keyboard resting on an old dresser.
The backing track to the diabolical "Upward Infection" by Futret uses a organ.
If the opening of Vangelis Papathanassiou's Nucleogenesis 1 (from the Albedo 0.39 album) hasn't been used for this purpose, it should.
Siena by Turmion Katilot has a example of this at a couple of parts in this song.
Unquestioned maestro of organ composers J. S. Bach both played this trope straight and averted it. The aforementioned Toccata and Fugue BWV 565 (probably an arrangement of a solo violin piece) certainly has a dark and evil feel to it, but Bach's other organ music (especially his chorale preludes) shows the entire array of characters possible in music.
It should also be mentioned that there are variations in the composition itself - most shows and films only play the toccata, the most "evil-sounding" part, when the whole work (toccata + fugue) is actually over eight minutes. While the beginning of the toccata and the end of the fugue do sound quite dark, there are parts in the fugue that actually sound quite whimsicial, and even upbeat at times.
Other Bach organ pieces that fit this trope include the "Great" Fantasia and Fugue in G minor and the "Little" Fugue in G minor. The "Little" Fugue was apparently evil-sounding enough to be used as boss music in Mega Man Legends.
The organ solo at the climax of the third movement of Ralph Vaughan Williams' "Sinfonia antartica".
Vernian Process. These guys love them some Ominous Pipe Organ music. Lead singer Joshua Pfeiffer even lampshaded it at the end of a show, introducing the band then declaring "...and we like Goth music, if you can't tell!" during the one minute, eight second organ outro to their song "Vagues de Vapeur."
"Jane Seymour" from Rick Wakeman's The Six Wives Of Henry VIII.
In The Phantom of the Opera, the Organ is prominently featured on the playfield; players shoot balls up its face to hit a set of musical targets, which makes the Organ open up to reveal a sinkhole underneath.
Prostetic Vogon Jeltz: (to Arthur and Ford) Think very carefully, for you hold your very lives in your hands. Now choose! Either die in the vacuum of space, or...(dramatic chord) tell me how good you thought my poem was.
Bleak Expectations: Pip Bin's first visit to Parliament as MP for Poverty St. Mary and Dreadfulness North is less than encouraging, not helped by the fact that he arrived right on time for Scary Organ Night, as demonstrated by organ music playing in the background.
Elisabeth uses this trope with aplomb in the Act I number "Alle Fragen sind gestellt", which also counts as Mood Whiplash from the tender love song that preceded it and Soundtrack Dissonance (a compelled-sounding choral piece predicting the singers' eventual doom at the heroine's wedding).
And the dead shall rise, and the living will be their slaves. She must be stopped!
One of the bosses in Castle Crashers alternates between fighting you and playing a pipe organ in a church. He cant be hurt while at the organ and as he plays the organ launches bombs in increasingly complex patterns.
While he's a general-purpose user of this, Neclord's appearance in Suikoden II is probably the crown of this trope. Entering a fog-shrouded, ruined castle on the lake's edge, surrounded by a graveyard containing the restless corpses of the castle-town's slaughtered inhabitants... ominous organ-music playing as you fight your way past undead ghouls and minor vampires, finding your way through the crumbling labyrinth of the castle's hallways, finally making your way to the top of the tallest tower, to find Neclord sitting with his back to you, playing the organ - and as he turns to face you, the music stops in mid-chord. Chilling.
In Suikoden I, he plays the popular Wedding March as a funeral dirge (appropriate considering what happens to his brides), and in both games his Leifmotif (Called "We Love Our Master") uses the Organ.
The heroes of Chrono Trigger have to play a few chords on an organ to uncover the hidden passageway in a (monster-run) church. Lavos's theme is a classic example of ominous organ music.
In the sequel/gaiden Radical Dreamers, a pipe organ song plays when you descend to Lynx's hiding place.
Damon Gant's theme in Phoenix Wright: Ace Attorney. He even has an enormous pipe organ in his office...the chief of police's office. It also seems to be modeled after the very one on this page image. Phoenix comments on what a massive waste of taxpayer money this is. According to Gumshoe, Gant goes so far as to use the organ for Cool and Unusual Punishment (he sits misbehaving cops in his office and plays it for several hours; the unfortunate victim is left deaf for a week).
Also, Richard Wellington's cellphone has the quintessential organ tune, Toccata et Fugue, as its ringtone. In the same case, it's used for major effect during the Phoenix Wright's nightmare and when Richard is found as the definitive culprit of the murder in the first case.
Tales of Phantasia has this as background music when you enter the cathedral that leads to Fenrir's cave.
Possibly lampshaded in Tales of the Abyss - The first time you fight Van, he's playing a pipe organ as you walk into his room and he gives his little speech.
Considering how music in general is one of the major themes of TOTA (Prophecies are called 'Scores' or 'the Score', the resident Crystal Dragon Jesus is the personification of sound, various church titles and ranks include Melodist, Maestro, Conductor, Cantor, etc.) and in fact is the key to using much of Auldrant's Applied Phlebotinum, this is perhaps more justified than many of the other examples on this page.
In Lunar: Silver Star Story (the remake), the dungeon music is replaced by Ominous Pipe Organ music between the penultimate and final bosses. It's truly great music to monologue over, as the Magic Emperor demonstrates.
And the original Final Fantasy organ themist has to be Golbez in Final Fantasy IV. His theme even shamelessly steals riffs from "Toccata & Fugue in D-Minor". The Nintendo DSremake has this lampshaded in the sound test by having Edward, who comments on the tracks, referring to the pipe organ as the hallmark of Golbez's theme.
Also, Chaos, the Big Bad of Final Fantasy I, features the Ominous Pipe Organ in his fight music. (Remakes only, the original has no boss music.)
An eerie, if not completely ominous pipe organ can be heard in church interiors in The Matrix Online.
Ys I and II: The 12th floor of Darm Tower features an ominous organ tune called "Devil's Wind" that drains Adol's HP and prevents him from progressing until he smashes one of the pillars on the outer gallery.
It is, however, on the movie soundtrack, titled Samael.
The chapel music in The 7th Guest. A different ominous organ tune is played during the "sacrifice" cutscene in the same room. Also, Dutton's leitmotif. You can even see a skeleton playing the organ if you interact with it.
Bonus points for Latin lyrics in the soundtrack version, "Chapel Pain".
The Disgaea series is rather fond of pipe organs, what with its demonic bent. Disgaea 3's "Fugue of Hell", Mao's leitmotif, is particularly noticeable in this regard.
Perfect Cherry Blossom, the seventh game in the Touhou series, has a very interesting example. Youmu's theme combines an organ with hard rock, and is very fast paced while still being ominous. But the thing is, not only is the character in question The Dragon rather than the Big Bad, but she's not evil in any sense of the word, even by Touhou standards. The third stage in the same game also has Ominous Pipe Organ music, which the creator himself has pointed out sounds like a Disc One Final Dungeon.
On the other hand, vampire Remilia Scarlet, from the same series, plays this straight - in the fighting spinoff Scarlet Weather Rhapsody, her already epic, piano-driven theme song Septette for the Dead Princess gets rearranged into a masterpiece that makes liberal use of organs, violins, piano, drums and electric guitar. Most notable is the kickass organ intro at the beginning, which follows the melody throughout the song and serves to drive the point home that you're fighting against a five hundred year old devil.
In the Heaven's Feel route of Fate/stay night, the BGM for much of the final battle (against the Angra Mainyu possessed Dark Sakura) is "All the Evils of the World", a very ominous remix of the (itself rather spooky) "Little Church on the Hill" which acts as the theme song for Kotomine Kirei. This further plays with the trope: Kotomine is a priest who works at a church, so having the pipe organs is appropriate and doesn't seem to suggest anything further. Turns out Kotomine's evil, and is The Man Behind the Man in two out of three routes.
Mother 3 had an organ play when you were in a shrine. That alone wasn't mysterious, until you take your time and if you listen through the whole song, they do a Dark Reprise of the "There's a Railway in Our Village!?" theme, which the real song plays later in the game after Porky's influence has taken over the town.
A creepy, if not disturbing example exists in Sonic Adventure 2/Battle's Chao Garden. A special organ jingle plays instead of the designated one for your Chao's new alignment if it evolves into a Chaos-type
A reed organ with fake front pipes appears in Assassins Creed III during The Mad Doctor's Castle. When climbed on to ascend through the ceiling it produces a brief cluster of notes (which is unlikely, since organs don't produce sound unless they've been turned on and one or more stops are drawn).
A occasional recurring element in music from the Soul Series. Hellfire, the Final Boss theme of SCII which is played during the battle against Soul Edge's true form, Inferno, may be the starting point of it. SCIII is not to be left behind in this regard, with Forsaken Sanctuary. Sacred Dawn, the Final Boss theme from SCV played during the battle with Elysium, Soul Calibur's own Inferno-equivalent, has an organ which is more in the background. No matter what though, they're all awesome.
The Big Bad of the first Pokemon Ranger game has an unabashedly sinister organ leitmotif. A longer version plays before the Final Boss... whose theme also happens to be an example. Worth noting is that the device he used to control the legendary beasts, including the final boss in question, Entei, actually resembles an electronic organ, and is operated by "playing" it!
In Dungeons of Dredmor, some background music tracks use this. "The Forsaken", which starts with a lone organ but later adds a harp and strings, and in "Death Walks Among You", the organ only comes up 2 minutes in, near the end. The songs are unusually creepy considering the humorous tone of the rest of the game.
The Cracked.com Harry Potter alternate timeline parody has a gag with this, Voldmort is sitting at an organ playing something vaguely sinister until it's revealed he's trying to play Take Me Out to the Ballgame and doing a horrible job.
Parodied in Animaniacs during their take on "The Three Billy Goats Gruff". Every time someone mentioned the [gasp] troll, there would be a sudden cut to Wakko playing ominous music on the organ. (Except when Wakko said it; then Dot covered for him.)
Dot: Well, somebody had to do it.
In an episode of Sponge Bob Square Pants Patrick encounters Spongebob parodying the infamous Phantom of the Opera scene because he believes the reason everyone is shunning him is because Patrick claims he's ugly (when actually it's just that he has rancid breath and Patrick has no nose to smell this). Made more hilarious by the fact that when confronted Spongebob is wearing gag Groucho Marx glasses.
For those of you interested, the episode in question is "Something Smells".
In the Phineasand Ferb episode "Bad Hair Day", Doof plays his evil jingle on the pipe organ.
Gargamel's Ghoullliope in The Smurfs cartoon special "Smurfily Ever After".
In the My Little Pony: Friendship Is Magic episode Castlemaneia the organ in the Princesses' old castle can activate various prank-traps when certain keys are pressed. The Mane Six (sans Pinkie Pie) walk in on the Shadow Pony playing it only to find out it was actually Pinkie Pie.
Played for laughs in the American Dad! episode "Phantom of the Telethon." Roger seeks to sabotage Stan's CIA telethon and dresses up as the Phantom of the Opera to do so. He orders a pipe organ in order to play while laughing maniacally down in the catacombs, but a handheld synthetic piano is sent instead. Roger is furious at first, but after tinkering with it, he happily accepts it. It can also make farts sounds.
When Danger Mouse and Penfold first encounter Wufgang Bach (who has stolen all the world's music in "Play It Again, Wufgang"), he is at a pipe organ playing ''Toccata And Fugue In D Minor" before it dissolves into a daffy rendition of "O Sole Mio."