Beware of any character whose name is simply "The Master." They're often in charge of things (duh) but most often these things include a reclusive mansion in the middle of nowhere, or a castle, or a laboratory, or all three! If they don't rule in the periphery of civilization like an old-school noble, they may rule right under our noses in civilized society. Whatever they're up to, expect them to have a big mustache, a great dining hall, and any number of Evil Plans.
Note that characters who have a name to go with "Master" are exempted from this—for example, Master So-and-So who teaches martial arts. Often a student will simply refer to their teacher as "Master," but that's also an exemption.
See also Names to Run Away From Really Fast, Spell My Name with a "The", Just the First Citizen.
Authority Equals Asskicking is usually in effect.
Not to be confused with the Paul Thomas Andersonfilm, or with the TV show Master Ninja (also known simply as The Master)
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Anime and Manga
Code Geass: Lelouch has a theme called "THE MASTER" for his most ominous, overlordly, badass scenes.
Maison Ikkoku: The bartender at the ChaChaMaru is known as "Master." Suppose this may double as Everyone Calls Him Barkeep, but he DOES fit with the big mustache and the great dining hall. As for evil plans, well, he has a crush on his boozy redhead slacker alcoholic waitress and eventually marries her, so he's got that going for him. "Master" is actually what Japanese people call bartenders in general; you can see it in a few other series, like Kimagure Orange Road.
Mad Max: Beyond Thunderdome: A character called Master was one half of MasterBlaster in the film. He was played by Angelo Rossitto, co-founder of the Little People Society of America and star of Freaks.
Barry Gordy's The Last Dragon: Sho'Nuff, The Shogun of Harlem insisted everyone call him "The Master".
In Knocked Up, Martin can only get out of the dirty man challenge by explicitly referring to Jason as The Master.
The Master and Margarita: One of the eponymous characters from M. Bulgakov's novel — though this Master is not a villain, but one of the most good and kind-hearted characters in the book. He was a writer, but after his book was banned, he went out of his mind, and started to call himself "the Master" (an important note: in Russian "master" means not "lord", but something like "maestro"). He was actually given the name by his lover (that would be Margarita) who was devoted to him and his novel. His real name is never revealed, but it's implied that his skill is so great that Master is the more fitting name anyway.
Despite not being a villain, he's still pretty scary in his own way, when you consider that the devil himself comes to Earth just to find him, and he seems to be channeling the consciousness of a biblical figure who's been dead for 2,000 years...
In The Master of the World by Jules Verne, the titular character is the inventor/pilot of the speedboat/submarine/automobile/aircraft called "The Terror" (it was 1904, folks).
The villain from Garth Nix's story "Hope Chest" is called The Master. He's a Hitler-like character in an alternate America.
A "stale beer with a martini olive" Spy Fiction series by William Garner featured a British intelligence chief who was referred to and occasionally addressed only as the Master. The main character had been one of his agents before the series began, and sometimes wound up reluctantly working for him again.
The Strain has an ancient evil vampire simply called The Master.
That's revealed to be a pseudonym, and his true name is Sariel/Ozaryel, and implicitly he's the Angel of Death.
On the rare occasions anyone's asked what he's the master of, his response has been that he's "the master of all matter" or simply "The Master of All." By the same token, the Doctor is "a doctor of many things" or "The Doctor of Everything" plus a couple of less-used versions referring to time-travel.
Doctor Who also had "The Master of the Land of Fiction" from The Mind Robber, who was usually called the Master for short. He wasn't a villain, though. However, he was controlled by a computer called the MASTER Brain.
On at least two occasions in the Second Doctor's run, the Doctor is told that "The Master" wants to see him (on one occasion it's the Master of the Land of Fiction, and on the other it's Professor Maxtible). In each case he reacts with alarm. Since the Master proper hadn't been invented then, his misgivings can only be down to his knowledge of this trope (in-universe, in the character's debut story, "Terror of the Autons", a Time Lord informs that the Doctor that the Master has taken to referring to himself by that title; though the Doctor knew the character before this, he is apparently unaware of the change in his moniker). After the Master proper had already been established, the Fifth Doctor, while playing cricket, was informed he played as well as "the Master", and got progressively more nervous until the other man clarified that he was talking about "the other Doctor — W. G. Grace".
He's also a very interesting foil of the Doctor himself.
It's been suggested that the Master's name comes from his degree at the Time Lord Academy. Bear in mind that a master's degree is just one step below a doctorate—this might explain the enmity between the Doctor and the Master!
Also in "A Good Man Goes to War" its hinted that the word 'doctor' which means man of knowledge or healer comes from The Doctor himself. So it would be fitting for the word 'Master' which means controller and man of knowledge to come from him as well.
Going by this name so amused The Master that even when he went incognito he often chose a paper-thin-disguise alias based on its meaning (Mister Magister, Professor Thascales, Col. Masters, etc.).
Occasionally, fanfics will make both Masters the same guy, with the explanation that the Doctor Who villain gave vampirism a shot in his pursuit of immortality. Sadly, there appears to be no team ups (or fights) between the two because they would be too confusing.
The Master (formerly Richard Grey) from Fallout 1.
Paper Mario: The Bonus Boss and most powerful enemy in the original game is known simply as The Master. He's the guy in charge at a martial arts dojo, so its clearly a translation of "Sensei" or something of that nature.
In Mega Man ZX Advent "Master" is given as the title to the members of the Sage Trinity. two out of the three are evil.
Megaman Legends 2 has "The Master" The last human being with everyone else in the game being robots or clones or robot clones.
In Assassin's Creed I, the leader of the assassins is named Al Mualim, literally 'The Master'. Turns out at the end of the game that he was just using you to give him undisputed control of the Piece of Eden, an ancient artifact capable of brainwashing the world.
ActRaiser subverts convention. You are the Master and you're not at all evil.
That is, in the Western version. In the Japanese version, the Master is known as God.
Street Fighter has a half example. In Japan the villain is named Vega. However, in america, he got a more famous name: Master Bison.
And from another Capcom game we got Grandmaster Meioh, commonly simply referred to as The Grandmaster. Of note is that "Meioh" isn't his name but is simply another title meaning "Dark King" or "Lord of Darkness".
Fansadox #37 has the titular psycho tattooed on his back the word 'Master' in Japanese (or so he says), and he likes (read: forces girls he rapes) to be called this. This becomes a plot point when the girls escape, they find the sheriff and demand the supposed rapist-slash-sadist show his back. Turns out he wasn't the psycho, but the sheriff himself. Prime example of Bondage Is Bad.