Breakout Villain

Not every hero has an Arch Enemy... initially. Sometimes, though, a villain will be introduced who ends up being a Breakout Character in his/her own right, and thus a Villain of the Week becomes the villain of the series.

This can be caused by many things, from Executive Meddling, to Writer Revolt, to unbridled fan response to the character, to the writers being blown away by the performance of the actor who shows up to play the role.

Note that this is the accidental creation of an archenemy, not Executive Meddling of "let's make an archenemy for X-character": a Breakout Villain is one who was meant to be a one-shot throw-away that, through fan/author/executive/all-of-the-above response became not only a staple villain, but the villain of the series.

In some cases, the character may never again appear in the original authors' stories, but because of the popularity of the character, subsequent authors or even the fans in general may make their parts bigger and more integral to the mythos in question, via subsequent stories, adaptations, or simply fanon.

Sometimes, these characters become antiheroes in their own right, with all the attendant risks. Most often, though, they retain their wonderful Big Bad status.

Compare Ensemble Darkhorse, Spotlight-Stealing Squad. Contrast with Token Motivational Nemesis, a major nemesis who is killed off as soon as the first story arc ends.

Anime and Manga

 * Yu-Gi-Oh!: Both Seto Kaiba and the card game, Duel Monsters (Magic and Wizards back then) were originally going to appear only once. Fans got interested, and sent a cavalcade of mail. Kaiba appeared again as the villain of an arc, and played a card game at the end. Fans went crazy. Then the Yu-Gi-Oh Duelist Kingdom Story Arc came out, one thing led to another, and before long, Kaiba was arguably the number-three character after Yugi and Jounouchi, and Duel Monsters was the focus of the series. If you tell someone who hasn't read the manga that Kaiba and Duel Monsters were originally one-offs, you may make their brain spontaneously combust.
 * Neon Genesis Evangelion - Kaworu Nagisa: Few villainous characters have appeared for so short an amount of time (approx. 12 minutes on-screen of the 24-minute episode), yet left such an impression on any one series. Since Kaworu's appearance, and death, in episode 24 of Evangelion, the fan response to his character has been so abnormally outstanding that Kaworu has appeared as a main character in nearly every subsequent incarnation/retelling/sidestory/etc. of the series, including the Evangelion manga series, Angelic Days manga, games, and the Rebuild of Evangelion series.
 * To Aru Majutsu no Index had Accelerator, who with his sheer creepiness, snark, creative use of the power to control vectors touching him and hell of an insane cackle was so popular among the fans that Kamachi Kazuma brought him back,.

Comic Books

 * Black Adam: Captain Marvel was such a happy, fun, feel-good-superhero series at first...then Black Adam came along. Originally intended as a one-shot baddy back in the 40's, Black Adam has come back in force several years before the Crisis on Infinite Earths, to become the most powerful villain/antihero of not only Captain Marvel mythos, but also one of the most powerful villains in the whole of the DC Universe. Heck, in recent years, he's proven to be more popular than the hero he was created to oppose.

It is all the more interesting in that Captain Marvel already had a designated "primary villain" in the form of Dr. Sivana, who debuted alongside him in Whiz Comics #2, bedeviling the Big Red Cheese with a whole deck of Villain cards throughout The Golden Age of Comic Books.
 * Most successful Batman villains are Breakout Villains.
 * The Joker: Believe it or not, the villain of villains, the Clown Prince of Crime, the one crazy bad guy who can make Satan pee in his pants just by laughing, was not originally intended to be the Batman villain, let alone the most well-known villain in comic history. According to the other wiki: "He was slated to be killed in his second appearance, but editor Whitney Ellsworth suggested that the character be spared. A hastily drawn panel, demonstrating that the Joker was still alive, was subsequently added to the comic." 60 years later, The Joker outshines Lex Luthor, Magneto, et all for "most recognizable villain in comics," and thanks to a certain recent movie, has also become infamous as one of the most heinously evil individuals in all fiction.
 * Harley Quinn's initial role was to do little more than help smooth out a punchline with a Joker character coming out of a cake, but eventually went on to be a comparable villain in much of the DCAU (and even the comics) to even the Joker.
 * The Riddler was featured in a whopping two stories in his debut year (1948) before being promptly forgotten for nearly twenty years. After being brought back into the comics (just in time for the sixties show), he climbed his way up to the highest tier of the Bat-Rogues almost overnight.
 * Scarecrow was featured in only two stories as well, neither of them memorable in the least. Then came a certain issue of The Brave and the Bold comic book that gave him his fear gas... and the rest is history.
 * For decades, Mr. Freeze was a joke villain from the 60's in the same league as Calendar Man and Killer Moth. Then the BTAS episode "Heart of Ice" aired, and he instantly became an A-list villain and one of the most haunting and tragic characters in Batman's rogue gallery.
 * In the third Two-Face story, Batman persuaded him to turn himself in and submit to any needed psychotherapy and surgery by loading a coin to land on its edge, and he did it and got better. They brought back another version and then had him revert.
 * Superman
 * Lex Luthor started out as a minor if powerful villain, with only two comic appearances in the first year he was created. Superman's original arch-nemesis was intended to be the now largely forgotten Ultrahumanite.
 * Though not a character, Kryptonite was first introduced in the radio series. This Achilles Heel became a defining element of the Superman mythos. (Something called "K-Metal", which amounted to the same thing as Kryptonite, figured in a comic book script well before the radio show, but the script was never published because Lois Lane found out Superman's identity.)
 * If you were to watch any modern incarnation of the Teenage Mutant Ninja Turtles, you would think arch-ninja The Shredder is the end-all-be-all of Turtles baddies. Originally, though? He died in the very first issue of the original comic, and was later brought back for a handful of issues--as a clone--only to be killed off again soon after, never to return.
 * Spider-Man's three greatest enemies (Venom, Doctor Octopus and The Green Goblin) were all designed to be throwaway characters, had radically different origin stories originally: Green Goblin was going to be a banker obsessed with physical money ("green goblin" is a colloquialism for greed), Doctor Octopus was going to ACTUALLY be an octopus-human hybrid who failed in the same way as Curt Connors did, and Venom was originally going to be Ann Brock (Eddie's wife) whose husband is killed and who has a miscarriage due to Spider-Man fighting Cardiac - and then she finds the symbiote. On top of THAT they're also villains of a character who himself was created by this very trope during the final issue of Amazing Fantasy #15.
 * The Iron Major became a popular recurring villain for Sgt. Rock, despite dying in his first appearance.
 * Doctor Doom is this to the Fantastic Four, appearing in their fifth issue, he took over their second annual by giving Death By Origin Story background for him and his parents, and has since then had his own book, own team-up series, and antagonized most of the Marvel verse by power hoarding Mc Guffins and being a Chessmaster Magnificent Bastard with Power Armor.
 * Lampshaded in Doom's third appearence. Stan Lee and Jack Kirby spend some time discussing how good of a villain Doom wound up unexpectedly being and lament killing him off so fast. Doom promptly storms in, very much alive, and berates them for doing the same.
 * The Angel gang in Judge Dredd - they were introduced as villains of the arc, and one by one were killed by Dredd as the "Judge Child" saga progressed. However, fan response was so positive that Mean was brought Back From the Dead, in one of the exceedingly few occasions that Tharg's rule against resurrections has been ignored. Mean has since become one of the iconic characters of the series.
 * In the Disney Ducks Comic Universe, Flintheart Glomgold started out as The Rival to Scrooge for title of Richest Duck in the World. Flintheart only appeared in three stories by his creator Carl Barks, but by his third appearance, he had ascended to Scrooge's Evil Counterpart and was one of the few villains to demonstrate murderous intent against Scrooge and his nephews. The Second Richest Duck in the World was mostly forgotten for the next twenty years, until Don Rosa reintroduced him in Son of the Sun. Comics, the cartoon series Ducktales, and video games have since portrayed Flintheart as a step above Scrooge's usual villains to the point of being his Arch Enemy.
 * Another breakout villain for Scrooge would be John D. Rockerduck. He was originally a one-shot character created by Carl Barks, but for some reason Italian duck artists made him a recurring character decades later.

Film

 * Star Wars - Boba Fett: Boba Fett's presence in the movies was... minimal, at best. But oooooh, has he become a staple of the Star Wars Expanded Universe. Much contention has been made over his survival after being ingested by the Sarlacc (Lucas says he died; Dark Horse comics along with most fans say he survived), but his popularity cannot be debated. Boba Fett is, to most fans, as integral to the plot as any other characters - in some respects, much more important and likable to the series as a whole.
 * Lucas' opinion has recently shifted to "Sure Why Not?," and he actually considered adding in a scene of him surviving in the 2006 DVD of Return of the Jedi. Tellingly, Boba has a bigger role as a little boy in Attack of the Clones than he did as an adult in the original trilogy.
 * Agent Smith from The Matrix was originally supposed to be a Starter Villain, but due to his popularity with fans he was brought back and incorporated in the storyline of the next two films as the main antagonist.
 * Pinhead of the Hellraiser series was originally just one of the group of monsters in the original film. He was even  But Doug Bradley's portrayal of him made him very popular with the fans, and Pinhead today is the de facto villain of the series, and pretty much its mascot.
 * Jason Voorhees in the original Friday the 13 th was . Then someone had an idea to bring him back in the sequel and things just escalated from there.
 * Khan from Star Trek started out as just another Villain of the Week for Kirk to defeat. He got to return in The Wrath of Khan as one of the series' most notable villains.
 * Though the first three John Carter of Mars novels form a loose trilogy, they don't really have a single Big Bad- the closest thing would be the Holy Therns, but they don't show up until the second book, and their leader Matai Shang doesn't put in a personal appearance until the third. For the film adaptation, both the Therns in general and Matai Shang in particular are Arc Welded into the first novel's basic plot, with the intention of making him the unquestionable Big Bad of the potential franchise.

Literature

 * Professor James Moriarty, created by Sir Arthur Conan Doyle to be a one-time opponent of Sherlock Holmes, and to bring about Holmes' demise. In fact, Moriarty was only given more than a passing mention three times in Doyle's work - the story where he appeared, and apparently killed Holmes; and the following story, which brought Holmes Back From the Dead, and in this it's only Moriarty's men; a third story, written much later but set earlier, uses him as a brief Diabolus Ex Machina. Every author, director, fan, etc. afterwards, though, has made Moriarty the villain of Sherlock Holmes, lifting him to the point of mythical status among literary characters; to the modern viewer, it's inconceivable to have an original Holmes movie or television series with original Holmes mysteries without having Moriarty as the central, most important villain.
 * Another "villain" to become central to the Holmes Universe (i.e. original canon and adaptations), despite her one appearance, is Irene Adler, who is the only woman to ever outwit Holmes. In Doyle's stories, he does make a few fleeting mentions of her as the only person whom Holmes never beat - though hardly as many as one might be led to expect by adaptations
 * Fanon has retconned both Moriarty and Irene into the Holmes mythos. There is now a timeline of cases where Holmes clashed with Moriarty's organization, and it's a popular theme in homages and pastiches that Sherlock and Irene had a tryst during Holmes's absence after Reichenbach.
 * Colonel Sebastian Moran, Moriarty's right-hand man. The story that brought about Holmes's resurrection established that he was there when Holmes killed Moriarty, even spontaneously attempting to finish the job, then proceeds to become a Breakout Villain himself. One of the few characters that gets mentioned in several stories, despite only appearing in one, to the point where he's sometimes Watson's full blown Evil Counterpart.
 * King Arthur - Mordred: In the early mentions of King Arthur in Welsh mythology, Arthur was slain by Medraut, later to be known as Mordred. However, Medraut's importance in the mythos as a whole was almost non-existent, save for that he killed King Arthur. Other villains had come and gone, and it seemed that Mordred was intended to just be another, though the only one who finally got lucky (although Arthur slew him in the same action, so his luck is debatable). Ask anyone in modern times, however, who is the villain of the story of King Arthur, and the answer you will get is "Mordred" almost all the time (though Morgan Le Fay is another name that also comes up quite frequently, and is, coincidentally, another example of this trope). Mordred has become so integrated into the mythos of Arthur that it is unheard of to not include him in any story involving Camelot.
 * Modern depictions of Mordred usually bump him up to being King Arthur's son with Morgan, which has a number of neat effects. First of all, it ups his status from being a random evil knight into Luke, You Are My Father. Second, it gives him an actual motivation - he wants to be recognized as the rightful heir but Arthur refuses. Third, it makes Arthur the architect of his own demise, directly. Fourth, it ties him in with Morgan Le Fay, the other popular Moriarty of the series, so everything's wrapped up in a neat little package.
 * This is the The Theme Park Version by way of the One Steve Limit. Originally, Mordred's mother was Morgan's sister Morgause, which ends up giving him an entire supporting cast in the form of his (half-)brothers at court - Gawaine, Gareth, Gaheris, and Agravaine. In Malory, at least, they're a bit of a Five-Man Band. The earliest mention of Mordred is a reference to "The Battle of Camlann" where "Arthur and Medraut died". From the context (or lack of same), it's not even clear that they were on opposite sides!
 * The Welsh Triads include Mordred in a list of heroes. The first unambiguous mention of Villain!Mordred is in Geoffrey of Monmouth's Historia Regum Britanniae (1100s). From there, Mordred got steadily more villainous: in Geoffrey he only speaks twice, in the Alliterative Morte Arthure (early 1300s) he's an angsty Worthy Opponent, in the Stanzaic Morte (late 1300s) he's distinctly worse, and by Malory's Morte Darthur (1470s) he's all the way into For the Evulz. As Malory's is the only version most non-medievalists have read, that's the characterisation that held.
 * In the end, calling Mordred a "breakout villain" is strange, to say the least. You go back far enough, and he isn't even a villain, but ever since Geoffrey brought him in his function has been constant: he kills Arthur. And, interestingly, that's all he does in most versions. He spends the entirety of Malory hanging around the background, getting constantly mentioned but never doing anything. A byproduct of the fact that there are no "tales of Sir Mordred" since all he ever did was stab his uncle and/or father in the back and try to force Guinevere into marriage.
 * Post Malory, however, there are some works that try to make Mordred into a full on Big Bad for the whole of King Arthur's story.
 * Speaking of which, why has nobody mentioned Morgan as a breakout villain? She goes from healer who preserves Arthur's immortality, to minorly evil witch, to full blown Big Bad in a great many modern takes on King Arthur.
 * The Lord of the Rings - Sauron originated as a relatively minor villain from the earliest version of the legend of Beren and Luthien, and the proto-Sauron was a giant cat, of all things. The character subsequently morphed into the Evil Sorcerer Thu, and from there into the demonic being known from The Lord of the Rings. In the process, he got promoted from one-shot villain to the God of Evil's Dragon to the Dragon Ascendant and Big Bad of the most well-known part of the mythology and the second most significant villain in the Middle-earth Verse.
 * The Wonderful Wizard of Oz - The Wicked Witch of the West, thanks to the popularity of the classic film, has become the most recognizable of Oz's villains and the Big Bad of most adaptations of the Oz series (i.e. the 1980s cartoon). In the original novels she only appeared in one chapter in the middle of the first book, during which she was Killed Off for Real; the closest thing the Oz books have to a Big Bad is actually the Nome King, who appeared in several books to cause trouble for the land of Oz.
 * Alice in Wonderland - The Queen of Hearts only appeared in the last third of the first Alice book and wasn't really as much a villain as she was a tempermental yet comic battleaxe, whose executions were never really carried out. However, Alice spinoffs like American McGee's Alice, The Looking Glass Wars and Tim Burton's new movie have made her the main villain, transforming her into an evil dictator who rules Wonderland with an iron fist and Alice's greatest nemesis.
 * Likewise, The Jabberwock, who only appeared in a poem in Through the Looking Glass where he was quickly killed, has become a significant villain in things like the aforementioned American McGee's Alice and Burton film, as well as a television adaptation in which it stalks Alice throughout.
 * Guy of Gisbourne originally appeared only once in the Robin Hood legend as a bounty hunter who gave Robin an extremely tough fight but was ultimately defeated and killed. He haas overtime been elevated to The Dragon or even Big Bad status in retellings.
 * Conan the Barbarian - Thoth-Amon makes only a passing appearance in a few stories, but both comic adaptations make him Conan's Arch Enemy.

Live Action TV

 * In Law and Order: Criminal Intent we have Nicole Wallace, AKA That Evil Aussie Chick. Now, this being a crime show, she doesn't get that many appearances, but if you can outwit Goren...
 * Doctor Who - The Daleks: Despite challenging the TARDIS for the title of the most iconic element of Doctor Who, they were created in defiance of co-creator Sydney Newman's insistence on writing a non-traditional Science Fiction serious which would avoid Bug-Eyed Monsters. This explains why they died at the end of their first story with no hint given that they might possibly return. Now these motorised pepper-pots have had more than twenty appearances and posed a threat to the Doctor exceeded only by other Time Lords and similarly Sufficiently Advanced Aliens.
 * A lesser but still relevant example: The Autons. They appeared twice, in 1970 and 1971, but are still remembered as one of the Doctor's iconic villains. When the series was revived in 2005 Russell T. Davies and co. were deliberating what classic Doctor Who-monster would be used in the first new episode to relaunch the series, the Autons were given that honor.
 * Lost
 * Benjamin Linus, or rather actor Michael Emerson, was originally scheduled for a three episode stint in Season 2. His performance won the producers' everlasting affection and it was expanded to the rest of the season, and then into a regular in Season 3. If this isn't reason enough to include him, in Season 4 one of his fake aliases happens to be Moriarty.
 * Dean Moriarty, though, making this an On the Road reference, as well as a nod to Sherlock Holmes. (The character from On The Road was named as a reference to the Holmes villain, it still works as a reference to both.)
 * Sigfried from Get Smart was originally meant to be a one-time villain, but then popped up again a few times, and is now considered the main villain of the series, even appearing (well, In Name Only) in the 2008 feature film adaptation.
 * Cavil on Battlestar Galactica Reimagined. In his original appearance, he actually seemed to be one of the nicer Cylons. Turns out he was lying about not supporting the genocide and was its main instigator. Then it turns out that
 * Scorpius from Farscape was supposed to be a one-shot first-season villain. The performance was so effective, however, that he returned, quickly usurped the then-Big Bad, and became the biggest Chessmaster this side of Xanatos.
 * Buffy the Vampire Slayer had Spike. Originally meant to be a one-season villain, and a Disc One Final Boss at that, he quickly went on to be one of the show's most popular characters, converting to full-fledged Anti-Hero by the fifth season, and continuing into Angel after the series ended.
 * Also, the First Evil was originally set to be the Bigger Bad--totally evil, but so vast that it wouldn't really show up very much. It eventually returned as the Big Bad of the final season, however, mainly due to its ability to appear as all the other dead (and undead) villains from seasons past.
 * Star Trek: Deep Space Nine - Although Gul Dukat appeared in the pilot episode, he was never intended to be a recurring character...but Marc Alaimo just played him so well.
 * Knight Rider - K.A.R.R. was originally a one-episode villain. He was introduced as K.I.T.T.'s Evil Counterpart and ultimately destroyed at the end of the episode. He was brought back in a second episode, "K.I.T.T. vs. K.A.R.R.", due to his popularity. Despite only appearing in two episodes, he's widely remembered as the heroes' Arch Enemy and plays a prominent role in both the video game and the recent reboot of the series.
 * Murdoc the Master of Disguise assassin on MacGyver. Originally a one-episode villain, his use of creative schemes and deathtraps made him a good foil for master-of-improvisation MacGyver himself, so they kept bringing him back about once a season (due to his Never Found the Body and Staying Alive tendencies), and he's now remembered as MacGyver's Arch Enemy.
 * Sylar on Heroes was originally planned to be the series' Starter Villain, who would be Killed Off for Real at the end of the first season. However, due to the character's popularity with fans, he was made into a main character and "The Face of Evil" for the series, to the point that pretty much every following Big Bad ends up getting Hijacked By Sylar in their season's finale.
 * In Sliders, the Kromaggs (an Always Chaotic Evil Alternate Universe race) eventually become this. Unfortunately it also marks the point where they become the Malignant Plot Tumor, since the show's original Walking the Earth appeal had to be downtoned to make place for more action scenes.
 * Barabas, the Demon of Fear, was a Monster of the Week villain who appeared in the 13th episode of Charmed. He proved popular enough that the writers ended up bringing him back several times (about once every other season). He never became a seasonal Big Bad, but is probably the show's most frequently-occuring nemesis right behind the actual Big Bads.
 * Smallville: Lionel Luthor, Lex's Corrupt Corporate Executive Abusive Dad was originally meant to appear in only a few episodes of Season 1 as a way of making Lex's Freudian Excuse seem more poignant. John Glover's performance was excellent, however, and the fandom embraced the Magnificent You-Know-What as a Love to Hate character of the first degree. Lionel was written into Season 2 as a major antagonist and Recurring Character, and became the Big Bad of Season 3. In the process he gained new dimensions to his character and his own Freudian Excuse becoming an Even Evil Has Standards Archnemesis Dad who was himself the product of Abusive Parents. He was later possessed by Jor-El and made a Heel Face Turn, becoming a dark Mentor figure to Clark. Killed Off for Real in Season 7 by Lex, Glover and Lionel returned to the show in Season 10 as Earth-2 Lionel, an Eviler Twin of our Lionel, who was The Heavy for most of the last part of the show. In some ways Lionel, and not as was originally intended, Lex, became Smallville's defining villain.
 * Emilia Fox as Morgause from Merlin was only supposed to be around for a couple of episodes, but ended up being so integral to the episodes she featured in that the writers kept her around for longer.

Video Games

 * Super Mario Bros. - Bowser: Before Super Mario Bros., the portly plumber tangled with a lot of nasty foes. Donkey Kong, Foreman Spike, and random unorganized critters (though some did look similar to Koopas). But once Super Mario Bros hit the scene, it was Mario's defining moment, and from that day forth, the Koopa troop and its fearless leader would be his most prominent nemesis. This seems even more dramatic in America, where Bowser was in fact absent for a game before making a triumphant reappearance in Super Mario Bros 3. In this case it was the unforeseen popularity of the game that caused Bowser to become a Breakout Villain.
 * In the original PS version of Resident Evil, Albert Wesker was just a standard horror movie stock character (the obligatory traitor who gets eaten by the monster in the end, basically Paul Rieser's character from Aliens). However, following his return in Resident Evil Code Veronica, he managed to pretty quickly be built up to be the Big Bad of the entire series over the course of the following decade up until his last appearance in Resident Evil 5.
 * While Revolver Ocelot manages to survive the events of the original Metal Gear Solid, there's really nothing to suggest that he is anything more than a mole planted into Liquid Snake's rebellion by the U.S. President. However, subsequent Metal Gear games depicted Ocelot as the ultimate chessmaster who shifts allegiances from one faction to another, while keeping his true motives to himself.
 * Warcraft - Sargeras started out as little more than a footnote in the lore, as a Sealed Evil in a Can demon lord whose powers Gul'dan tried to harness. The revelations of his origins as a fallen Titan and creator of the Burning Legion elevated him to Bigger Bad of the entire franchise.
 * Wilhelm "Deathshead" Strauss/Strasse of the SS Paranormal Division gets this in the Return to Castle Wolfenstein - Wolf 2009 series, mainly due to his status as being the sole surviving Nazi of any prominance in "Return" besides Himmler.
 * A remarkably well done example is Bishop Ladja of Dragon Quest V. In the original SNES game, while he did have some presence in the plot, he was ultimately a minor villain who showed only a mild evil and . The DS remake propells him into this, giving him a unique appearence, replacing King Korol with him as The Dragon, giving him much more screentime, and most of all, turning him from a run of the mill villain to arguably the biggest Complete Monster in the entire series.
 * SHODAN was so much of a standout villian in the first System Shock, that she was brought back for the second, where she became one of the most legendary villains in gaming history.

Webcomics

 * In Order of the Stick, Nale was the only member of the Linear Guild originally slated to escape from the first battle with the heroes. However, fans really liked Thog, so the Giant decided to spare him and, while he was at it, Sabine as well, developing her and Nale's relationship into a case of Unholy Matrimony.

Western Animation

 * Ixis Naugus was on his way to becoming this on Sonic the Hedgehog (SatAM) when Sonic and friends defeated Robotnik, but Cancellation screwed him over. The Archie comics took note of this however and made him a recurring villain, even if not enough to rival Eggman as Sonic's true arch nemesis.
 * Kim Possible's Shego was originally "just a henchman" to Dr. Drakken, but later developed into a competent but unambitious villain who entertained herself (and the audience) with her incessant verbal jabs at Drakken and Kim. Drakken's own standing has curiously enough has also benefited from her popularity: even though he gets out-shined by his own assistant on the popularity polls it was thanks to this dynamic that he became the second most important villain in the series.
 * In the original Mirage Comics version of the Teenage Mutant Ninja Turtles, the Shredder was actually a fairly lackluster Starter Villain who managed to get himself Killed Off for Real at the end of the very first issue. In later issues a colony of sentient worms would take up the mantle of The Shredder (it's a long story), but even they only appeared in a few issues and played a rather minor role in the comics plotline. However, the 1980's cartoon adaptation made him the Big Bad, and he's been the Turtle's Arch Enemy in every future adaptation of the series ever since.
 * On Gargoyles the Archmage was originally only supposed to be a Villain Of The Week, but creator Greg Weisman liked David Warner's voice acting so much he decided to bring him back, making him the villain of the three-part "Avalon" arc through a Stable Time Loop and a couple Artifacts of Doom.
 * Mad Stan from Batman Beyond was originally a one-shot joke villain thrown in to make Terry miss his date with Dana. The fans loved him, and he eventually became a regular member of the Rogues Gallery.
 * Negaduck from Darkwing Duck. After the Negaduck I episode, Tad Stones (the Show Runner) said he liked Negaduck and wanted him brought back for more episodes; this resulted in Negaduck II, who the fandom embraced as perhaps not just the most popular villain but the most popular character on the show, period. When the revival comic book came around, the writer has said that he intended to have a F.O.W.L. story for the second arc and a Negaduck story for the third arc, but sheer fan demand made him swap the order.
 * Sleeping Beauty gave us Maleficent, who has since become the de facto villain to use in Disney crossovers, most notably in Kingdom Hearts.
 * In The Powerpuff Girls, The Rowdyruff Boys were originally one-shot evil spear counterparts of the titular heroines that got Killed Off for Real at the end of the episode. Fan popularity ensured that they were brought back several times.