Disc One Final Boss

"He's not the Final Boss. The game has 3 discs, and you're on Disc 1."

""There's all sorts of stories where you think you've beaten the Final Boss but then it just moves up to the next level!""

- Haruna, Mahou Sensei Negima

A driving force early in a story. The heroes seemed to have defeated them, but then the audience realizes that the show is only in midseason (or as the title suggests, the first disc of a multi-disc RPG).

The real villain, The Man Behind the Man, will show up later. This may lead to the plot being Hijacked By Ganon.

A cross between a Red Herring and The Dragon, with a little bit of Your Princess Is in Another Castle thrown in. It takes its name from the video game trope of a Final Boss, not a management figurehead -- as much fun as it'd be to find your boss's boss is bringing about the Apocalypse. See also Disc One Final Dungeon. Compare Decoy Protagonist.

Spoilers abound, obviously.

Anime and Manga

 * Dragonball Z has a lot of these, most notably Raditz from the Saiyan Saga and the Androids from the Cell Saga.
 * In what is probably an instance of playing with this trope, the jaw-droppingly powerful vampire/sorceress Evangeline A.K. McDowell in Mahou Sensei Negima likens herself to both intermediate and final bosses from a video game, and refuses to say exactly which she is.
 * Negima likes this trope. Haruna uses this as a metaphor (also quoted above) for the fact that Nagi had multiple, progressively stronger enemies.
 * In the first season of Tenshi Ni Narumon, Dispell seems to be the Big Bad. It turns out, however, that he is literally a puppet of his "sidekick," Silky.
 * Mermaid Melody Pichi Pichi Pitch uses this in both its seasons; in fact, in the second season, it was effectively used three times,
 * Reached ridiculous heights in Digimon Adventure 02. The Digimon Emperor was the Disc One Final Boss under Arukennimon...who turned out to be reporting to Oikawa...who then got Hijacked By MaloMyotismon (BelialVamdemon). Oh, and then there was this guy called Daemon thrown in there somewhere, although he never received any plot resolution.
 * Played more realistically in Digimon Adventure 01 with Devimon, the Big Bad for the first quarter of the season - when he's defeated, he reveals that there are other, more powerful enemies out there (and gloats at how the heroes only barely defeated him).
 * Really, all Digimon-series have this. Tamers had the Devas, whose leader was ultimately revealed to be just a Well Intentioned Extremist fighting against the real enemy, the D-Reaper. Frontier had Cherubimon acting as the main antagonist for the majority of the series, then Lucemon showed up. Savers had Kurata, only once he was killed, Yggdrasil showed up...
 * Averted on Digimon Xros Wars where introduced villain Bagramon stays the main threat of the series until the very end, breaking the tradition.
 * In Higurashi no Naku Koro Ni, it seems that the curse of Oyashiro-sama is to blame for the main characters going crazy and the bloodshed that follows...Surprise!.
 * Naruto does this, where we find out that instead of, it's who is the true leader of , though it's slightly subverted in that this is revealed sometime before the former even begins to directly fight the heroes. Though the manga has turned this on its head too with the reveal that  leaving us to wonder who the Big Bad really is.
 * Orochimaru, the Big Bad in part 1, suffers Villain Decay after the Time Skip, due to the long-term side effects of, with both replacing him as the major threat to Konoha.
 * In Code Geass Suzaku of the Counterattack, this happens . The viewer expects Lelouch to be the villain, but.
 * Not to mention,.
 * In Yu Yu Hakusho, Zeru acts as the leader for Team Rokuyokai during the Dark Tournament. When Hiei kills him, Team Urameshi thinks they have the round in the bag, until the real leader shows up, killing two of the team's fodder in the process: Chu, who appears to be a joke of a fighter, but is in reality every bit as powerful, if not moreso, than Zeru.
 * The Big Bad of Slayers' first season seems to be, but its actually.
 * In the second season, Gaav is the Disc One Final Boss, who gets executed by the true Big Bad,.
 * Subverted in the third season with Valgaav, who seemingly gets killed off partway through. Just when it looks like Dark Star is the Big Bad,.
 * Zuuma in the fifth season.
 * And in the fourth season, Gioconda is the Disc One Final Boss to
 * In the Diamond Is Unbreakable arc of Jo Jos Bizarre Adventure, the story focuses on trying to get revenge on Red Hot Chili Pepper for killing Okuyaso's older brother. But he turns out to be far too dim-witted and easily beaten for a Jojo Big Bad. Say hello to Yoshikage Kira instead!
 * in Death Note.
 * In Sailor Moon R, Rubeus appears to be the Big Bad but it turns out midway that he was answering to Prince Diamond, who was being used by Wiseman who was the true Big Bad of the season and had been there since the start of the story arc.
 * Also, turns out to be this in the manga as it is outright stated (but only implied in the anime) that   Pretty intense.
 * in Tengen Toppa Gurren Lagann turns out to be this.
 * In Star Driver, was built up to be the Big Bad, but  hints at the fact that someone else is going to take up that role.
 * In Fairy Tail, just when
 * , the Bigger Bad of most of the series and the Big Bad of the Tenrou Island arc, is disposed of like garbage by right after his defeat.
 * In Rave Master,
 * In Yu-Gi-Oh Marik Ishtar is arguably this to himself. He's the Big Bad for most of Season 2, and while not an especially great duelist and something of a Dirty Coward, reveals himself to be an excellent Manipulative Bastard and plotter with well-developed Mind Rape capabilities. Than his Morality Chain, Rashid/Odion is rendered comatose, and he suffers a Split Personality Takeover by his Super Powered Evil Side, Dark Marik, who kicks normal Marik out of their shared body and takes over as the Big Bad of Seasons 2 & 3. In addition to being a better duelist than the original Marik, Dark Marik proves himself to be far more evil, as well as a Combat Sadomasochist and Blood Knight of the first order.
 * Agon Kongo was arguably one of these in Eyeshield Twenty One. From his very earliest appearance he was built up as the player to beat, and his team, the Shinryuuji Nagas were an undefeated juggernaut. At the Kantou Regionals it was expected that the Nagas, and Agon in particular, would plow through all the other teams and reach the finals as they had done for the last nine years running. Instead they go up against the protagonist's team, the Devil Bats, in the first match of the Regionals and are knocked out; Marco Reiji's Hakushuu Dinosaurs take over as the team to beat afterwards.
 * Shin from Fist of the North Star.
 * In Angel Beats Angel is initially set up as the main (and only) enemy of the SSS The really big twist however is the fact that she turns out to be

Comicbooks

 * in a Boba Fett miniseries released in 1998 (later collected in TPB format as Death, Lies, and Treachery. The real villain is.
 * in Gear., who initially appeared, at best, as an unimportant dupe in 's plans, turns out to be the real Big Bad.
 * In the Our Worlds at War DCU miniseries event, gets upstaged by  in the middle of the series.
 * "The Doctor" (aka Dr. Fu-Manchu) in the original volume of League of Extraordinary Gentlemen.
 * The Big Fat Kill, a Sin City miniseries, features Jerkass Jack Rafferty and his Mooks harassing Dwight McCarthy's girlfriend and then escaping to Old Town to cause more trouble. By the end of the first issue, you're left wondering what sort of craziness is going to go down once Dwight ends up between Jack and the girls of Old Town. What follows is a No Holds Barred Beatdown as Miho takes Jack apart in sadistic fashion. The conflict comes from the fact that, which leads to the real Big Bad,  , stepping in with Wallenquist's enforcers.

Fan Fiction

 * In Total Drama Battlegrounds, when Sandra was introduced, everyone thought she would be an even worse Manipulative Bitch, Alpha Bitch than Heather and then.
 * A Dark Knight Over Sin City starts with Batman tracking down the Yellow Bastard. Once he catches up to him,  It's soon clear that The Joker is the final boss.
 * Starkits Prophecy tries to set up TiggerStraw as it's Big Bad, with HolyLeaf as his dragon. Then
 * The Legend of Spyro a New Dawn begins with three Big Bads, Deadlock, Empress Tyrania, and Boss Kaze with Deadlock as the true main antagonist, but Tyrania and Kaze serve as the main villains for most of the first half, at which point they're killed off and Deadlock returns to being The Heavy.
 * The Pony POV Series begins with the Discorded Series, which like the series proper has Discord as the Big Bad. In the main timeline, he's defeated and sealed just like in the show, leading to the Reharmonizing Series, where who the main antagonist is gets a bit...Trickier.
 * In the "Origins" arc, one could argue that Discord's father Havoc serves this role.
 * In Naruto Veangance Revelaitons, about 20 chapters in, Naruto turns evil and helps kidnap Sakura for Madara, which seems as though it might be the climax. However, a mysterious Omniscient Council of Vagueness is introduced in the course of Ronan's attack on Madara's hideout, and serves as the main antagonists.
 * In With Strings Attached,  is revealed to be the Big Bad behind most of what happened to the four through the Second and Third Movements. However, after their indirect and unknowing defeat of him, he flees. All seems rosy, except that there's one more Movement to go, and   steps in to make things difficult for the four--proving to be worse in many ways, too. Unusual in that the two are in no way related, or even have any awareness of each other.
 * In the Azula Trilogy, General Azun is the first Big Bad, and is a very credible threat, a fanatic with a growing army of Fire Nation imperialists determined to restore the Fire Nation to its conquering ways. However, he is defeated at the climax of the first story, and the rest of the trilogy make it clear that he was just one Unwitting Pawn of many of the true Big Bad,.
 * Invader Zim the Series: Relationship Sue (and yes, that is her name) is the Big Bad of the story's first major Story Arc, but after her defeat at said arc's climax she disappears. By the time she returns, the Rogues Gallery has grown so large that she's just one antagonist among many, and eventually ends up Demoted to Dragon for, who establishes himself as the new Big Bad when he gathers most of the other antagonists into a Legion of Doom during the latter end of the story.

Films -- Live-Action

 * Star Wars:
 * The Phantom Menace ends with Yoda and Mace Windu wondering whether the Sith that Obi-Wan slew was the Big Bad or just a Disc One Final Boss. (The audience, having seen him taking orders from a man he calls "master" earlier in the film, knows the answer...and those that hadn't probably could've puzzled it out from the "Episode I" aspect.) However, the in-universe possibility they consider is that they had killed the Big Bad, meaning that the former Disc One Final Boss was now the new Big Bad.
 * Count Dooku and General Grievous are this for the first half of Revenge of the Sith.
 * Jabba the Hutt in Return of the Jedi.
 * The Big Bad in Last Action Hero appears to be the mob boss, with Benedict as his dragon. As the far more competent Benedict starts to figure out what's going on, he and becomes the real threat himself.
 * Especially tricky because the movie is almost over when he's finally taken down: is not the Big Bad of Paul Blart Mall Cop.  The new villain then gets taken down almost instantly.
 * In the classic Rankin/Bass Christmas special Santa Claus Is Comin to Town, the Winter Warlock is hyped up as a terribly powerful, evil being and set up as the villain. However, he is convinced into a Heel Face Turn by Santa in mid-film, and the dictator who had appeared toward the start of the film, Burgermeister Meisterburger, becomes the movie's Big Bad.
 * Betty in Kung Pow: Enter the Fist, with The Evil Council as the real Big Bad. Or at least they would, if the second film was ever made.
 * The first half of Home Alone 2 is mainly about Kevin trying to make sure the hotel staff doesn't wise up to the fact that he's staying in the hotel alone, but after they discover what he's up to and he escapes from the hotel, the rest of the movie involves his conflict with Harry and Marv.
 * Thor begins with the Frost Giants invading Asgard. Thor goes to their king, Laufey, believing he was behind the attacks. It is soon revealed that there is a traitor in Asgard and that Laufey was in cohoots with him. The rest of the movie deals with this character as the Big Bad while Laufey disappears for much of the action.
 * In Gremlins 2 the gremlin Mohawk, who's been pretty non-interested in leading the other gremlins throughout much of the film, gets killed while the greater part of his brethren are still creating mayhem. The Brain Gremlin effectively assumed his place beforehand.
 * Kill Bill has O-Ren Ishii as literally the last boss of "disc 1" (volume 1). In true ironic Tarantino scene order, she's actually the first of the main victims of the bride in the storyline.

Literature

 * Mistborn combines this one with Well Intentioned Extremist and, of all things, Big Good..
 * Depending on how the Alloy of Law era books go, seeing as has been, the final Big Bad may end up being that of the overarching Cosmere,.
 * Thought Tywin Lannister was going to be the main antagonist of A Song of Ice and Fire? Nope! It's actually shaping up to be.
 * All the plotlines of Kitty Takes a Holiday seemed to be wrapped up after the apparent Big Bad is killed. But  that takes up the last third of the book.
 * New Jedi Order gives us every character who looks like a Big Bad. The Man Behind the Man?
 * In order, the major bosses go: Prefect Da'Gara, Commander Shedao Shai, Supreme Commander Nas Choka, Warmaster Tsavong Lah, Supreme Overlord Shimrra, and finally  . Nom Anor breaks the pattern- while never technically in charge, he bedevils the heroes across the series and is the most visible and developed villain.
 * Salamander initially sets up Maridon and his pawn Coelus as the villains. By a third of the way through, Maridon is dead and Coelus has gone from Reluctant Mad Scientist to The Lancer.
 * In Warrior Cats, Brokenstar at first seems to be the Big Bad, but then Ravenpaw reveals Tigerclaw is evil. Later, Tigerclaw becomes Tigerstar, and Firestar sets out to defeat him. The stakes are set for an epic battle at Fourtrees...
 * Also in Warrior Cats: Power of Three, at first it seems  However, in Eclipse,   He's on the cover of Long Shadows and the blurb only talks about him. Also,   But then,   Then he gets hijacked by   So then Hollyleaf says that   So the heroes spend Sunrise on a journey to   And finally, we find out the final real not fake this time big bad. Who is it?
 * The first book of The Wheel of Time introduces the reader to an enigmatic, powerful figure who goes by Ba'alzamon, one of the lesser-known names of the Dark One, with every implication that he's the Big Bad. At the end of the third book (of fourteen) he's killed off, and it's revealed that he's not and never was the Dark One but rather his Dragon Ishamael, who'd been using one of his boss's names to rally his followers and hunt down his enemies. The real, far more powerful, Dark One is still out there, and as of the second half of the series Ishamael is Back From the Dead too in a new body, now going by Moridin- but no longer presenting himself as Big Bad.
 * After Ba'alzamon's death, the series gets a second Disc One Final Boss (Disc Two Final Boss?) in the form of Sammael, one of the Forsaken who uses trickery to get himself set up as de facto ruler of a powerful nation, allowing him to take over the role of the most visible villain. He holds the title for several books, but gets defeated by the midpoint of the series.
 * Wizard's First Rule, the first book of the Sword of Truth Series, ends with the the defeat of Darken Rahl, the worst guy anybody knows. Then come 10 more books that gradually reveal and portray Richard's struggle against a much worse enemy:
 * The Voyage of the Jerle Shannara has Antrax who essentially takes over as the Big Bad of the middle book in the series, and is then killed off. Uhl Belk and The Wisteron from The Heritage of Shannara might also count.

Live-Action TV

 * 24 begins each season with henchmen taking orders from a boss, who reports to yet another boss, and so on until we meet a boss of sufficient charisma to drive the rest of the season.
 * And then sometimes, that boss will report to someone from the NEXT season, and it goes on and on and on...
 * Emperor Gruumm is played as the main villain of Power Rangers SPD for the first half of the series, then starts making veiled references to a "Magnificence" which he worships. Only in the final episode is this revealed to be "Omni", a giant malevolent brain which Grumm has been secretly serving as lieutenant.
 * "Veiled" is being nice. "Confusing" is more accurate, considering half the time Grumm implies that the Magnificence is a Doomsday Device he's building, not a person. You get the impression that the writers couldn't figure out what he was talking about either until the last two episodes.
 * There's also several instances of the Big Bad not being the Big Bad, but getting taken out about 1/3 of the way through the season. Diabolico and Morticon were this way. If the main villain is defeated too early in the series, sometimes he gets better, but sometimes someone else comes along. And sometimes someone else comes along, and disc one boss gets better later.
 * The third season of Burn Notice sets up
 * Avoided in Babylon 5 -- just six episodes into the fourth season, the Shadows are persuaded to leave the galaxy and never come back. "Aha," the audience thinks, "we've only just started the season, so we must see them again at some point." No, we don't. They really are gone. Much of the rest of the series deals with cleaning up what they left behind.
 * The Buffy fandom refers to these guys as "Little Bads". They show up early on during the season and cause a great deal of trouble for Buffy and crew, but get incapacitated or killed off sometime after the season's midpoint, after which the real Big Bad takes center stage.
 * Spike and Drusilla cause the main trouble of early season two. Spike reappears crippled in episode 13, and in the very next episode, Buffy and Angel have their little moment of romance, which triggers Angel's Curse Escape Clause and results in the reemergence of Angelus, who becomes the Big Bad for the rest of the season.
 * Mr. Trick in the third season is more of a fake Dragon. He joins up with The Mayor shortly after his arrival in Sunnydale, but is killed by Faith, who takes over his position with the Mayor.
 * In season 4, Dr. Walsh and the Initiative filled the early villain role, though Dr. Walsh wasn't actually out to get Buffy until she became too much of a threat to the Initiative's plans. Then episode 13 comes along in which Walsh betrays Buffy and is subsequently killed off by the true Big Bad, Adam.
 * In the 6th season, Warren and his two cohorts appear to be the Big Bad for the season...right up until Warren shoots through a second-floor window while trying to kill Buffy, and the bullet meant for her kills Willow's girlfriend Tara instead. This proves to be a colossal mistake.
 * In an example that doesn't follow the formula, in the first episode of the 5th season of Buffy the Vampire Slayer, Dracula is introduced in such a way to make it appear that he'll be a major force in the season, especially with his ability to reform after being killed...then leaves Sunnydale forever at the end of the episode. The actual Big Bad, Glory, shows up in episode 5.
 * In a particularly elegant example of misdirection, the entire ad campaign that had been running in the weeks leading up to the premiere played up Dracula as the season's Big Bad.
 * Cross-promotion with the Vlad miniseries on a neighboring station owned by the same conglomerate.
 * The Beast from Angel appeared to be the major force of destruction that all the prophecies warned about, and it took the characters quite a while to figure out that it was working for a supernatural being more powerful than itself -- and longer still to figure out the identity of this more powerful Big Bad.
 * In fact, the Beast even manages to be a Disc One Final Boss to ITSELF..
 * Lost: At first it looks like Tom Friendly was the show's Big Bad, only to have him be reduced to the role of The Brute in the Others' Five Bad Band under supposed Big Bad Benjamin Linus, who in-turn was the alleged Dragon to Jacob. Jacob, it turns out is actually, and . Other pretenders to the Big Bad throne include Charles Widmore, Alvar Hanso, and Richard Alpert.
 * D. Gibbons/Dyson Frost on FlashForward..
 * In Tensou Sentai Goseiger, there are three Disk One Final Bosses. The first is Warstar, the next is the Yuumajuu, and the final one is Matrintis..
 * Similarly, in Hyakujuu Sentai Gaoranger, three Highness Dukes each take their turn at the top of the Org hierarchy.
 * Ninja Sentai Kakuranger has Young Noble Junior/Gasha Skull, prince of the Youkai Army Corps. He's killed about three fifths of the way in, and his death provides the last bit of power needed to release the seal trapping his father Daimaou (Arch Demon), the true Big Bad.
 * The Doctor Who serial The War Games has a series of villains of increasing threat, but once the War Chief shows up you're sure it's him...and then the Time Lords execute and exile the Doctor.
 * The Invasion of Time is a particularly effective example. The serial deals with the Doctor's fight against the Vardans, which plays out over four episodes (the most common length of a serial) and reaches a clear conclusion at the end of episode four with a typical final scene full of goodbyes, when suddenly, and the serial continues for an additional two episodes.
 * In the episode "The Long Game", the evil owners of Satellite Five are destroyed, with the implication that mankind's development will speed up after the Editor and the Mighty Jagrafess stunted it. Instead, it's learnt the Daleks have been manipulating the Earth, with the antagonists of the episode being just a small step, causing the planet to fall into depression, transporting humans to deadly game shows. The Daleks make themselves known when the Doctor is taken back to Satellite Five 100 years and five episodes later in "Bad Wolf".
 * Smallville: Slade Wilson is a General Ripper who causes serious problems for the main cast in the first half of Season 10, leading the Vigilante Registration Agency in its attempts to force Superheroes to comply with the VRA's dictates. He kidnaps members of the Justice League and subjects them to Cold Blooded Torture, nearly kills Clark with Kryptonite, and . Yet despite this list of achievements he's still the Unwitting Pawn of Darkseid and his defeat marks the foiling of only a part of the true Big Bad's plans.
 * Both Brainiac and Lex fill this role in Season 8. They're both major villains from previous seasons who return to the show after a huge plot build-up, inflicting massive damage in the process. Brainiac drives most of the plot in the first half of the season, before being defeated in episode 11. Then, just as everyone is getting their breathing back to normal, Lex remerges, permanently ruining Clark and Lana's relationship and nearly taking half of Metropolis with him before being uncerimoniously blown up by Oliver. It's shortly afterwards that the real Final Boss emerges: Doomsday, whom both had considered little more than a pawn.
 * And season 10 has another example right at the beginning: while Clark is hovering between life and death after his battle with Zod in the previous season finale, Jor-El warns him of a coming evil, and he has a vision of what appears to be Lex. Returning to life, he is then confronted by a demented, deformed clone of Lex, who he quickly defeats - only to find out that Jor-El didn't give a damn about the clone. He was talking about Darkseid.
 * Lionel Luthor is this in Season 4. Having gone to prison at the end of Season 3, he spends the first half of Season 4 screwing with the cast from behind bars. After his release, one would expect him to pick-up where he left off. Instead he makes an attempt at going straight, and Geneveive Teague takes over as Big Bad.
 * Supernatural: Crowley, having become  during the Time Skip between Seasons Five and Six, seems set up to take over the role of Big Bad. However, halfway through the season,  . Now, the role of Big Bad seems to be falling to the newly introduced being known as "The Mother of All".
 * However, in "Mommy Dearest", just a few episodes before the season finale
 * And then, in the season finale, it turns out that
 * In Kamen Rider OOO, had pretty much been the main villain most of the series, and if not him, then the Greeed as a whole.
 * A very common trope in Survivor, due to the way the game can play out. Editing can sometimes mislead the viewer into thinking that a character will be important and/or unstoppable, only to be either a) taken out by a twist, b) taken out by the even bigger threat, or c) their tribe has enough of them and decides to get rid of them:
 * Silas Gaither in Africa, the leader of the Samburu, controlled the game after eliminating tribal leader Carl, and him and his "Mallrat" alliance, made up of younger and lazier kids, were the most despised group at that point on the show as they picked off the older members. Then comes the first ever Tribal Swap, sending Silas and the last two remaining elders over to Boran, where everyone hated him enough to throw the immunity challenge and vote him out.
 * Boston Rob filled this role in Marquesas. He was a fairly strong strategist before the merge, and once the merge started he continued to strategize by trying topple the other strategic mastermind John by planting seeds of dissent in the heads of John's alliance-mates Kathy and Zoe. His attempts backfired and got him voted out...but not for nothing: in the next episode his remaining alliance-mates convinced Kathy along with outsiders Paschal and Neleh to join together and vote against John.
 * Shawn in Pearl Islands, at least for Jonny Fairplay. When Rupert, Christa and Sandra are forced to chose between keeping Fairplay or Shawn for the merge, they chose Fairplay over Shawn since he's "more trustworthy". Fittingly, Fairplay signs his vote for Shawn with a "F#%k You!".
 * "Rocky" in Fiji. He was disliked for his bossy and rude attitude but survived because he was strong despite being on the Can't Catch Up tribe. He even survives over the much more likable Anthony because he was strong and could possibly win them the much-needed immunity. Through a combination of twists (Lisi being sent to exile and would join the tribe that lost immunity, making them break even) and tribal switches, and with the merge just around the corner, his tribe finally decides they had enough.
 * Jaime Dugan in China. She masterminds the elimination of one of Fei Long's strongest members, but then gets the Humiliation Conga edit after mistaking a wooden tile for a hidden immunity idol and being blindsided at the merge.
 * Ace Gordon was the master strategist of Gabon...at least until Fang's last Tribal Council. Thanks to some quick thinking by the eventual villain Kenny, he and Crystal managed to flip Sugar onto their side by convincing her Ace was only using her for her hidden immunity idol. At a 5 person tribal council, Ace is sent home 3-2 over Crystal.
 * Brendan Synnott appeared to have Tocantins in hand...until the first post-merge Tribal Council. Because he mishandled allies Taj and Stephen - who he'd joined up with during the stays at Exile Island - they along with J.T. joined up with Coach's "Warrior Alliance" and blindsided Brendan, getting rid of his idol in the process.
 * Boston Rob again in Heroes vs. Villains - when Coach sits on the fence when the Russell/Rob feud reaches its climax, his indecision allows Jerri to flip and gets Rob voted out 4-3-1 only one Tribal Council before the merge.
 * A Dual Boss of sorts in Nicaragua - Marty Piombo and Brenda Lowe were both the huge power players of the season, eliminated one after the other after the merge. Marty is eliminated when Jane finally convinces the majority to get rid of him after slandering her at the previous tribal council, and Brenda is voted out next Tribal Council when everyone realises how powerful she's become and don't want her to get any further.
 * One World features maybe the epitome of this trope in the context of Survivor in Colton Cumbie, a Camp Gay Smug Snake Manipulative Bastard Ascended Fanboy who, over the course of the pre-merge portion of the game, took control of his tribe, acquired a Hidden Immunity Idol, was the focal point of much of the editing and looked poised to be one of the most loathsome villains the show has ever seen... and then he got appendicitis and had to be medivaced from the game, after which point the tribes merged.
 * The Vampire Diaries does this in season 2 when most people thought Katherine was the main villain. It was actually the top vampire Klaus.
 * In the first season finale of Merlin, Arthur and Merlin go up against the Questing Beast. Merlin kills it before the ten minute mark, and the rest of the episode revolves around the fatal wound that it delivers to Arthur.
 * True Blood did this in their second season. The main plot of the season seemed to revolve around Sookie, Eric and Bill rescuing Godric from religious fanatics in Dallas. When they finally invaded the Fellowship of the Sun's church mid-season, they had a face to face with Reverend Steve Newlin.. but he is defeated rather easily and moreover, Godric manages to pull off a peaceful resolution. Returning to Bon Temps, Sookie and Jason found it to be overtaken with people acting like idiots.. only to discover that Maryann Forrester, a seemingly innocent social worker who was introduced in season 1, was a bloodthirsty maenad hellbent on cutting out the heart of Sookie's boss and friend Sam Merlotte. Maryann's defeat didn't come until the final episode of the season, subsequently.

Videogames

 * In Mario & Luigi: Superstar Saga, you defeat the Big Bad, Cackletta, halfway through the game. However,
 * The King of Fighters 2001 reveals that the Zero fought in the previous game was actually a stand-in for the real Zero that is fought in 2001.
 * And once you beat Zero in 2001, his boss Igniz appears...who then kills his own boss to remind you that Igniz is indeed the SNK Boss.
 * Used in several Final Fantasy games.
 * Final Fantasy III. You play through an entire world, discover it's a floating island, find a land frozen in time, battle your way through everything Xande, the guy responsible for all the misfortune in the world, could throw at you. You fight through 2 dungeons before you can reach him, without save points along the way,
 * Final Fantasy IV. For much of the game, Golbez seems like he'll be the Big Bad,.
 * Final Fantasy V: Some people were fooled into thinking that the fight against was the final battle, despite the 12 legendary weapons having not been unlocked yet.
 * Emperor Gestahl in Final Fantasy VI.
 * Kefka is a subversion (double subversion?), since he starts out as an underling for Gestahl and is faced several times early in the game. He even gets defeated pretty easily near the end of what might pass for Disk One.
 * President Shinra in Final Fantasy VII, who.
 * Another example from Final Fantasy VII is when Sephiroth is set up as a Disc One Final Boss because Its Personal, he has been hunted into the extremely bleak Impact Crater where Jenova first came to the planet and everything is set up for an epic Boss Battle, ending in the foul villain's much deserved death, and presumably The Reveal of the Man Behind the Man, because you're still only at the middle of Disc 2 out of 3. . The story goes on after a two-week Time Skip, which somehow manages to make everything even worse.
 * A more literal version would be the fight against JENOVA-Life immediately after Aerith gets stabbed through the chest with a seven-foot katana.
 * In Final Fantasy VII Advent Children Kadaj is the leader of the Remnants of Sephiroth, a trio composed of himself and his brothers, Yazoo and Loz. He spends the entire film antagonising Cloud Strife and Rufus Shinra, enacting one scheme after another to try and find Jenova's remaining cells and achieve reunion with her. Finally, he faces Cloud in a Sword Fight and after being defeated opens the box containing Jenova--and is promptly replaced by Sephiroth, who was manipulating Kadaj as part of his plan to come back from the dead.
 * The Sorceress Edea in Final Fantasy VIII, who's the boss of Discs 1&2, but then turns out to be just a puppet for something far worse. She later joins the heroes as an ally, sans most of her superpowers.
 * This is sort of arguable. Ultimecia is still the villain all the way through. The twist is Edea's past/identity and the possession - there's not really an actual villain change since everything 'Edea' said and did in the first 2 discs was still Ultimecia.
 * ...and again in Final Fantasy IX, with Queen Brahne who is -- as usual -- killed by Kuja, who'd previously seemed to be The Dragon. Of course, he's a White Haired Pretty Boy, so she really should've seen it coming...
 * Happens up to three times in FFIX, in fact, since Kuja himself is then set up to be a Disc One Final Boss when he's revealed to be working for Chessmaster Garland...and then subverted  And AGAIN,
 * And Beatrix, the literal final boss of disc one.
 * However, this trope was actually subverted by Final Fantasy I, in which the first boss, the original Garland, turns out to be the vessel of the Big Bad, Chaos.
 * Square loves this a lot. In Final Fantasy XI
 * The little known Game Boy title Final Fantasy Adventure (which is actually part of the Secret of Mana series) features an obvious Big Bad simply named "Dark Lord" and his Dragon Julius. Unexpectedly, not only does the player face off with Dark Lord at the halfway point of the game, he's not even challenging. The Big Bad turns out to be Julius after all.
 * Diablo II was divided in four acts. One final boss per act. And in act II, the NPC insisted that you may come in time to destroy Diablo. If you count the extension, Diablo himself was the penultimate boss.
 * Dragon Quest III was perhaps the first to do this, and one of the only ones to do it convincingly. After the entire world so far is explored, the apparent Big Bad, Baramos, is destroyed, and the apparent ending has started...the real Big Bad, Zoma, shows up from his home in the Hollow Earth and seeks vengeance for his defeated Dragon, requiring the hero to go into the Hollow Earth after him.
 * Dragon Quest II had The Man Behind the Man Malroth, and Dragon Quest had (in Japanese) the Dragonlord's pet dragon, which became your standard One Winged Angel in the English version.
 * Dragon Quest VII was very convincing as well; after you've recreated the entire world, you finally go to face the Demonlord. After a big battle, you beat him, so now you can resurrect God and get to the ending...
 * Dragon Quest VIII featured a villain Dhoulmagus who stole a magical sceptre and went around killing people. After chasing him all over the world and going through a rather difficult boss battle, it turns out the sceptre made him do it, and the game is less than half over -- now you have to go after the real Big Bad, a Sealed Evil in A Can named Rhapthorne.
 * Dragon Quest IX has King Godwyn, ruler of The Empire. He has all the trappings of a Big Bad: A fancy, foreboding dungeon, extremely powerful monsters and minibosses, and even a One Winged Angel form. Surely, he's the main villain, right?
 * Unfortunately, he does a poor job of hiding this. He isn't even mentioned until shortly before you meet him, where he takes credit for only the most recent plot developments. A single glance at his castle tells you that
 * Dragon Age 2 is an interesting example. It spans three time periods, each with their final boss. However, no one in their right mind would actually think something as bland as the Rock Wraith was the final boss...and they'd be right. It's genuinely surprising, then, for people taken in by the marketing, that the leader of the strange race of grey-skinned horned men, the Qunari Arishok, isn't the final boss. If you look carefully, however, you can see all the hints the developers planted towards the real Final Boss...
 * Legend of Dragoon does this multiple times. It starts with (arguably) Fruegel, then Emporer Doel, the literal Final Boss of Disc1- of 4. Then you persue the man who'd been maniputating Doel accross two more contries where he unleashes similar manipultions before taking him down around 2/3 of the way through Disc3, though he is still the final boss of that disc as the rest of it is devoted to revealing the identity of the man he had been working for, where to find him, and what his plot is. Furthermore, this man turns out not to be the man he said he was when he takes off the mask he was wearing, nor is he the man he looked like under it, since he was actually possessed by somebody else entirely.
 * Batman Arkham City has The Joker (and his hidden Dragon ) pop up again once the Big Bad, Hugo Strange has been taken care of. Unlike most examples of the trope, however, going after Joker was mentioned as a necessity beforehand (due to his kidnap of one of Batman's allies.)
 * In Baten Kaitos Origins, you spend about 78% of the game fighting the sinister Lord Baelheit (and another 20% being Mental Time Travel in which you fight against Wiseman, an apparently unrelated villain millenia in the past). Then, in the last hour of the game, you
 * Eternal Wings has.
 * Inverted in Overlord where you discover at the end of the game
 * Happens roughly a million bajillion times in Tales of Symphonia, which was made of Your Princess Is in Another Castle. Particularly with Remiel. While you know that Lord Forcystus isn't a final boss by any means, you literally do fight him at the end of Disc 1 (Symphonia uses two discs on Game Cube).
 * Vesperia has it too, with the second part concluding with an epic battle against The Man Behind the Man, . In fact, this boss is easily the most evil character in the entire game; in comparison, the final boss is just misguided.
 * The giant living brain Agathos in Adventures Of Rad Gravity. After you beat him, he returns to human form, and reveals that
 * Oddly enough, shows up in Bomberman 64. Altair is hyped up for the entire game to be the Big Bad, except if you've gotten all of the Gold Cards. If you do that, instead of fleeing after you've beaten him,  After that, all of the hint-givers in the previous levels tell you that you should die because it would be easier.
 * In Might and Magic IV, the Big Bad is Lord Xeen, who is only able to be harmed with a special weapon and can eradicate you at a touch. Once you kill him, another Big Bad shows up and proclaims you have defeated his general. Cue sequel.
 * Actually, both Might and Magic IV and V when installed combine into a larger game called "World of Xeen" where it turns out both respective games' villains are actually pawns of
 * Anyone who's not Wily in the Mega Man series,
 * Anyone who's not Sigma in the Mega Man X series,
 * Fortunately the Mega Man Zero and ZX series kept it fresh with each game.
 * Castlevania, particularly the Metroidvania-era games, is a big fan of this one, with the twist that frequently, the Fake Boss can be the final boss, depending on what you've managed to do throughout the game. This being a videogame series about the eternal war with a certain vampire, however, the Disc One Final Boss tends to be hijacked by Dracula when you do things right.
 * Symphony of the Night: Alucard's final foe appears to be, and if he's defeated normally, Alucard gives a solemn monologue and a Downer Ending. If he puts on a certain piece of equipment, though, he can see that his foe
 * Aria of Sorrow: Graham Jones inherits the powers of Dracula, and has an epic battle with Soma. If Soma defeats him normally, the game ends with Soma and his friends escaping the castle, but with him getting a strange feeling. If Soma equips three certain souls, however, and defeats Graham,
 * Dawn of Sorrow: The game ends rather anticlimactically if Soma just defeats Dario straight-on, with the other cult members escaping the castle and Soma getting another weird feeling as he leaves. If he gets another certain soul, however, he can After a long series of events that result from this, he eventually goes to The Very Definitely Final Dungeon and does battle with
 * Portrait of Ruin: If Jonathan and Charlotte beat the vampire sisters head-on, Brauner stops them and flees the castle with them, leaving 's wish unfulfilled and sending the duo on what would likely be a country-wide hunt for the vampire and his hostages.
 * Order of Ecclesia: If Shanoa defeats Albus without having saved all the villagers, she goes home with all the Dominus glyphs for the ritual . If she does manage to save all the villagers,
 * Castlevania 64: Used on two different occasions during the game. The first example is the Behemoth encountered in the Castle Center, which uses the same battle theme as the final boss. The second is atop the final stage, which has a unique battle theme to himself. Notably, both of these Disc One Final Bosses can become the game's final boss by either playing the game on Easy Mode for the Behemoth, or for, by taking too long to reach the final stage.
 * Lords of Shadow: Gabriel spends over 75% the game adventuring, fighting, and 'taming' monsters, all to defeat the three Dark Sides of the Holy Order and claim their ressurection powers. When he defeats what seems to be the final darkside, a personification of Death,  Gabriel
 * Basically, if Dracula isn't declared in charge from the get-go, the villain's plan will usually involve reviving him and/or taking Dracula's powers. Dracula worshippers hoping to revive the dark lord get exactly what they wanted. Dracula ursurpers, not usually so lucky. Either way, they're demoted to Disc One Final Boss or The Dragon in the process.
 * In Prince of Persia: Warrior Within and the ensueing boss battle takes place. The fake aspect is that this battle occurs halfway through the game and the Prince's troubles don't dissapear afterwards.
 * Legend of Legaia pulls two of these.
 * The 5th Strong Bads Cool Game for Attractive People installment: 8-Bit is Enough, has a fake final boss against the supposedly invulnerable Trogdor; who gets defeated with a single slash, emitting final words of "I could not handle your style!". Even Strong Bad himself concedes that it was easier than expected. Cue walls coming down and Ultimate Trogdor appearing.
 * Banjo Kazooie led to you believe that the final showdown with the Big Bad, Gruntilda, is a quirky board game/quiz show where you test your memory about the game and run through a few minigames. After you beat it, she skedaddles, Banjo and Kazooie rescue Tooty, and the whole gang goes back home for some well-earned rest and relaxation. The credits roll...and as soon as they're done, Banjo and friends are shown busy throwing a party when Tooty pops up and tells Banjo to get back out there and finish off Grunty. What ensues is probably the most epic final boss battle in the history of the N64.
 * Lampshaded in the sequel when Grunty does the same thing, but after the quiz, Grunty has no idea what to do next, so Kazooie suggests that she run off again like in the last game before they beat her up. The next game has a challenge that feels very much like the ending: you have to incorporate pretty much every different aspect of the vehicles you've built before into one multitasker, complete with mid-challenge quiz (as featured in Banjo-Tooie). Once you beat it Grunty requests a final battle, although it can easily be won using overwhelming firepower.
 * Happens a lot in The Legend of Zelda games:
 * to  in A Link to the Past.
 * , to  in Majora's Mask.
 * in Oracle of Seasons, and  in Oracle of Ages, are fake bosses to , who are also fake bosses to.
 * in The Legend of Zelda Twilight Princess, to
 * to  in The Legend of Zelda Skyward Sword.
 * Okami features two very convincing instances of this with Orochi and Ninetails. Both of them are heavily foreshadowed and reside in their very own big honking evil lairs, each of which constitutes a Point of No Return and has its own ridiculously dramatic lead up sequence. Of course, the fact that Ammy hasn't learned all of the skills necessary to restore her godhood and there's a lot of empty space on your weapons screen should be a dead giveaway to the status of these (admittedly imposing) nasties.
 * Considering that you have twelve of the skills by the time you face Ninetails and Issun making a comment about how their adventure is almost over, it was fairly believable.  However, there's still empty space on the weapon screen, sooooo...
 * Done even more convincingly in Okamiden. You've got all the brush techniques, all the divine instruments (bar the one you get for New Game Plus), and the dungeon does what is probably a first for the genre: it comes in 2 parts. The threat level is high as well, King Fury has a Humongous Mecha Moon Rabbit that will destroy Nippon. You beat King Fury, and hey, who's this guy called Akuro?
 * A becomes bit of a recursive subversion too:
 * Jade Empire has perhaps too many of them, from Gao the Greater as the boss of the river town to Death's Hand as the first apparent Big Bad, then through Sun Hai as the second apparent Big Bad and Sun Li the Evil Mentor as the actual final boss.
 * In Bioshock, Jack battles his way to the apartment of  in order to kill him, only for   Only then does poor Jack realize that
 * Maleficent is not, in fact, the last boss in Kingdom Hearts, despite what everything up until that point has led you to believe.
 * To tell the truth, the whole Ansem part had been added at the last moment, because the staff was thinking the scenario was too simple and would offend the FF fans. It didn't stop them.
 * In 358/2 Days, is not the last boss, despite having all the trappings of one. No, there's still an epilogue chapter, with the true (and less challenging) final boss fight with, as you re-enact the Deep Dive trailer.
 * In Coded, likewise is a Sequential Boss which behaves very much like the final boss. However, the final boss of the game is actually.
 * Metroid has the Mother Brain, a Load Bearing Boss with its own final dungeon. After the escape from the exploding dungeon you are treated with victory music and a victory cutscene! ...As long as the game in question wasn't the Zero Mission version, in which it quickly turns sour as your escape ship falls under attack and you lose all your equipment and have to work through part of the Very Definitely Final Dungeon without it.
 * Due to the branching storypaths, most villains in the Nasuverse will fall under this.
 * Tsukihime: In the near-side routes, Nrvnqsr plays this role before Roa takes the stage. SHIKI is quietly killed off and replaced by Akiha in Kohaku's route, which is the last one.
 * Fate/zero quietly shoves Tokiomi Tohsaka, Rin's father and they guy everyone expected to be a very serious contender, to the side and Kotomine takes his Servant.
 * Fate/stay night: In the Fate route, Berserker is this, and in Unlimited Blade Works, Caster is the disc one while is the disc two. In both routes, Gilgamesh is the True Final Boss, and in Heaven's Feel Zouken makes it to the end, at which point Sakura effortlessly destroys him and True Assassin. She also ate Gilgamesh about halfway through. Nom nom nom. The two big fights are against Sakura herself, the love interest, and Kotomine, who really ought to be dead. Obviously, he isn't because that wouldn't be interesting enough.
 * Played with in Kara no Kyoukai, where Souren Araya really was the Big Bad, and was killed off in Movie 5. The two remaining movies explore loose plot threads and places as Araya's final pawn and the last threat to Shiki.
 * Throughout Guild Wars Nightfall, you're trying to stop Varesh Ossa from completing her final ritual to release her god, Abaddon. The game even does a good job of disguising the mission where you confront Varesh as the final mission before pulling a Your Princess Is in Another Castle in the ending cutscene: Varesh's rituals weakened Abaddon's prison enough that he can punch through unless you take the fight to him.
 * Chrono Cross is clearly building you to take on Lynx/ and Fate itself, whatever that may be. The final boss is something of a Giant Space Flea From Nowhere because while Lavos is mentioned a couple times, it never does anything throughout the entire game.
 * Speaking of the Chrono series, Chrono Trigger deserves a mention. Crono and company ventures into 600 AD to stop Magus from summoning Lavos and to stop it from raining destruction upon their future. It turns out that Magus was only trying to summon Lavos to kill it himself. Queen Zeal, on the other hand. wanted Lavos's power.
 * Somewhat subverted as Lavos is predicatably the Big Bad of the game and everyone is its genetic livestock.
 * This happens a couple of times in the Wild Arms series, but the most infamous example is probably in the third game, when the party finishes Part 3 by fighting against the Blue Menace,, that had been foreshadowed the entire game. When the epic battle with him is concluded, the game goes into Part 4, which is only a few hours long and introduces, and puts an end to,
 * Wild Arms 2 does this with Vinsfeld, who is literally the final boss of disc one. Defeating him even brings a full and concrete end to his plans, allowing for a completely unrelated and not even foreshadowed threat to become the focus of disc two.
 * The Monster Scout Championship Finals in Dragon Quest Monsters: Joker. Interestingly, the game doesn't play it as a twist. Your suppossed goal is to win the championship, but from the very start it's apparent that behind-the-scenes intrigue and the Incarnus' mission are guiding the plot.
 * Disgaea 3 Absence of Justice makes a big deal of how the final boss is going to be, but it turns out  However, you can actually beat the "fake boss" on a second playthrough and get a secret ending.
 * And in Disgaea Hour of Darkness, you go through the whole game believing that the final boss will be, only to find out at the end there's still one more battle...not to mention, Vyers/Mid Boss is a parody of this.
 * In Prototype, the game is not over when you kill . To be sure, the infection slackens off considerably when you do, but there's still Blackwatch to deal with.
 * In The World Ends With You, everything in the game seems to build up to it being done when you defeat . After all, it's . However, after defeating him, . Finished? OH NO.
 * Lord Darin from Fire Emblem 7 is by far the most direct opponent for the first half of the game, and when you finally face him on the battlefield it's in what can only be described as The Very Definitely Final Dungeon: the gate where dragons were thrown out of the world, and through which the Black Cloaks plan to let them back in. Though this is somewhat of a subversion as you know Darin is not the Big Bad by this point, it still plays out like the end of the game: after defeating Darin, you meet the real Big Bad, learn his evil plan, stop his evil plan, which proceeds to go quite literally nuclear, annihilating the Complete Monster in the process, and rescue the Mysterious Waif. Then, your Disappeared Dad, who had been used as an Unwitting Pawn to provoke a war, knifes the Big Bad in the back before dying himself and leaving you heir to the province he rules. Everything seems pretty adequately resolved and- wait, what? Chapter 20?
 * Before the main story, you play through Lyn's Story, whose villain is Lundgren, the scheming power-hungry great-uncle of Lyn. Every chapter builds him up to villain status, including Kick the Dog moments and earning Complete Monster status, culminating in finally getting to kick his ass in the story's Final Chapter. Afterwards, the main story starts proper.
 * Emperor Vigarde is sorta-kinda played as the Big Bad of Fire Emblem 8, being responsible for the war you're trying to end - I say 'sort of', because you only get to fight him on one of the two main characters' different routes. Not that you've defeated all the evil Generals yet, but assuming you played Ephraim's route first, it ends when you DO defeat him and he...vanishes? Turns out the Emperor was really Dead All Along, and his son Lyon is the one that started the war - and Lyon is himself possessed by the Demon King, the true Big Bad of the game.
 * Radiant Dawn loves this trope, considering that it's split into four different parts, each one with different baddies. The first part has the the second part has  the third part  and the fourth part has
 * Ace Attorney Investigations: Miles Edgeworth sets up Case 5
 * In the fourth case of the first Phoenix Wright Ace Attorney game, you manage to expose the true murderer of Robert Hammond,, and when everything seems to be over, , and you have to find the true murderer from that incident.
 * Pokémon has arguably been pulling this since Pokémon Red and Blue, when the final boss was not the final member and leader of the Elite Four, but the Champion that had previously defeated him and won the title. Fifteen years after the games were first released, though, no one is surprised by it anymore.
 * In Pokémon Gold and Silver, the champion himself is an example of this trope. After the build up of the eight gyms and Elite Four, you'd think this was the end...but after you beat him, you can visit the setting of Red and Blue, complete with all eight gyms still intact. After this, you'd think the sixteenth gym leader would be the final boss...but there's still one more boss to face: Red, the player character from the original games.
 * Bonus points for having the Champion and sixteenth gym leader be.
 * from Pokémon Mystery Dungeon Explorers of Time/Darkness/Sky. The game's real final boss is.
 * And the postgame of Red and Blue features a new mon you haven't faced before, though if you still have your Master Ball, he's an Anticlimax Boss more than anything.
 * General Scales in Star Fox Adventures.
 * The beginning of Assault plays up Andrew Oikonny to be the main villain only for him to get shot down by the real antagonists, the Aparoids.
 * The NES Ninja Gaiden trilogy has this for the second and third games. In II, Then in III,
 * In the original Time Crisis, after saving Rachel from the Big Bad Sherudo, The Dragon, Wild Dog, kidnaps her and becomes the True Final Boss.
 * In Arcanum of Steamworks and Magick Obscura, you finally corner ultimate evil devil-figure Arronax within the prison dimension he's on the verge of escaping from to lay waste to the world.
 * The first three sectors of Iji set you up to find Krotera, who you fight as soon as you see. Of course, that's all to set up the arrival of.
 * Persona 4 has a variation on this trope, in that the game's story is a murder mystery, so
 * Later on, there's a Disc Two Final Boss, in the form of.
 * Star Ocean Till the End of Time has the Vendeeni, The entire first disc you have four goals unrelated to the idiots of Elicoor II, 1) Get off of Elicoor II, 2) Get your Girlfriend back (she acts as if they are cousins, but it says in the manual that she is just your Girlfriend), 3) Get your dad back, 4) Destroy all of the Vendeeni for taking your Girlfriend. There is no legitimate boss at the end of the first disc, but right at the start of the second you beat up the leader of the Vendeeni and then new enemies pop up from nowhere and start blowing up bits of the galaxy.
 * Just because it must be said, this doubles as a Forced Level Grinding point of the sort that The Goomba can stomp you because the monsters stop being normal stuff that, say, can't blow up bits of the galaxy and start being stuff that can, say, blow up bits of the galaxy and that the developers thought that it would be a GREAT idea to make all of the bosses after that point get turned into normal enemies with no loss of strength whatsoever immediately after their battle.
 * Interesting examples in the Blaz Blue series: The final bosses in the arcade versions of both games appear to be the main villains, but become this in the story mode of the console version. Translation: When Calamity Trigger was ported to consoles, final boss Nu-13 effectively became The Dragon to an NPC, who was made the final boss of Continuum Shift, only to himself become The Dragon to another NPC upon that game's console release. Confused yet?
 * That last part might just be a subversion.
 * An case in the first two Golden Sun games, since they're essentially one complete story - would be a straight example if the games were just one. You fight and defeat Saturos and Menardi - up to this point the main threat - at the end of the first game, and after they proceeded to go One Winged Angel on you. You think it's over, their evil plan is thwarted even though two lighthouses a lit. Becomes a subversion when after Felix declares he will continue their plans himself, he's knocked into the sea and the game ends. Then The Lost Age comes around - Saturos and Menardi's ally Alex becomes effectively the Big Bad for the next game and Felix becomes the protagonist lighting the lighthouses. Of course, Alex then proceeds to become The Unfought, subverting this trope even further - on the other hand, one of the major themes of the dualogy was about people from different backgrounds putting aside their cultural or philosophical differences to save the world from a greater threat. As the Wise One reveals at the end of the game, the true enemy isn't each other, but the evils within humanity in general, which led to the sealing of Alchemy - and the gradual entropy of the world - in the first place.
 * If you see the first game as self-contained, it's arguably a subversion. Saturos and Menardi are set up like a Disk One Final Boss (since they appear at the very beginning of the game to wreck your village), but turn out to be the actual Final Boss. Interestingly, if the first game has a Disk One Final Boss it's probably the fight with Saturos alone at Mercury Lighthouse.
 * True enough - to think that Felix looked like he would end up being the Big Bad after their defeat, only to reveal it's the game's end. Regardless, Venus Lighthouse sort of functions as the Disc One Final Dungeon as well - the only reason people don't realise the story is over is because in a normal story, all four lighthouses would be visited before everything is said and done. Of course, Golden Sun - for all its traditions - has a funny way with subverting storytelling expectations ...
 * The Z-Master in Super Robot Wars W plays this role. His strength is quite hyped up, his show's plot has been the most important so far, has much higher HP than anything up to now (Aad anything in quite a while, for that matter), The Fight of the Courageos Ones plays in the background and your Original Generation main character gets an Eleventh Hour Combining Mecha to help defeat him. However, some series haven't got finished (Or started, for that matter) yet, and if you watched Gao Gai Gar, you know this isn't over yet, plus there's the whole thing this game features sequels...sadly (to Z-Master), you fight him again later as a Degraded Boss, albeit with the same base stats (but higher level, of course).
 * From the same game, Pasder can be considered a Disc 0.5 Final Boss, for very similar reasons.
 * Similar to the Golden Sun example above, Super Robot Wars Z 2 is a two-part game; the Big Bad of Hakai-hen, Gaioh, is a Disc One Final Boss to the final boss of the second part, whoever it may be.
 * Complete Monster Fassad from Mother 3. You encounter him near beginning of the game, as in before the Time Skip, witness him as he He remains The Unfought until he seemingly dies at the end of chapter 5, but by that point, the player party has become aware that Fassad is a relatively low-level operative in the Pig-mask army.
 * Children of Mana pulls this twice, once with the Mana Storm and then with the Mana Lord.
 * In Wings of Liberty, the first third of the Starcraft II campaign,
 * Phantasy Star IV does the rather expected example of the first bad guy, Zio, being a minion of Dark Force, the perennial boss of the series. But after beating Dark Force a few times, you finally find out about his master.
 * Benny serves this role in Fallout New Vegas. He kills your character in the opening cinematic (You get better), and you spend the first half of the game chasing after him and trying to figure out what his plot is and why he put a bullet in your brain. By the time you finally deal with him, though, you've learned that a major conflict is about to ensue between the region's 3 major superpowers, and you get to decide which one wins.
 * Touhou Seirensen ~ Undefined Fantastic Object managed to have the Final Boss be the Disc One Final Boss, with Byakuren having nothing to do with the UFOs while Nue, the Bonus Boss, was the one who started the protagonists on the fruitless quest for treasure by planting the seeds of non-identification.
 * Metal Gear Solid Peace Walker does this twice. The whole game appears to be building to a battle with Coldman, Peace Walker or both. You fight Peace Walker at the end of Act 3, after which there are some plot twists. A few stages later, at the end of Act 4, and you fight Peace Walker again after one of the longest, most action-filled stages in the whole game, and everything looks like it's resolved. In fact, there are six more missions and the average game's worth of plot twists before the real final boss.
 * Both New Super Mario Bros games do this. In the original game for the Nintendo DS, it was Dry Bowser, and in the Wii sequel, it was the third battle against Bowser Jr.
 * The old Super Mario Bros game does it, too. Every fourth level until World 8 finishes with Mario defeating Bowser and saving the Princess...except, he has really only defeated a mook disguised as Bowser, and has only rescued a Toad who thanks you and then tells you that you ain't done yet.
 * The Lost Levels does it as well.
 * In Super Mario Bros 3, this is done with Ludwig von Koopa, the oldest Koopaling. You get a letter from "the Princess", but it's actually from Bowser! He's kidnapped Peach!
 * In Super Mario 64, you face Bowser (the real one) three times, and the first two times have this written all over it. This is also true with Super Mario Galaxy and Super Mario Galaxy 2.
 * Super Mario Land plays with this. While you don't face Tatanga until World 4, you still get the same "Thank you Mario", only instead of "but our Princess is in another castle", you get Daisy turning into a mook who runs away.
 * Bowser again in Super Mario 3D Land. The first time you defeat him, the captive Peach actually turned out to be a cardboard cutout.
 * In Jak II, Jak ascends the Big Bad's palace for a showdown only a third of the way through the game.
 * The Thief in Ratchet and Clank Going Commando.
 * The Marquis de Singe seems to be the Big Bad for the first four chapters of Tales of Monkey Island. In the climax of Episode 4, Guybrush finally defeats de Singe and cures the Pox of Lechuck...only for Lechuck to show up and reclaim his voodoo power. Lechuck resumes his role as the Big Bad in Episode 5.
 * Portal 2: The game has 9 chapters. You face GLaDOS in Chapter 5. It doesn't take a genius to figure out that this won't be the end.
 * You don't get to know how many chapters there are before you start though, unlike Valve's previous games.
 * Red Faction 2: You know that villainous dictator you've heard so much about, has fucked your country up almost beyond repair, and you have been gearing up to assassinate? He's not the Big Bad - he gets his Karmic Death halfway through the game, and you spend the rest of it fighting the anarchic new regime led by
 * This seems to be a running theme in the Red Faction series. Almost every game's Big Bad (Capek, Sopot, and Adam Hale) end up getting killed about halfway through the game, with the rest of the game spent dealing with the aftermath of their evil schemes.
 * In Drakensang about halfway through the level you find out that there's a young purple dragon named Japhgur who's raiding the country. However after you kill him there are still a lot of things to do.
 * Heavy Weapon has X-bot, at the end of the Disc One Final Level. When you beat him, you are teated to a scene showing your tank driver celebrating, untile he learns that it was a diversion and that the enemy had amassed a reserve army 10 times the size.
 * Lufia 2 Rise of the Sinistrals and Lufia the Legend Returns have Gades, a god of destruction, who firstly appears to be a Big Bad of the game, but defeating him only reveals that there are three more of his kinds. Subverted in the first game, where the heroes already know Gades has friends,
 * In Saints Row the Third, Phillipe Loren is set up as the Wicked Cultured, mafioso-like leader of the syndicate, but is killed in a mere handful of missions. In his place.
 * Fossil Fighters fakes you out with Blambeau, and his Olympus Mons, Frigisaur. He's the head of the Goldfish Poop Gang that's been chasing you everywhere throughout the game, he's trying to take over the islands, and in order to stop him, you have to get your own godlike powerbeast from the climactic Mt. Lavaflow. Afterwards, you'll fight the final stage of the tournament To Be a Master, so clearly he's the final Big Bad, right? Not even close.
 * The second game does it twice. The first time is when you confront Don Boneyard, who is once again head of the Goldfish Poop Gang. However, someone who played the first game might quickly catch wise to the fact that he's not the real villain. However, it catches you again when you go to face the real Big Bad for the first time. It plays up the confrontation bigtime, you prepare to seal him in a can... However, you don't succeed in catching him, and have to go to the Very Definitely Final Dungeon to finally get him.
 * Dark Lord Gaol from Kid Icarus Uprising, a Tin Tyrant who leads the Underworld Army's attack on the human world. Why is this not a spoiler? BECAUSE YOU DEFEAT ON THE SECOND LEVEL IN THE GAME.
 * Bruno's chase after the medallion to awaken Lares and Take Over the World is the major conflict of Solatorobo, and he's set up to be the final boss.
 * Epsilon in Mega Man X Command Mission. Unsurprising for a Mega Man X game, however the Man Behind the Man is not the one fans had come to expect...
 * Happens in Persona 3. After beating, the main characters think the Dark our is finally over. Obviously there's still a bit more to the game, what with STREGA possibly still out there and you never finding out more about Pharos... And you still haven't found out who the Big Bad is yet.
 * In Kirby 64 The Crystal Shards, the game ends after beating Miracle Matter, If you collect all of the shards and beat Miracle Matter again,

Western Animation

 * In Legion of Super Heroes Imperiex is the Big Bad for most of the second season. In a possible nod to the Our Worlds At War storyline in the comics
 * Admiral Zhao in Avatar: The Last Airbender. Actually, defeating him was necessary to make the hero important enough to make the Big Bad focus on him.
 * Before Zhao, Zuko was the main enemy to the group, Zhao just turned out to be even worse. After Zhao's defeat, Azula took his place, but the True Final Boss was always Ozai, no matter who he sent after the group.