Malignant Plot Tumor

You are watching a movie, or reading a book and everything is going along swimmingly. There is an A-plot and maybe a B-plot and a C- and D-plot thrown into the mix too. While the storyline isn't too obvious, it's pretty clear that the climax is going to be with the Big Bad that is the focus of the A-plot. But there is also a small E-plot, it's so small you might not even notice it, but as the story goes on, it grows and grows until the main characters are forced to completely forget about all the other problems and focus completely on this growing threat. Despite its dire sounding name, this trope can be used with excellent results. Ergo, this might even be a Benign Plot Tumor.

Compare to a Plot Tumor, where the growth of one aspect above all others is unintentional, and Halfway Plot Switch, which is somewhat like this, but more abrupt and leads to Genre Shift. See also Arc Welding. Don't confuse with the Bait and Switch Boss, which is oftentimes entirely unrelated to plots and subplots.

WARNING: SPOILERS AHEAD

Anime and Manga

 * Yu-Gi-Oh! Duel Monsters: The Spirit of the Millennium Ring appears as a villain from season 1 but ends up being the Big Bad in the last season after other more prominent antagonists are "defeated".
 * In Naruto, the Uchiha slowly but surely take over the entire plot. Big Bad Madara Uchiha is introduced much later in the manga but is shown to be responsible for almost every bad thing that happens, from Akatsuki, the relationship between Naruto and Sasuke, and what happened to Naruto's parents, to even the Tailed Beast. And all things not tied to Madara, are tied to the Uchiha.
 * The Chimera Ants in Hunter X Hunter. Started out as a minor side plot, has since turned into the longest arc in the manga.

Comics

 * Valiant Comics' 1990's revival of Magnus, Robot Fighter initially picked up right where the Silver Age series left off, with a decadent upper class humanity becoming increasingly dependent on robots and vulnerable to antisocial ones; the robots chafing under humanity's rule and sometimes becoming extremely dangerous; the vast slums on the Earth's surface, beneath the gleaming towered cities, where life is terrible; and Magnus trying to find a way to set things right for all three factions. It had always been a cool premise with a lot of potential, and at first the Valiant title explored it in much more depth than the original Gold Key Comics version had. Then the Malev Robots from space invaded, conquering Earth and derailing all of the above-mentioned premise. All that mattered after that was everybody fighting space robots.

Film

 * The later two Matrix movies seem to be about the showdown between the machines and free humans, but while those two sides are busy fighting, Agent Smith is busy replicating, and by the end the warring factions must agree to a truce to deal with Smith.
 * The first part of The Birds is mainly about the romance between Rod Taylor and Tippi Hedren, which ends up completely drowned out by the titular bird attacks by the end of the movie.
 * This also happens in the Z-List The Birds tribute/rip-off Birdemic. The first half of the movie is a rather bland romantic comedy. The second half is a laughably bad horror movie with terrible CGI birds.
 * Many people forget that the first half hour of Psycho is a heist plot involving Janet Leigh embezzling money from her boss. She buys a new car, gets briefly followed by a cop, and then stops at this little motel for the night . . ..
 * Similar to the Hitchcock examples above is Red Eye, which starts out like a romantic comedy before revealing that the male lead is a Psycho for Hire here to present the heroine with The Sadistic Choice. There are still a bunch of people, though, who are mad that the movie didn't end with a kiss.
 * In M. Night Shymalan's The Village halfway through the movie from focusing on Lucius' trying to unravel the village's secrets to Ivy going on a perilous journey to find medicine before it's too late.
 * The main plot of Stealth was about an AI fighter jet which goes rogue and attempts to start a nuclear war with subplots about the military contractors who wanted to figure out how it gained independence and one of the other fighter pilots being shot down over North Korea and running from the army. Halfway through, the AI pretty much gives up for no reason, making the military contractors the main plot point, before that is resolved anticlimactically so that the climax can take place in North Korea.
 * Monty Python and the Holy Grail has a scene where a modern historian explains the setting of Arthurian-era Britain, but then has his throat cut by a passing knight on horseback. Just another absurd gag in a movie full of them, except that we see cutaways to the police investigating the crime throughout the film. They show up at the end and arrest Arthur and his retinue for it, conveniently preempting a big final battle scene that the production didn't have the budget to stage.
 * The Dark Knight started out as basically a turf war between Batman, the cops, and organized crime. Then some clown decided to get involved, whom everyone brushed off as little more than a nuisance. At first.

Literature

 * Matter by Iain M. Banks starts off apparently about a deposed prince gaining back his throne from the Evil Chancellor on a quasi-medieval planet, while more advanced aliens manipulate things behind the scenes. Then an archaeological dig is mentioned a third of the way through the book. Then later, the heroes find something in the city. Then with maybe four chapters left, the thing they find turns out to be Sealed Evil in a Can, whose first act is to kill all of the characters involved in the struggle over the throne. All but one of the surviving characters die trying to prevent it from blowing up the world.
 * Perdido Street Station by China Miéville starts off looking light - the A plot is going to be a scientist helping a bird man to fly again, with a B plot of his girl friend making a sculpture with her spit (don't ask). But then one of the caterpillars the scientist was studying while researching flight hatches, and pretty much every thing else is pushed to the side as the moth starts eating people's dreams, in a bad way.
 * Perdido Street Station has this to a ridiculous degree; by the end of the book we've gone through four or five major plots, any of which on their own could have taken up an entire book. It doesn't help that a lot of them get Left Hanging.
 * The Night's Dawn Trilogy by Peter F. Hamilton (especially book 1) seems to be about smuggling, politics, and revenge. That is until, half way through the first book, out of left field, the dead come back to life.
 * The Vord from the Codex Alera series are a classic example of this. They're introduced in the first book as the nasty but apparently unintelligent and unimportant guardians of the MacGuffin of a Sidequest. In the second book they prove to be very intelligent (though only collectively) and become a major threat, only to apparently be completely wiped out. In the fifth book, they're back with a vengeance, having been building up their forces massively in the background and forcing Tavi, the Canim and Lord Aquitaine to team up to stop them.
 * The entire Lord of the Rings trilogy essentially springs from a minor plot point (the ring) in The Hobbit.
 * In A Song of Ice and Fire The Night's Watch and their undermanned defence of the Wall initially seems, compared to the epic civil war in the South, like a pretty minor plot which we're only seeing because the son of a main character is up there. It gets a bit more interesting when the Others show up, but the sheer world-endangering Eldritch Abomination nature of their threat is only gradually revealed to the reader, and is still unknown or unappreciated by the vast majority of the characters. It takes the reader from rooting for whichever claimant they like the most to which one seems most able to defeat the Bigger Bad.
 * The first Sword of Truth novel is interrupted about 2/3 of the way through by a lengthy torture/brainwash/seduce sequence which is a sharp departure from its previous standard fantasy fare—and is by far the most arresting thing in the book.

Live Action Television

 * While fans will debate endlessly about whether Joss Whedon was winging it or not, most Buffy seasons are good examples, particularly season 6. The Big Bad looks like it's three fairly Harmless Villains. But there's a subplot about Willow being addicted to magic, which is fairly minor at first, but by the end of the season, one member of the trio has been flayed alive, and everybody is too busy trying to prevent Willow from destroying the world to care about the two others.
 * Seasons 2, 3 and 4 also show this pattern: a bunch of threats at the beginning of the season that end up being eclipsed by some bigger one.
 * Season 2 had the most rational explanation that there wasn't really a singular Big Bad throughout the season until, and once he did, everything else paled in comparison for the rest of the season...and maybe even for the rest of the series.
 * Season 2 also had to switch gears near the start because over the summer between seasons 1 and 2, the actor who played The Anointed One had grown too much to believably have him as the same unaging child vampire. The Anointed One was going to be the Big Bad of season 2.
 * The 2000-era Battlestar Galactica drew most of its plots from conflicts between humans and Cylons, infighting within the fleet, and the overarching Myth Arc of finding a way to Earth. Along the way, however, seemingly minor details come up about the titular warship:
 * The miniseries establishes that she's old and about to be decommissioned.
 * Battle damage accumulates on the hull as the series goes on.
 * A third-season episode involves a malfunctioning airlock threatening lives, along with remarks on how Galactica would be in need of a major overhaul under normal conditions.
 * A similar remark about equipment malfunctions occurs the next season.
 * Finally, it is revealed that Galactica has started to fall apart from all the wear and tear over her many years in service, and the last few episodes of the series see many plots put on hold as the ship's critical condition begins to dominate the series.
 * In Season 4 of 24, the raid on the Chinese embassy doesn't seem like a big deal at first, but wait until the end of season 5.
 * The Kromaggs from Sliders grew from a a semi-recurring menace into the series' Big Bad. It had little to do with the original premise and was relatively poor-received.
 * Kirsten Cohen of The OC drank on-screen enough for Television Without Pity to have started a "Kirsten Cohen drink watch '03." But at the end of season 2, she immediately switched from frequent wine drinker to inst-alkie complete with Wangst.
 * In the last half of season two of Blakes Seven Travis has been court-martialed by the Federation and is just as much a wanted man as Blake. Initially he cooperates with Servalan covertly, but by the penultimate episode he hints he's got a new agenda, which is fully revealed in the season finale and forces Blake to abandon the goal he's been attempting to achieve all season.
 * The second season of True Blood is mostly about Sookie helping Eric and the Dallas vampires find the missing sheriff, Godric. Meanwhile, there's a subplot going that has Tara moving in with a social worker who is secretly a maenad. For most of the season, the maenad, Maryann, isn't really much of a threat; she mostly just prances around holding sex parties and trolling Sam, committing a couple of murders while she's at it. However, after the Dallas plot is wrapped up, Maryann becomes the Big Bad and the main cast must team up to
 * In the book season two was based on, the Maryann character shows up in one scene near the beginning, then Sookie (being the first-person narrator) takes the story with her to Dallas. When she comes back to deal with the maenad in the climax of the novel, readers might be forgiven for forgetting she was ever there in the first place. It's especially aggravating because in the book version the problem is resolved when
 * In Doctor Who's third (revived) series, the entire plot of Utopia and the plight of humanity becomes negligible when a certain tenacious character makes a surprise return.
 * Lost is naturally a big offender here. Just a small spoiler-free hint: The Final Season  is not really about castaways trying to survive after the crash and to get off the Island anymore.

Music

 * Played for laughs in "Jack Sparrow" by The Lonely Island. The song was supposed to be a generic club rap with a hook by Michael Bolton. Turns out said hook was Michael Bolton singing a chorus about Captain Jack Sparrow which more or less takes over the song. He switches it to Forrest Gump, Erin Brockovich and finally Scarface by the song's end.

Toys

 * Bionicle web serials tend to choose this route. More often than not, they set up a basic plot-setting, and either shove it aside or wrap it up within the first couple of chapters, to concentrate on something barely related. Sometimes, these plot threads connect, other times, they just sort of get forgotten.

Video Games

 * A subplot about Alchemiss' power increasing in Freedom Force vs. The Third Reich takes over the third act of the game, as Alchemiss goes insane and nearly destroys the universe.
 * In the Marathon trilogy, an evil trapped inside the sun since forever is briefly mentioned once in a short piece of religious text of an alien planet in the second game, for the purpose of fleshing out a cultural Backstory for the game's real plot.
 * The evil organizations in all of the Pokémon games come into play as extremely minor obstacles in the way of the player's true quest (which is To Be a Master and Gotta Catch Em All), but swell in importance, numbers, and ferocity as the player progresses, and eventually eclipse the original quest in importance (at least for a little while).
 * The fifth generation games, as some feel, was the first generation to avert this, by basically having the plot involving the evil organization introduced in the first town you visit and remain important throughout the entire game.
 * Well, only if you believe that Colosseum didn't try for it first - you don't even get far from Pyrite before you realize Cipher is Serious Business. Done well, on the other hand, is a matter of opinion.
 * In Ultima III the Great Earth Serpent was just an obstacle guarding the entrance to the Big Bad's castle, which you needed a password to get by. In Ultima VII Part Two: Serpent Isle you learn that the serpent in question was a cosmic force of balance, and removing it from its proper place threatens to destroy the entire universe as the serpents of Chaos and Order struggle unchecked.

Web Comics

 * Sluggy Freelance Dr. Schlock's evasion of Heretti-Corp dated back to when he was forced to work for them, and even when hC became the main plot, Schlock was still a minor supporting character. His fugitive flight from them took over more and more panels until "broken"
 * Initially, CRFH focused on three very different losers trying to live together while occasionally dealing with wacky supernatural baddies. At one point, The Devil showed up, grabbed a character's soul and then was quickly dispatched. The devil is mentioned another couple of times, but doesn't appear again for a while. Then, it turns out one of the characters is a pawn in his plan to destroy the world, and all the other characters join forces to stop him.

Western Animation

 * The Family Guy episode Da Boom features half-octopus Stewies multiplying out of control and eating most of the characters.
 * "We don't know that they ate them!"
 * The Simpsons loves this trope, a good example is A Tale of Two Springfields. It starts off being about a badger infesting a dog house, but when Homer tries calling animal control, he gets distracted by the fact that the area codes have changed. Lampshaded when the badger looks through a window growling menacingly, but Homer shrugs it off, saying there are more important things to deal with now. Lampshaded even more at the end, when all of Springfield is focused on the resolution of the episode's major plot, and an army of badgers seize the opportunity to take the town by surprise.
 * In Futurama: Bender's Game the titular game starts as Bender tries playing an RPG and his imagination goes overboard. However, this is but a loosely connected sidestory to the main plot about dark matter (fuel). Then, right as that plot is reaching its climax, the messing with quantum physics caused the dark matter Bender had on his person to suddenly get sucked into his fantasy.
 * Fairly Oddparents: For most of the "Wishology", the head of the Mecha-Mooks was simply a recurring opponent. However, after seemingly falling into the background, he suddenly goes rogue and absorbs the entire planet. With the revelation that he proves the trilogy's true Big Bad. Considering all the parodies in said films, he is likely a direct Shout-Out to Smith.
 * Spider-Man: The Animated Series: we get a double whammy, First with the portal machine that a Villain of the Week built, and the Carnage Symbiote, who is really only fought once or twice in the series. Not only is it used to  but the final battle of the show involves   The Word of God supposedly says that a reason the show ended with an unresolved plot was that after   they couldn't think of anymore compelling plots for the webhead.

Other

 * In the Mars Attacks! bubblegum cards series, the Martians invade! And they release giant bugs to mop up humanity! And then disappear for most of the cards, as all but two deal with the giant insects until humanity suddenly decides to attack Mars for the last five.