Plot Tumor

A single plot element that was once a minor part of The Verse swells in importance as the series progresses, growing more in focus and elaboration to the point that it becomes the focus of major arcs and plot development. As a result, the Plot Tumor's tentacles get wrapped around other elements of the work, either via retcons that connect the Plot Tumor to things it wasn't originally conceived for or just by crowding out other elements in the story.

Typically this occurs when the creative reins pass on from one writer to the next, as writers forget the original quirks of the element or their creative juices enable them to actualize the untapped story potential of taking a small but notable aspect and expanding on it. However, it's most visible in Derivative Works, where a single element that was important in the source material's success becomes the major focus of the adaptation, especially if late-to-the-party fans or non-fans of the original don't realize the Plot Tumor was once a small part of the original storyline when the work was first being published and it can seem almost unnatural for it not to be part of the status quo of a derivative work.

Keep in mind, however, that Tropes Are Not Bad and fandoms expound on minor details just as much as canonical writers; sometimes with the latter ending up into the former.

Compare: Adaptation Decay, Flanderization, Romantic Plot Tumor, Never Live It Down, and Motive Decay. A Malignant Plot Tumor is the single-plot counterpart, where a minor plot at the beginning crowds out the other plots at the climax. Contrast Adaptation Induced Plothole.

Anime and Manga

 * Duel Monsters in the original Yu-Gi-Oh manga was just supposed to be a one-shot deal, but eventually became more and more important to the plot. The same thing happened to Kaiba, who went from Monster of the Week to Big Bad to Anti-Hero and finally to The Rival.
 * The mystical aspects of the game has also become this; originally just a bunch of dark magic from Ancient Egypt that the game's creator was tricked into bringing back through the game, it eventually evolved into an entire series of Alternate Dimensions full of monsters, and eventually into a power that's Older Than They Think and is part of the Earth itself.
 * Ki Attacks and powering up in Dragonball Z. At the beginning of the original Dragonball, there were no Ki Attacks, and the first of them, the Kamehameha, didn't appear until the middle of the first arc. Even then it sort of the trump card, and wasn't played terribly often. As the series progressed though, the KameHameHa became a more standard attack, and Ki Attacks became more and more prominent. Then DBZ came along and it became the main premise behind practically everything the fighters did. They could fly, teleport, power up, etc., all based on Ki manipulation. Ki Attacks eventually led to Beam Spam, and the ability to power up that was introduced early in DBZ became the method by which nearly every Big Bad but the last one was defeated, by digging just a little deeper and becoming just a bit more powerful.
 * It's also interesting to note that Dragonball started as a homage to Journey to The West, then it got a little martial-arts focused and drifted so far you almost forgot the original purpose of the story was to find the Dragon Balls. By two-thirds of the series gone past, the balls were so easy to recollect again by the good guys, and the bad guys were no longer focused on getting wishes from them and settled for the destruction of the world and the rest of the cosmos.
 * The Uchiha clan in Naruto, and Sasuke in particular, have done nothing but become more prominent in the story as time passes. It's gotten to the point where the Uchiha clan is responsible for the entire plot of the manga. Sasuke started out as merely The Rival to Naruto (though he clearly had greater story importance than other such rivals due to also being Naruto's teammate) who wanted to avenge his clan, but as the Uchiha presence expanded, so has his. He's arguably had more face time in the manga than the actual protagonist (he hasn't, though he's had more than every other character despite being largely absent for the first three arcs of Part 2). It's a sore spot between fans whether this is a good thing, a bad thing, or something in between.
 * Yukito Kishiro derailed Battle Angel Alita: Last Order for a two-volume gothic vampire story which acted as last-minute background for "Fata Morgana" (a nanotech super-program). It would appear the Fata Morgana became such a Plot Tumor due to Kishiro's understandable reluctance to pull a Deus Ex Machina on his readers, but it's still not the most elegant arc of the series).
 * More or less the same thing has happened to Bleach, with the early substitute shinigami stories fading into endless tournament-like fight arcs.
 * Given the amount of panels and empty surrounding space they receive, the speech bubbles themselves have been ballooning into strangling whatever plot they were supposed to be driving, extending any event by months or even years. Plot carcinogen?

Comic Books

 * In the Silver Age Superman comics, Kryptonite went from a simple Achilles Heel to a rainbow of Green Rocks that could do anything, and were present in ludicrous quantities. This was toned down Post-Crisis, but Smallville seems to have taken it back up.
 * Currently, it was brought back in the comic books as well.
 * Lampshaded in an issue of Superman/Batman where Superman is almost accidentally killed because it was cheaper for a film company to use real kryptonite rather than make a prop.
 * X-Men has dined out for years on the idea of prejudice against mutants - to the point where its the major thread of nearly every adaptation and any attempts to even tone down "Mutant Hysteria" (much less eliminate it) have been swiftly written out. When it was first conceived, anti-mutant prejudice was based on fears of mutant supremacy: that mutants like Magneto would eradicate/replace normal humans as the next stage in evolution, especially since anyone's child could be a mutant. As currently written, the Fantastic Racism is apparently so ingrained that it's become even stronger in the face of the mutant population being Brought Down to Normal in the Decimation arc.
 * One might also look at the entire character of Wolverine as a Plot Tumor. Moving from a loner and a minor member of the team till gradually we find that he is the main character of the movie series (with the team leader gone for nearly two entire films), and his name in the title of a new series.
 * Another Plot Tumor could be the whole idea of the mutant hunting robots, the Sentinels. The anti-mutant groups have no problem with gigantic robots, filled to the brim with all weapons of mass destruction, roaming the world in search of mutants and not stopping till they found even a mutant or mutants with the power of, oh say, glow in the dark, and destroying everything and everyone in the way until said mission is done?
 * The Flash and the Speed Force. The Speed Force started as a way of Arc Welding all of the unrelated super-speedsters while providing them with a universal Hand Wave for the ways that they make physicists cry. It eventually gained enough properties, applications, and relevance that it now dominates the Flash mythos.
 * This happens to a lot of heroes with power sources that can be even remotely anthropomorphized, with the power source becoming used in more and more story elements instead of just being left in the background. For example, a lot of recent Marvel Family stories are more about the Wizard and/or the gods who empower Captain Marvel and less about the Captain himself, Green Lantern comics are frequently dominated by the Guardians and Lantern politics rather than heroics, and Animal Man eventually started drowning in "the Red" (which eventually led to Animal Man ditching superheroics completely in favor of animal activism).
 * In one issue of The Authority Swift has a one night stand with Grunge from Gen 13. Later this become source of drama between Grunge and his girlfriend in Gen 13.

Film

 * An in-universe example from Rubber where a group of spectators are watching the "film"

Literature

 * The Holy Grail in Arthurian literature grew to be the entire raison d'etre of the Arthurian Court, taking on aspects of various magic hamper/magic mill myths, and creating a mythological snarl whose origins modern scholars are nowhere close to deciphering.
 * For that matter, King Arthur himself suffers from this. His origin as a British post-Roman warlord is so obscured by later accretions of folklore and myth that entire books have been written that try to pry as much detail out of the meager historical documents available from Dark Age Britain.
 * Recent historical surmises place him as actually being Welsh and called "Owain Ddantgwyn", or "Owen White-tooth".
 * J.M. Barrie's novel Peter Pan has Peter saying that you fly by thinking happy thoughts. The book goes on to reveal that Peter made that up as a joke, and that the real secret is pixie dust. In every later version of the story, you need both pixie dust AND happy thoughts.
 * Another is when Peter says Neverland is located "second star to the right and straight on 'til morning." The book immediately follows up by saying again that Peter is just making it up, pointing out that nobody could possibly find Neverland with these directions. Again, most adaptions assume that is literally where Neverland is located.
 * Oh, it's even worse. The "star" part was added in adaptations. When Wendy asks Peter where he lives, he says "Second to the right and straight on 'til morning," which is not only impossible, but nonsensical.
 * Yet another example: Saying "I don't believe in fairies" causes a fairy somewhere to die, and you have to actually believe what you're saying. A lot of recent adaptations seem to assume you can shout this at specific fairies to kill them and you don't have to really believe your own words, just say them.
 * This was actually subverted in the movie Hook. When Peter yells "I don't believe in fairies" at Tinkerbell, she pretends to drop down and play dead, he panics, and starts clapping furiously to bring her back. Meanwhile, Tinkerbell is basically just screwing with him, and it's possible that the fairy-death-by-lack-of-belief thing is just a myth.
 * When J.R.R. Tolkien was writing The Hobbit, he was also designing the fantasy world of Middle-Earth in his spare time, just for fun. For his own amusement, and to flesh out the world of The Hobbit a little more, he put a few references to Middle-Earth into the book, but he wasn't seriously thinking about adding hobbits to his private World Building project. However, when he decided to write a sequel to The Hobbit, the Middle-Earth references increased exponentially, to the point where the book (The Lord of the Rings by name) was as much a sequel to The Silmarillion (at that time unpublished) as it was to The Hobbit. Some massive amounts of Ret Conning were needed to make the two stories fit into the same setting.
 * Another, perhaps even more surprising, Tolkien example: The One Ring (and Gollum). In Tolkien's first version of The Hobbit, Gollum willingly handed over the Ring to Bilbo as a prize for besting him in the riddle contest, it was just a plot point to give Bilbo the invisibility powers. Tolkien had to back and make Gollum far more sinister and un-sportsmanlike about the whole thing AND add in that he freaked out about losing the Ring, considering that the follow-up to the Hobbit, The Lord of the Rings,the importance of the Ring has swollen so much that the story pretty much entirely revolves on the corrupting power of the One Ring and Middle Earth is inadvertently saved because of Gollum's need to have his precious.
 * In the Honorverse, Manpower Incorporated, a genetic slavery organization, was originally a minor background detail, with the focus of the series being on the increasingly escalating war between the protagonist Star Kingdom of Manticore and the antagonistic People's Republic of Haven. Starting around the tenth book in the series, however, the Mesa system, which is both home to and arm-in-arm with Manpower, became the Big Bad of the Honorverse. The shadowy cabal that controls Mesa was eventually revealed to be closing in on the end of a centuries-long plan to control the known galaxy via long-term political and military manipulation of every other government, all so they can reintroduce widespread genetic engineering to the galaxy and eliminate any opposition to it.

Live Action TV

 * Doctor Who has a couple of examples.
 * The Cybermen's allergy to gold went from "could be choked by powdered gold dust" to "tossing a gold coin at them is like shooting Kryptonite bullets". When the new series reintroduced them, this tumor was quietly excised. Supplemental material mentions that the allergy to gold was discovered early in the Cybermen's R&D process and eliminated then.
 * In the sonic screwdriver's original appearance in Fury from the Deep, and later in The War Games, it was used for unscrewing things. It only gradually became a do-anything device.
 * It was actually written out of the show because it was becoming a Deus Ex Machina, before being reintroduced for the Eighth Doctor... and becoming a Deus Ex Machina. It got so bad that they had to introduce a second Deus Ex Machina ("deadlocking") to counteract it. And now it doesn't work on wood either.
 * The Kromaggs on Sliders.
 * When Ellen DeGeneres came out of the closet, then character on her sit-com, Ellen, did the same. It had been stated that the show would continue normally and that her being gay would not take over the show. However, in the fifth and final season, half the episodes focus on it.
 * The surreal comedy episodes of The X-Files became the series' plot tumour in the sixth season especially. Whereas previously there'd been two or three per season that were refreshing escapes from the show's usually dark and disturbing subject matter, it was a bit much to get a silly comedy episode every single week. (The other perspective was that this was a relief from the conspiracy arc that didn't seem to know where it was going, but that's a matter of fan opinion.)
 * Archie Kennedy in Horatio Hornblower became a rather inconvenient character-flavored plot tumor (and nearly a Romantic Plot Tumor if you squint) as a minor character cobbled together from several bookverse extras and who proceeded to swell vastly in importance as the highly non-canon best friend of a hero not known for having extroverted besties.

Machinima

 * The Freelancer program of Red vs. Blue began simply as independent soldiers who worked for the paying side and to introduce the AI programs. The mini-series Out of Mind expanded this to being a special program to combine AIs with soldiers and the AI revolt. The Recovery One and Recollection trilogy further expanded it to be not only a program designed to win the great war with unscrupulous methods, but all the cause of the Red vs. Blue war and all the events of the first five seasons. Finally, the ninth season had the plot equal parts silly comedy and the darker Freelancer backstory.

Multiple media
""Whoever wrote this episode should DIE!""
 * Franchise Star Trek across its many incarnations and writers has had a lot of these.
 * The "Brain Bugs" from The Wrath of Khan went from a moderately small concept to a much larger one as successive generations of fans got a hold of the writing jobs.
 * Incidentally, "Brain Bugs" is sometimes used as an interchangeable term for Plot Tumors; whether or not this is influenced by Wrath of Khan is up for question.
 * The Jefferies Tubes started out as fairly realistic maintenance tunnels that the odd tool or piece of equipment were in. This is realistic because sometimes with complicated engineering not everything is within arm's reach. These mutated over generations to labyrinths of tubes where everything important was kept - Fair to say no engineer would design something this malevolent.
 * The Star Trek Voyager episode "Macrocosm" Lampshaded this when Janeway gives the Doctor a rather complex set of directions through the tubes and the Doctor asks who designed the ship.
 * Parodied and Lampshaded in Galaxy Quest.


 * The Borg started out as technophiles who were only interested in stealing interesting technology and ignored life forms unless they became a danger, but they gradually mutated into Night of the Living Dead-style zombies. The first trip aboard a Borg Cube showed that Borg reproduced naturally and put implants into their infants. Meanwhile Picard was chosen to become Locutus as a mouthpiece for the Borg to announce their intention to conquer and enslave humanity. By First Contact, they were able to assimilate on the fly, injecting nanites directly into people to begin the assimilation process (though full assimilation was more involved). By the time Voyager encountered them, they were primarily interested in assimilating life forms regardless of their technological level, and eventually the Borg were revealed to be unable to actually understand anything without assimilating it.
 * The Vulcans have also gone through this. One of the complaints about the Vulcans on Enterprise was that they were portrayed as capable of deceit and underhanded behavior, the complaints arising because people took one character, Spock, who was in fact notably atypical, and used him as the archetype for an entire species. However, when you look at how Vulcans were portrayed in the canon, you saw Vulcans acting in quite un-Spockish ways, even as far back as his "wife" in the original series who manipulated things to get out of her arranged marriage.
 * Transporters were created as a last-minute cost-cutting cop-out to prevent expensive effects shots of shuttles landing on planets, but soon became a rich source of plots, with whole episodes centered on the zanier aspects of their operation, even though the unintended applications make them outrageous and are best ignored to begin with. See Misapplied Phlebotinum.
 * Perhaps the biggest one was the way the Prime Directive grew in importance until Enterprise was doing an episode where the Family-Unfriendly Aesop was that the only moral thing to do was to stand by and let an entire species of advanced, peaceful aliens die out when you could easily save them. Worse, the Prime Directive didn't even exist at the time that series was set. That species was allowed to die out because the character had somehow got it into his head that "evolution" is some kind of omniscient God who must not be disobeyed.
 * Klingons as Space Vikings. The movies and TNG portrayed them as possessing a much more nuanced culture that happened to have a warrior past. By the time Worf started as a regular on Deep Space Nine, every Klingon went everywhere with his sword, and no woman ever held a position of power.
 * The entire Dominion War arc that practically was Star Trek Deep Space Nine.
 * Star Wars has several examples. It can be argued that lightsaber combat qualifies, as it was never paid that much attention in the original trilogy compared to the prequels (and in the Expanded Universe, there are seven forms of lightsaber combat, each explored in detail). However, a more glaring example is the evolution of Boba Fett -- starting with a non-notable background character with almost no dialogue, whom the audience liked for his "cool" armor, and ending up with the Mandalorians, an entire society of proud warrior race guys like him, who have played a major role in at least two galaxy-spanning conflicts to date and basically became the Star Wars answer to the Klingons (not to mention ).
 * The Star Wars video games, having a relatively limited amount of iconic canonical material to draw on, have become almost comical in the way various memorable elements of the movies show up over and over again in different, unrelated games. For instance, there are now, in the non-canonical parts of the EU at least, at least five different sets of Death Star plans that have been stolen five different and mutually exclusive ways by five different heroes or sets of heroes.
 * In turn, writers who try to make sense of EU have come up with the explanation that the Empire did not keep a full set of the plans in any single location, but that several stolen pieces were necessary to put together a complete picture of the Death Star and learn about the vulnerabilities.
 * See also how thanks to the video games' endless reliving of the Battle of Hoth, what was, in the movies, a one-time, fairly cool longshot that happened to pay off - the snowspeeder managing to trip the AT-AT with a tow cable - has now become the de rigeur, recommended means for killing AT-ATs.
 * This was nicely subverted in one of the X-Wing novels, where it is demonstrated that real starfighters find AT-ATs target practice, even without using single proton torpedoes to blow them to bits. Of course, this also causes the Fridge Logic to attack since Luke's X-Wing was sitting around doing nothing on Hoth...
 * Not to mention Force Lightning: It's used six times in the six movies - three times by Palpatine (Return of the Jedi, twice in Revenge of the Sith) and three times by Dooku/Darth Tyrannus (all in Attack Of The Clones). Both major league Sith Lords. In the games, anyone who has a smidge of Dark Side can throw lightning around with impunity and on a vastly greater scale, too.
 * In Jedi Starfighter, Jedi can use lightning with no karma meter to speak of. Timed correctly, you can destroy five fightercraft at once with it!
 * The planet Tatooine is a particularly malignant plot tumor in the Star Wars Expanded Universe. Initially introduced as a thoroughly unremarkable backwater world ("If there's a bright center to the universe, you're on the planet it's farthest from"), it's since been featured with varying degrees of prominence in almost every Star Wars game and, in the end, appeared in five of the six films. Its appearances in the Expanded Universe may even outnumber those of Coruscant, ostensibly the capital planet of the galaxy.
 * If the player character in Knights of the Old Republic follows a certain sidequest with the Sand People, there is an implication that Tatooine is the original human homeworld.
 * Tatooine assumed this importance as early as Return of the Jedi when we find out Jabba lives there - a crime boss so powerful and infamous that C-3PO has heard multiple horrible legends about him.
 * Hoth suffers from the same disease as Tatooine, to a lesser extent. It's an utterly unremarkable, nigh-uninhabitable snowball of a planet whose sole significance was a major Rebel base built there specifically because it's the last place anyone would look. And yet almost every Star Wars game features a Hoth level. (Which would be excusable if the game were set between Episodes 4 and 5 - most are not and have a Hoth level anyway!)
 * So, Obi-Wan cuts off a guy's forearm in Episode 4. Then Vader cuts off Luke's hand while dueling in Ep5. Finally, Luke returns the favor in Ep6, which also reveals that Vader (or his arm, at least) is mechanical. One might think that all these dismemberings are just a natural consequence of a guy swinging a freaking laser sword, right? Not according to the Expanded Universe, which insists that cutting off an opponent's hand is specifically a display of one's mastery and superiority, complete with a silly Jedi name for this move. Not that Luke would have known that. Or that going for the limbs is a pretty sensible and relatively unimpressive move when they're being extended toward you and your blade could carve them like warm butter. Although perhaps taking JUST the hands should be considered impressive (rather than lobbing off half the arm).
 * Cutting off a hand, or "cho mai", is a gesture of respect, as well. What? There's also cho mok, cutting off a dude's arm, and cho sun, cutting off miscellaneous parts of a dude. Yes, they all have pseudo-Korean names.

Newspaper Comics

 * Few people realize that the comic strip Beetle Bailey was originally about the title character attending college. Him joining the army (in 1951) was originally going to be just a one shot story. He was in college for only six months before leaving forever.
 * Blondie was originally about a flapper girl from the twenties of the same name. After the Great Depression hit, the focus of the comic turned to her inept comically-oversized sandwich-eating husband, Dagwood Bumstead.

Toys

 * Pretty much every single Transformers series since about 1992 where Takara (the Japanese toy company that shares the rights to the Transformers brand with their American partner Hasbro) had a major say in the direction of the toyline/story development has over-emphasized the role of Convoy (better known as Optimus Prime outside Japan) and his derivatives (Hasbro, on the other hand, despite also putting an "Optimus"/"Prime" character/toy in every series whenever possible, puts a little more emphasis on character diversity). This is particularly glaring in short-lived toy-only lines with no television show to back them up, which will often start with a new Convoy toy... then maybe a different character as the second toy if they're really lucky, or another Convoy-related toy of they're not so lucky... and then the line ends and gets replaced by a new line that starts with the next Convoy all over again. The most noteworthy example would be the "Robot Masters" line from 2004, which, during its 25-toy-run, had no less than seven toys with the word "Convoy" in their names (including redecos). One of these "Convoy" toys was even a retool of a Megatron toy and was intended to actually be a form of Megatron.
 * Prime's role can be over-emphasized in America, too; The most recent movie had a villain who could only be defeated by a Prime.
 * A more notable example in the Transformers mythos: The Autobot Matrix of Leadership. The term "matrix" originated with Optimus's "creation matrix" in the comics, in which it was simply used to create new characters toys. It was then introduced into the movie with its current title, serving only as a MacGuffin to defeat Unicron (note that prior to Unicron mentioning it, Megatron had absolutely no use for it); it quickly became the central do-anything power source and all-purpose MacGuffin for the cartoon. Several series have even had Megatron and other Decepticon leaders dip into Motive Decay by having them all lust after the Matrix. In All Hail Megatron, Megatron's acquisition of the Matrix was treated as "game over" for the Autobots, and Starscream was able to win over the Decepticon army just by possessing it.
 * Considering that in everything except the G1 cartoon, Beast Wars and Beast Machines, the Matrix contains part of the essence of the Transformer god and creator, Primus, it's understandable that the Decepticons would want it. Still though...
 * For that matter, the Primus/Unicron conflict. In G1, Unicron was "merely" a humongous planet-devouring Transformer, who got defeated in the very movie he appeared in. Eventually, however, he was retconned into a "multiversal singularity" existing in every Transformers continuity at once, along with his good counterpart, who was introduced into the mythos even later. Eventually, fans got so sick of Primus and Unicron that Transformers Animated very pointedly avoided mentioning either of them.
 * Sparks. They were a creation of Beast Wars; nothing in G1 pointed to the idea that an actual object was required to keep a Transformer operational, any more that one normally would for a machine. The Dinobots and Combaticons were built on site with no access to any "life-giving" entities, the Stunticons and Aerialbots were animated by Vector Sigma, and Optimus Prime was simply repaired into full working order by a random Quintesson after dying (twice, at that). By the time of the movie and Animated, the BW idea of sparks firmly secured their place in the mythos, to the point of postulating that all Transformers were creations of the AllSpark.

Video Games

 * Neverwinter Nights 2, starting with the Ember Trial, seems to force one quest on the player after another, leading to the question "Whatever happened to going to the Jerro Estate?", it takes most of part II for the answer to that question
 * The Insult Swordfighting in Monkey Island was meant to be a parody of the witty banter found in high adventure movies, but by the time Escape from Monkey Island came around, there's apparently an Insult version of nearly every sport available floating around the Tri-Island Area.
 * Sometimes the earlier games in Zelda series seem to be set in an almost separate universe than the more modern ones. Originally, the Triforce was a mysterious triangle that granted magical abilities, and there were only two of them, not three. Come The Legend of Zelda a Link To T He Past, however, and it's the Cosmic Keystone of the entire Zelda universe with omnipotent wish-granting and reality-warping powers. The significance of the Triforce mark was also different. From The Legend of Zelda Ocarina of Time onward, the Triforce mark on one's hand signified which piece of the Triforce one had and would glow when its power was being used. The first appearance of this mark was in Zelda II the Adventure of Link, and it showed up on Link's hand before he even had the Triforce of Courage. It just marked him as the hero destined to claim it.
 * Likewise, the Master Sword being the only sword able to kill Ganon is a relatively recent idea. In its first appearance in A Link to the Past, the Master Sword was a powerful weapon to defeat evil, but in order to kill Ganon you had to stun him with the Master Sword, then actually harm him with a Silver Arrow. After Ocarina of Time the relationship has been reversed, and the Light Arrows are needed to stun Ganon so you can harm him with the Master Sword. Sometimes you don't even need the arrows at all. The Master Sword meanwhile has been given increased importance, and it's a Comic Keystone just as important to the world of Hyrule as the Triforce now.
 * Although, in Ocarina of Time, it was required only to seal him away; you're able to harm Ganon with the Biggoron Sword.
 * The Metal Gear games were once about bipedal nuclear tanks but ever since Metal Gear Solid 2 Sons of Liberty introduced the Patriots, everything, even retroactively, has something to do with them.
 * In the earlier games, Unusable Enemy Equipment was handwaved by the fact that the weapons were keyed to their users via Nanomachines and won't function for anyone else. In Metal Gear Solid 4 Guns of the Patriots, the entire plot revolves around the weapon-identifying nanomachines (hence the subtitle) and the computer system that regulates them.
 * In the first Sonic the Hedgehog game, the Chaos Emeralds were merely bonus items to collect. They gained the ability to transform Sonic into his Super Mode in the Genesis sequels. The 3D games saw them turn into MacGuffins around which plots of entire games were based, and the emeralds gained the power to energize weapons of mass destruction, bring the dead back to life, and seal away monstrosities that live inside the planet.
 * Dragons were mostly background lore in the The Elder Scrolls series. Come The Elder Scrolls V Skyrim and pretty much anything can be explained (retroactively) via dragons. Liches, zombies, the Blades, an important part of the Empire's history...etc. Even door keys in several dungeons have the shape of dragon claws.
 * The Cerberus group in the Mass Effect series. Initially it was just a shady group with a couple of hidden bases. Come Mass Effect 2 they're an almost all powerful organization that are central to the plot. While it may have been planned that they would have such a large role it still felt like a Plot Tumor for those that didn't take part in the optional quest of the first game.
 * Legendary Pokémon. Gen I: 4 rare Mons only available at the ends of several dungeons (Seafoam Islands, Power Plant, Victory Road and Cerulean Cave). Gen II: 3 randomly appearing Mons out of nowhere and two special Mons that require special items to catch. Gen III: Creators of the planet added. Gen IV: We have Dialga, Palkia, Giratina and Arceus.

Webcomics

 * Sluggy Freelance has had a couple of these, thanks to being Kudzu Plot incarnate.
 * The Dimension of Pain was originally just a concept that fueled roughly a week's worth of strips. Then Pete Abrams decided to make it a Running Gag, having the Dimension of Pain demons show up each Halloween to claim Torg's soul. Each Halloween arc got longer than the last, and eventually the demons caught on so much that they were made the stars of their own B Side Comic Strip "Meanwhile in the Dimension of Pain." Then eventually even that wasn't enough, and the Dimension of Pain demons became the main antagonists of the massive "That Which Redeems" arc.
 * Although Pete Abrams has stated he knew the demons would be invading the Dimension of Lame when he left them a potential means to do so, right in the first story.
 * There's also Bun-Bun's grudge against Santa Claus. At first there were just a handful of strips around Christmas each year where Bun-Bun would try (and fail) to kill Santa Claus. The feud kept escalating, however, with more and more side characters (the Easter Bunny, Santa's black ops elves, aliens with a weakness against Nerf) getting involved, until it eventually exploded into Bun-Bun amassing an army and going on a holiday killing, world conquering rampage in the three month long "Holiday Wars" saga (which itself launched the even longer "Oceans Unmoving" arc).
 * Both of these Plot Tumors, however, seem to have been successfully removed. The Dimension of Pain has not been seen for years, ever since "That Which Redeems" concluded. And, while Bun-Bun still makes the occasional attack on Santa Claus, holiday figures and black ops elves have long since ceased to play a prominent role in the story.
 * Although with the 4U city mutants and the mutagen causing squid on a stick, the Dimension of Pain looks to be moving back towards being important. Timeless space also managed to be fit in.
 * Concession started off as a comic strip about a bunch of anthropomorphic characters who worked at a concession stand at a movie theater (The author actually based it around the stupidity he experienced, working in customer service is a good way to get material for comic strips). But if you look at the most recent comics...you'll not really see that much about an actual concession stand. For awhile, the actual concession stand was more or less put to the side, and until it got wrapped up in the massive Plot Tumor, it didn't even play a role beyond the occasional appearance of a main character who was still employed there. Immelmann has actually admitted that it's only really about concession stands In Name Only and centers around the character Joel and his plot, it even says so right in the "About" section.
 * In Sam and Fuzzy the original comic was mainly a slice of life style that was mainly a gag a day style. Then ninjas were added. And a demonic refrigerator. After that, things got weird. Now the whole story revolves around the weirdness and the weirdos and pretty much every arc has ninjas in it due to Sam becoming the Ninja Emperor.
 * The "Patriarchy" in Sinfest during fall of 2011 quickly grew to overtake the strip, turning the focus to the actions of Trike Girl and the ramifications of said actions on the world. As of early 2012, things seem to have calmed down a bit. Sinfest runs into this trope a lot, due to the author Writing By The Seat Of His Pants. "Patriarchy" is notable for taking over so much in such a short time period, but there are plenty of other examples:
 * Possibly the first was the Devil's "crisis of faith", which spun so far out of control that the author didn't know how to end it. Big D was AWOL for several real-world months before it was revealed that he just went on vacation.
 * The "Reality Zone" was introduced for a one-off Sunday strip, then became a recurring plot element.
 * A 2010 storyline had Squig becoming a hobo and Walking the Earth meeting all sorts of weird cameos, eventually winding up lost in a desert and pining for home. The author was eventually able to tweak an unrelated storyline to get Squig home.
 * And the big one: The Fuschia/Criminy subplot, which became the strip's chief attraction for awhile and still pops up frequently to mess with the status quo.
 * The trolls in Homestuck could be considered this. Most fans don't even remember that they didn't appear until Act 3 and they were retroactively added into the earlier story through flashbacks.