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- 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".
- The Chimera Ant arc in Hunter × Hunter started off as a side story, but eventually ended up ballooning to 132 chapters and lasting seven years real time because of numerous hiatuses.
- 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 then 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.
- The later two The 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.
- Cutler Beckett and the East India Trading Company in Pirates of the Caribbean. The company is more-or-less mentioned in passing in the first film, before becoming much more of a threat in the following two films. By the time At World's End rolls around, the combined threat of Beckett and Jones was enough to ultimately unite the world's pirate forces, who up until then were crossing and betraying each other on a regular basis.
- 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. Most people only know the film for the bird attack portion, leaving them quite confused by how long it takes to actually get to it.
- 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 Marion Crane embezzling money from her boss and making her escape. The entire plotline is completely abandoned once she's murdered partway through the film. The emphasis then transfers over to Norman Bates and how he's eventually captured.
- Red Eye starts out like a romantic comedy before revealing that the male lead is a Psycho for Hire here to present the heroine with a Sadistic Choice.
- In M. Night Shyamalan'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 village's secrets are still revealed as a result of Ivy's journey, however.
- 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 is persuaded into giving up, making the military contractors the main plot point, before that is resolved anticlimactically so that the climax can take place in North Korea. At the very least, the way the runaway AI was talked down involved a big emphasis on teamwork, which is brought up again in the in-universe justification for the pilots breaking ranks and embarking on the rescue mission to 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.
- In the Tim Burton Charlie and the Chocolate Factory, this begins to surface as the tour is about to begin and it's revealed that Willy Wonka has a hard time saying the word "parents". Starting at about the halfway point of the film, the audience is privy to Flashbacks of his childhood that reveal he had a Fantasy-Forbidding Father who ultimately abandoned him alternating with the tour scenes. Finally, Charlie is the last kid standing and Mr. Wonka intends to make him his successor...and the plot tumor turns out to stand in the way of the novel's ending. Mr. Wonka reveals that a condition of his offer is that the boy abandon his family, as his traumatic childhood has led him to think that it only holds one back. Charlie must decline, and Mr. Wonka slips into a depression of sorts even as Charlie's family's fortunes improve without him. Finally, Mr. Wonka consults Charlie, who convinces him to reconcile with his father. Only then does the Happily Ever After of the novel commence.
- In the Marvel Cinematic Universe, the plotlines involving Thanos and the Infinity Stones has steadily growing in importance. Phase One only involved the Tesseract in two movies (without revealing its greater significance) and revealed Thanos in The Stinger in one. Phase Two has three movies that each introduce a new Infinity Stone, with Guardians of the Galaxy also explaining what they are and giving more screentime to Thanos. Phase Three escalates even further, as the Avengers have now realized what they're dealing with and Thanos has vowed to take action personally, culminating in Avengers: Infinity War where they'll go head to head.
- 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.
- Tad Williams's Otherland involves a huge number of characters, and starts off rotating between their not-immediately-connected stories. The serial killer Johnny Dread is among this cast but doesn't play a particularly prominent role in the first volume. However, he grows in power and significance to be the main antagonist that everyone is fighting at the climax, even overshadowing the creator of the virtual world they're in.
- 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 for a mysterious crime boss. But then one of the caterpillars the scientist was studying hatches and starts Mind Raping everybody. Everything else gets pushed to the side when it turns out that the moth is just about the deadliest thing in the world.
- 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 Side Quest. 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, and later one of the claimants to the throne decides to assist the Watch, 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 Others.
- The Gray King in The Lies of Locke Lamora goes from background menace to Big Bad. The B plot almost literally murders the A plot and takes its place.
- 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 Angel went evil, 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.
- 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.
- 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 poorly-received.
- Kirsten Cohen of The O.C. 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 Blake's 7 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 save the townspeople's souls from her control and stop her from killing Sam in a ritual sacrifice.
- 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 the maenad kills the people she came to kill, then moves on to menace some other town.
- 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. Or so you think. In the next couple of episodes, just when you've gotten used to the idea that the certain tenacious character is the big threat, it turns out that we aren't quite done with the far-future plight of humanity — and they aren't quite done with us...
- Lost is naturally a big offender here. Just a small spoiler-free (not) hint: The Final Season and the two that preceded it is not really about castaways trying to survive after the crash and to get off the Island anymore.
- Dexter Season 7: For the majority of the season, the focus is on Hannah McKay and Isaak Sirko, both jostling for position as Dexter's main antagonist. Meanwhile, in the background, Maria LaGuerta investigates the accusations leveled at her late friend and former lover, James Doakes. Come the final episode, Isaak's dead, Hannah's in jail, and Maria's figured out who the REAL Bay Harbor Butcher is.
- In Babylon 5, mysterious alien vessels are introduced about halfway through the first season. Their first appearance is in the appropriately named episode Signs and Portents. We don't even learn the name of the race that uses these strange-looking ships until after a few appearances. As the series progresses, we slowly learn more about them, until by the time Season 3 rolls around, the Shadows have become the series main antagonist, and the show's Myth Arc is in full swing.
- Star Trek: Deep Space Nine:
- The Dominion, first introduced as a background plot reference in a comedic Ferengi episode, would go on to almost conquer the Klingons, the Romulans and the Federation. They were also aided in season 7 by the Breen, a race which started as a bit of a throwaway joke.
- Dukat. His final arc started as the E-plot, something to give comic relief while everyone else was fighting the Dominion. Then things escalated. And again. And ag- say, did he just figure out how to free the pah-wraiths? Which he considered gods in a previous episode? Oh shit...
- In Kamen Rider Gaim, the protagonists are originally concerned with the competition between local street dance crews, though they do notice some odd monster attacks on the rise. About a third of the way through the series, the "dance crew" storyline is officially retired as the show focuses more on the invading monsters, and it's eventually revealed that this is a Cosmic Horror Story with the power to reshape the world at stake.
- This trope also applies to two of the secondary characters, Kaito and Mitsuzane. Kaito starts out as simply the head of a rival dance crew, who is a Social Darwinist but otherwise pales in comparison to the other threats out there, and even frequently allies with our hero Kouta when their goals align. But when those other threats are dealt with, he becomes the Final Boss since he, like Kouta, has been growing in power the whole time wants to use it to tear down and replace the world order. Similarly, Mitsuzane begins as Kouta's friend but gradually starts to hate Kouta, fall into madness, and make more extreme plans to shape the world to his whims. Subverted when, just before the final battle, his schemes finally catch up to him and blow up in his face, leaving him psychologically broken and a non-threat.
- 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 (1983) by the song's end.
- Frequently happens in Legend of the Five Rings due to the audience participation model used to determine the storylines. Actions taken by players very early on in an arc can come to dominate the storyline late in its lifetime. The most memorable example is probably the first published story arc, The Clan War. It starts with the (at the time) six Great Clans coming into conflict with one another as they attempt to assume dominance while their emperor lies close to death, some of them consorting with the Empire's ancient enemy, the Shadowlands, in order to do so. The storyline concluded with the Shadowlands and its leader, Fu Leng, firmly established as the undisputed Big Bad of the setting and the Great Clans forced to cease their war in order to wrest control of the empire back from Fu Leng and his undead hordes.
- A more subtle example occurred with the subsequent storyline, The Hidden Emperor. This storyline contained several confusing, seemingly-unrelated subplots with the abduction of Emperor Toturi I at its heart. At different points in the story, the Dragon Clan, the Kolat, and the resurgent Shadowlands all seemed poised to emerge as the masterminds behind all the chaos. It was quite a surprise when the shapeshifting ninjas who had been a part of the setting since day one were revealed to be a Hive Mind under the command of an Eldritch Abomination who had instigated everything as part of their master plan to unmake all of reality.
- 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.
- 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. Or so you think until it turns out that the "religious texts" were actually accurate historical recordings, and the enemy's eventual attempt to destroy the sun (with a likewise briefly mentioned WMD) releases the chaos god. The entire third game revolves around putting it back.
- The evil organizations in all of the main series 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.
- 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.
- In World of Warcraft Warlords of Draenor the original goal of the players was to destroy the Iron Horde, with Gul'dan and the Burning Legion being part of a side plot. Due to the Iron Horde weakening quickly Gul'dan stepped in and seized control, making him and the Legion the true enemies of the expansion.
- 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" when he took over Heretti-Corp.
- Initially, College Roomies from Hell!!! 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.
- The Family Guy episode Da Boom features half-octopus Stewies multiplying out of control and eating most of the characters.
- The first episode of Season 14's "Coon & Friends" trilogy in South Park was about Cartman trying to get Captain Hindsight to join his superhero team, with BP's recurring drilling accidents being the B-plot. Then BP unleashes Cthulhu and the last two episodes focus mostly on him, tying up Captain Hindsight's story in the second.
- 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. The badger looks through a window growling menacingly, but Homer shrugs it off, saying there are more important things to deal with now. 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.
- The 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 Dark Is Not Evil 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 kill Mary Jane but the final battle of the show involves Carnage coming out of nowhere and trying to use the machine to destroy the entire multiverse. Word of God supposedly says that a reason the show ended with an unresolved plot was that after saving all existence they couldn't think of any more compelling plots for the webhead.
- Avatar: The Last Airbender:
- In the first season, Prince Zuko is initially the main villain, while the other major recurring villain, Commander Zhao, is mostly just his far less sympathetic rival. Midway through the season, however, Zuko has started to get Character Development shifting him towards Anti-Hero territory (though he doesn't fully get there until the second season) while Zhao gets promoted to Admiral, letting him take over as the main villain in time for the Season Finale.
- Also, while Fire Lord Ozai is identified as the Big Bad pretty much from the start (albeit in a Orcus on His Throne sort of way,) the first season contains one brief shot of a rather sinister-looking girl, who is then identified in The Stinger as Zuko's sister. She is not named, doesn't speak until Season 2, and seems to serve no purpose beyond looking a bit creepy. The girl is Princess Azula, who may technically be The Dragon to Ozai, but is so competent in that role that they sometimes appear more like a Big Bad Duumvirate, and she remains a very serious threat even after Ozai himself takes an active role.