Dragon Ball 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.
In season 1 of Tenshi Ni Narumon, Dispell seems to be the Big Bad. It turns out, however, that he is 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, where the viewer thinks that Michel is the villain, then it's Fuku, then it's the fire spirit known as "him", then it's Fuku again who is controlling Michel to be the final boss.
Quite common throughout the various Digimon anime universes:
Starts out realistically in Digimon Adventure 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).
Reaches ridiculous heights in Digimon Adventure 02. The Digimon Emperor is the Disc One Final Boss under Arukenimon... who turns out to be reporting to Oikawa... who then gets Hijacked By MaloMyotismon. Oh, and then there was the Dark Ocean master and this guy called Daemon thrown in there somewhere, although they never received any plot resolution.
Digimon Frontier has Cherubimon acting as the main antagonist for the majority of the series, then Lucemon shows up.
Digimon Savers has Merukimon, who gets overshadowed by his psychotic lieutenant Gotsumon and another Mega level Digimon, Saber Leomon, both of whom are replaced by Kurata, who later makes a Big Bad Ensemble with one of the Demon Lord Digimon, Belphemon. Once they were killed, Yggdrasil appears...
Finally averted with Digimon Xros Wars where Bagramon is introduced as the villain early on and stays the main threat through the first two arcs. (The third arc comes after a Time Skip with less focus on an ongoing plot and no main villain until near the very end.)
Naruto does this, where we find out that instead of Pain, it's Tobi AKA Madara Uchiha who is the true leader of Akatsuki, though this is revealed sometime before the former even begins to directly fight the heroes.
Also subverted later on. It's revealed that Tobi was impersonating the real Madara Uchiha, whom was was revived as an all-powerful immortal zombie beforehand. Even as we learn that Madara was Tobi's mentor and trainer, they're operating under Teeth-Clenched Teamwork more than anything else, so while Tobi is still the Big Bad, he's sharing it with Madara, just like he shared it with Kabuto beforehand.
While Emperor Charles zi Britannia was always more of a Bigger Bad, he gets several episodes that somewhat heighten his threat level to Lelouch. As the target of Lelouch's rage, Charles dies five episodes before the finale, leaving Schneizel as the Final Boss. On the other hand, Schneizel was always a more direct and frustrating opponent to Lelouch than Charles ever was.
In Suzaku of the Counterattack, this happens twice. The viewer expects Lelouch to be the villain, but Emperor Charles Zi Britannia is soon introduced as a potential Big Bad, only for Schneizel to assassinate him.
In YuYu 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 Rezo/Shabranigo, but its actually Rezo's clone.
In the second season, Gaav is the Disc One Final Boss, who gets executed by the true Big Bad, Hellmaster Fibrizo.
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, it turns out Valgaav merged with Dark Star and returns to become the real Big Bad after all.
Zuuma in the fifth season.
And in the fourth season, Gioconda is the Disc One Final Boss to Zanaffar.
In the Diamond Is Unbreakable arc, 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!
The second seriesseries Battle Tendency began with Joseph Joestar being attacked by former Joestar ally Straights, who had become a vampire by the same means as series one Big Bad as well as Big Bad of later series Dio Brando. But Straights' tenure as villain was cut short only a couple chapters later when he killed himself. The real main villains of series two were in fact the Pillar Men who eat vampires, and against whom the ripple technique is of limited effectiveness most of the time.
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, Galaxia turns out to be this in the manga as it is outright stated (but only implied in the anime) that Chaos is the the evil behind all evils of the entire SERIES and sent every villain Sailor Moon had fought up until that point. Funny thing is, Chaos cannot be defeated as he/she/it is the root of all evil. Pretty intense.
In Star Driver, Head was built up to be the Big Bad, but his defeat at the hands of Takuto only halfway through the series hints at the fact that someone else is going to take up that role. This is subverted, as Head ends up being the Big Bad anyway.
In Fairy Tail, just when the team thinks they've beaten Oracion Seis, their leader's Super-Powered Evil Side kicks in. Subverted in the Edolas arc. You're led to believe that Queen Shagote is the Big Bad behind King Faust, but Faust is the actual Big Bad.
Master Hades, the Bigger Bad of most of the series and the Big Bad of the Tenrou Island arc, is disposed of like garbage by Zeref right after his defeat.
Shin from Fist of the North Star. He's set up to be the antagonist until episode 22, where he gets killed in a somewhat anti-climatic duel between him and Kenshiro. It isn't until episode 44 that the actual antagonist of Raoh is revealed.
The original manga take it a step further: Jagi (good-for-nothing black sheep turned unhinged psycho killer), Amiba (good-for-nothing Toki wannabe who murders countless victims in his experiments), and Uigur (sadistic petty tyrant) all are shown to be great threats before Raoh enters the picture. Shin actually gets it even worse; he's eventually revealed to have been manipulated by Jagi.
In Angel Beats! Angel is initially set up as the main (and only) enemy of the SSS later on it is revealed that she is simply another human soul like the rest of them only wanted to help them move on from purgatory. She becomes their friend and ally in the fight against that Shadows. The really big twist however is the fact that she turns out to be the main Heroine and Otanashi's Love Interest.
One can actually make a case for Kaiba being this, in the Yu-Gi-Oh! manga. His second appearance (his first is as just a Monster of the Week) has him a far greater threat that any opponent Yugi and his friends had faced so far— previous enemies were (with some exceptions) just school bullies, while Kaiba actually tries to kill Yugi and his friends, and for an incredibly petty reason to boot. His climactic showdown with Yugi has a ton of buildup, the heroes get some Character Development for the first time, and at the end, Yugi learns of the existence of his other self, at a point in the story where nothing suggests that said other self is anything more than a Split Personality. Millenium Items other than the Puzzle had been revealed before this point, but not how many there are or any hint that Yugi must eventually acquire them all. The arc has enough of a denouement that a reader completely unfamiliar with the franchise could probably believe that Death-T is the final arc... only to discover that the series lasted for another 33 volumes.
In Attack on Titan, Annie, Reiner, and Bertolt turn out to be this. What exactly is worse, has only been hinted towards so far. But the implications are not good for humanity, if claims of them merely being "small fries" turn out to be accurate.
In Saki, Koromo Amae is built up as a fearsome mahjong opponent, and the greatest obstacle the protagonists will have to overcome if they want to win the prefectural tournament and advance to the nationals. The first anime series concludes not long after the main characters win the tournament, and Koromo's teammates mention that they were eliminated early on in the tournament, giving some indication of how difficult things will get for the protagonists.
The Big Fat Kill, a Sin City miniseries, features Jerk Ass 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 Jack was a cop, which leads to the realBig Bad, Manute, stepping in with Wallenquist's enforcers.
A Dark Knight Over Sin City starts with Batman tracking down the Yellow Bastard. Once he catches up to him, he finds out the Yellow Bastard has been killed by John Hartigan. It's soon clear that The Joker is the final boss.
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. Loneliness, Trixie's Enemy Within, serves as the Big Bad of the story arc to save Trixie, eventually being destroyed by Trixie herself. Then Fluttercruel ends up accidently doing a Break the Cutie on Fluttershy which "Discords" her for real, causing Fluttershy to transform into a Superpowered Evil Side called Princess Gaia, a Well-Intentioned Extremist who begins trying to draw everypony into her Lotus-Eater Machine and serves as the second Big Bad. However, Discord has already been confirmed to escape sometime in the future to be the True Final Boss.
"Origins": Discord's parents Havoc and Entropy serve as joint-Ultimate Evil for the first half of the arc, but after the Alicorn/Draconqeui War they disappear from the story, allowing Discord to take center stage.
The Shining Armor Arc: Makarov and the Wolf are the greatest threats to Shining's continued existence, but the Wolf is also a threat to Makarov as well, for all the damage he's caused to the timeline. Ultimately, it erases him, before turning out to still be after Shining as well, since he's not supposed to exist either.
In With Strings Attached, Jeft 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 Brox 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, Zhan Zheng.
Doumon in Theory of Chaos. While the readers know from the beginning that she's working for someone else, it's quite a shock when Takato's Superpowered Evil Side comes out halfway through, casually offs her, and then nearly kills the other Tamers. Doumon's master, Daemon, doesn't take the stage until the very last scene and serves as Big Bad for the final story instead.
Earth and Sky: Diamond Tiara starts out looking like the Big Bad, using the Flim-Flam brothers to try and ruin Harmony Aeronautics, but by the time the Pegalathon starts has lost complete control of them and is stuck pulling what strings she can for her benefit. And then she gets kidnapped by the changelings and replaced by Chrysalis, beginning her road to a Heel Realization and a Heel-Face Turn.
Star Wars: Paranormalities: Maesterus is made out to be the main villain and the leader of the Valkoran Empire throughout Episode I. Even when the Forceless Collective enters the story, he's still the most active villain. By the end of Episode I, it is revealed that he was really being controlled by Valkor and upon realizing how truly evil Valkor and the Forceless Collective are, he performs a subverted Heroic Sacrifice by throwing Forceless Archfiend Belluzub into Krantisi's sun.
In The Prayer Warriors Threat of Satanic Commonism, John Lennon is killed about 3/5 of the way through that installment, and the remaining chapters deal with the effort to defeat Stalin.
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 thenew Big Bad.
Especially tricky because the movie is almost over when he's finally taken down: Veck is not the Big Bad of Paul Blart: Mall Cop. Commander Kent, the SWAT guy that took over the hostage negotiations and was chasing after Veck with Paul, was actually working with Veck all along. 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.
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. He makes a return toward the end of the film and is promptly killed off without ever having fought the main character.
In Gremlins 2: The New Batch 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. The most dangerous gremlin in the film was likely the Spider Gremlin, but even then, the movie was far from over after it was killed.
Kill Bill has O-Ren Ishii as 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.
In G.I. Joe: The Rise of Cobra: James McCullen (played by Christopher Eccleston) is most definitely this. Because of the heavily publicized fact that Joseph Gordon-Levitt (a more recognizable Hollywood name than Eccleston) was playing the villain, even those who were unfamiliar with Joe mythology couldn't help but understand that McCullen was just a placeholder until the Big Bad revealed himself.
Iron Man 3: The trailers imply the Mandarin as being the Big Bad. He's not; he's simply a washed-up actor posing as a decoy.
Subverted in Elysium. At first, Kruger seems like this, but then is revived and kills Delacourt, making her the true Disc One Final Boss.
In The Wolverine, Shingen is built up as the Big Bad Logan has to stop in order to save Mariko's life. Logan kills Shingen, only to reveal that the true final boss is Ichirō Yashida, whose after Logan and his quick healing ability that makes him immortal.
The rival band manager in Miami Connection, who gradually loses his importance to the story after siding with Big Bad Jeff.
Phenomena features an odd one. According to the prophecy Phenomena does the chosen children have to kill Tarkan on the Gredom Fields. But in the 2nd book does it turn out that Tarkan is merely The Dragon, and King Sherpa, the king from the country in the north is the Big Bad they have to defeat there since he's the one behind Tarkan. Gets even more complicated when on the Gredom Fields does King Veha defeat Tarkan, and Alk kills Sherpa with his bare hands. If this wasn't confusing enough does the story not end there as it's still ongoing into "Phenomena: The Dark Chronicle.
In Inheritance Cycle, the Big Bad Galbatorix doesn't show up until the final few chapters of the final book. Before then Eragon concerns himself with hunting down the Ra'zac, the henchmen who killed his uncle.
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... Wait, who's Scourge?
Also in Warrior Cats: Power of Three, at first it seems Tigerstar's ghost is going to be the Big Bad this time. However, in Eclipse, a new villain named Sol appears and takes over ShadowClan. He's on the cover of Long Shadows and the blurb only talks about him. Also, in the prologue, the original leaders show up to talk about much of a threat he is. But then, he's defeated less than halfway through Long Shadows. Then he gets hijacked by Ashfur? Wait no, Ashfur's dead and his killer must be caught. So then Hollyleaf says that the killer is Sol. So the heroes spend Sunrise on a journey to capture Sol. But then Midnight says that Sol didn't kill Ashfur. And finally, we find out the final realnot fake this time big bad. Who is it? Would you believe it's Hollyleaf?
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 DragonIshamael, 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.
The Haruhi Suzumiya novels don't usually use Story Arcs, but this trope has happened at least twice:
The very first novel is self-contained, and could easily be considered a standalone work, so Haruhi herself could be considered this when she almost recreates the world at the climax.
The Anti-SOS Brigade in general, and Fujiwara in particular. Their plot is the focus of three novels and is foreshadowed even earlier. Fujiwara and Kuyou's attempted deicide makes them the first real threat in the series. They're this trope because the climactic battle fooled so many readers into thinking this was the end of the series that Word of God had to step in and state otherwise.
In Sukhinov's Emerald City Decalogy, Corina is this. She gets a lot of development early on (even being Villain Protagonist for a while), and then is deposed in the book 2. For a while it looks like she may return to a threat status, but she is quickly Stuffed into the Fridge, and the actual Big Bad takes over.
The first twelve books of The Dresden Files revolve around the war between the White Council wizards and the Red Court vampires, with the amorphous Black Council serving as the ostensible Bigger Bad. As of the end of Changes, the Red Court has been wiped off the face of the earth, leaving the series in need of a new major threat that is ultimately provided by The Outsiders and Nemesis, the latter of which is either a tool of the Black Council or the weapon that created it to begin with.
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...
Played especially straight in Season 1, where the creators prepared for the possibility that they wouldn't be allowed to bring the season to its proper close and set episode 13 up to be capable of serving as a finale if need be, with Ira Gaines serving as the final boss.
Angel: The Beast 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. After discovering that Angelus has knowledge of the Beast that has been retconned out of all memories and records on Earth through powerful magic, they enlist the help of a mystic who creates a dream sequence in which they find a magical sword that can kill the Beast, so that Angel will experience the perfect happiness needed to bring Angelus back. So Dream Beast bites the dust...and then Angelus awakens and the Beast still needs to be dealt with. With the added fun of having Angelus around.
Avoided in the fourth season. Just six episodes into the 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.
Played straight with the main villains of the first season — the Raiders get taken out by the Shadows when they first show up, and the Home Guard terrorists become irrelevant once President Clark, who supports their ideology but has far superior power and resources, takes office.
Battlestar Galactica (Reimagined): During the first half of the first season, the "Skinjobs" running the Cylon force seem to be operating on an equal footing, with no hierarchy and all decisions made collectively. Then we are introduced to D'Anna aka Cylon Model 3. The next time we see 3 interacting with other Cylons, she seems to be taking a more dominant role - the majority of agressive decisions are made by her, and other Cylon models seem rather intimidated by her presence. Then the season 2 finale introduces Brother Cavill, aka Model 1, who, amongst other things has the entire Model 3 line 'boxed' when D'Anna sees the faces of the final five, and quickly becomes the dominant model at least, amongst those who don't side with the humans in Season 4, firmly establishing himself as the Big Bad.
In the third season of Breaking Bad, "The Cousins", a pair of Salamanca Cartel enforcers who sneak across the border hoping to kill Walt and Hank, are introduced in the season opener and set up as the season's biggest threat. Midway through Season 3, in "One Minute", they're both betrayed by Gus Fring—leading to their deaths, and setting Gus up as the Big Bad of Season 4 as he begins plotting Walt's demise.
Buffy the Vampire Slayer: The 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 realBig Bad of the season takes center stage.
Happens twice in Season 2 alone, first the Anointed One who takes charge after the Master's defeat, who himself is killed by Spike a few episodes in. Spike and Drusilla then cause the main trouble of mid 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 acolossalmistake, as Willow snaps out, kills Warren, goes after his buddies, and then tries to destroy the world.
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.
Adam from Season 4 (who is the only big bad who is killed in an episode other than the finale) acts as a disc one final boss the the first slayer who believes Buffy's has too many shortcomings to do her job properly.
Burn Notice: The third season sets up Psycho for Hire Gilroy as the scary Big Bad for most of the season. Then, the episode right before the finale, he's killed and Simon—who was more-or-less a living MacGuffin beforehand—turns out to be the real villain.
Chuck: In season one and two we have the leaders of FULCRUM, towards the end of season two we have their main boss, Ted Roark, and in season three we have his boss, The Director, while Shaw becomes the Dragon Ascendant for the last half the season. Then in the last four episodes of the series it's discovered that Nicholas Quinn was secretly the driving force behind Fulcrum and the Ring.
Defiance: Nicolette is set up in the pilot as the Big Bad, being behind both the Volge attack and the conspiracy to get at whatever is buried underneath Defiance. However, near the end of the season, Doc Yewll decides she's gone too far past the Moral Event Horizon and kills her, making it look like suicide. This now leaves Datak, the corrupt Earth Republic (represented by Colonel Marsh), and possibly Yewll herself as potential Big Bads.
As of the season finale, Datak was reduced to being Colonel Marsh's puppet and killed him in retaliation, meaning the E-Rep will probably kill/arrest him and Stahma, while Yewll turns out to be The Atoner. So it looks like the Earth Republic as a whole will be the Big Bad after all.
Doctor Who: The 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. (Indeed, the War Chief turns out to merely be the Dragon/Starscream to the War Lord, resulting in the last two episodes consisting of the War Lord killing the War Chief and the Time Lords killing the War Lord before they turn their attention to 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 the Sontarans show up, revealing the entire Vardan invasion to be a set-up to disable the defense system, 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".
FlashForward (2009): D. Gibbons/Dyson Frost. Not only was he not the real Big Bad, but he was actually trying to defect to the heroes' side in order to prevent the impending apocalypse. Too bad he got shot.
Kamen Rider OOO: Kazari had been the main villain most of the series, and if not him, then the Greeed as a whole. Then towards the final act, Dr. Maki takes the role by force and killed Kazari.
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 the Big Good, and the real-true-honest this time Big Bad is an entity so far only known as "The Man in Black" / "The Smoke Monster". Other pretenders to the Big Bad throne include Charles Widmore, Alvar Hanso, and Richard Alpert.
Merlin: In the first season finale, 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.
Power Rangers S.P.D.: Emperor Gruumm is played as the main villain 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. note Okay, this takes some explaining. As early as the Shadow Ranger's debut, he started talking to someone we can't see that clearly terrified him (making you wonder if earlier evil monologues of his weren't actually monologues.) However, first the Magnificence is this being. Then The Magnificence is something he has to build. Then his master starts being called Omni as if he had been all along. Then it turns out that Omni has no body and The Magnificence will be Omni's vessel. Which jibes quite well with Gruumm's actions, so he knew what he was doing...the writers just screwed up the names. (They also couldn't decide what a Troobian - nominally Gruumm's faction, but vaguely defined and applied to Gruumm-related and non-Gruumm-related bad guys - was. And with this, the Bruce Kalish Dork Age is well underway.)
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.
Revolution: For most of the first season, General Sebastian "Bass" Monroe and Randall Flynn have proven to be serious threats, the former in charge of his own republic along with men and weapons, and the latter having the inside track to getting the power back on along with power pendants that he supplies Monroe with from episode 11 onward. The first season finale first has Bass running off without any power and his Republic is taken over by his former subordinate Tom Neville. Second, it has Randall, upon the power being turned back on, using the opportunity to launch Intercontinental Ballistic Missiles to wipe the Monroe Republic and Georgian Federation off the face of the earth, and then committing suicide with his own gun. Finally, it turns out that Randall had been working for the U.S. government in exile all along, and now that he has completed his mission in getting the power back on, the government intends to come back into the U.S.A. and take back what's theirs.
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 kills Hawkman in a Sword Fight right before being trapped in the Phantom Zone by Clark. 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'srelationship 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.
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.
Sons of Anarchy: Lee Toric in season 6. After being set up as the Big Bad at the end of season 5 and driving the plot for 4 episodes of season 6 he is killed off suddenly and the focus shifts to the club's conflict with Irish and Tyne Patterson's attempt to take down the club.
Supernatural: Crowley, having become King of Hell 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, he's killed off by the Winchesters and Castiel. 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 not only is the Mother killed, but we discover that Crowley is still alive. So, this is a case of the apparent Disc One Final Boss turning out to be the true Big Bad after all, with the person we thought was the Big Bad turning out to actually be the Disc One Final Boss...anyone got anything for a headache?
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.
In Hyakujuu Sentai Gaoranger, three Highness Dukes each take their turn at the top of the Org hierarchy. The finale has all three revived and later fused into the final villain, Senki.
Mahou Sentai Magiranger starts with General Branken running the show for Infershia. He dies around Episode 17, with the next leader being Meemy, the traitorous Heavenly Saint Raigel, for a Disc Two Final Boss. Then he dies, predicting the rise of the Hades Gods and, wouldn't you know it, up they come with Dagon swiftly making it clear that he is the leader here. However, from the first few minutes of Episode 1, it's made clear that the guy all of Infershia is ultimately answering to is Beast Emperor N Ma, making Branken and Meemy and DagonThe Dragon.
In Tensou Sentai Goseiger, similar to Gaoranger, there are three Disk One Final Bosses. The first is Warstar, the next is the Yuumajuu, and the final one is Matrintis. The final big bad is Buredoran, who was with all these groups all this time.
Kaizoku Sentai Gokaiger has the rather pathetic "Well Done, Son" Guy Prince Walz Gill, son of fearsome Emperor Akudos Gill of the Space Empire Zangyack, leading the Empire's invasion of Earth. In #38, distraught over the loss of Barizorg, who he considered his only real friend despite being a subservient cyborg servant, Walz Gill decided to fight the Gokaigers himself, which resulted in his death. After Walz's death, the Emperor steps in and takes direct leadership of the invasion, becoming the true Big Bad.
Averted Trope in Tokumei Sentai Go-Busters, which starts with the Big Bad position being held by a computer virus called Messiah, leader of the Vaglass organization. Messiah met a premature demise in #30. Rumours of a total retool of the show proved to be false however. It is revealed that Messiah survived, living on through the 13 Messiah Cards, each of which has the potential to become a Metaroid which can be possessed by Messiah. However, with Messiah's current state, his holographic servant Enter seems to be becoming more in control.
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.
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. Guess what Coach's nickname for him was?
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 GaySmug SnakeManipulative BastardAscended 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.
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 bent 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.
The Vampire Diaries: Does this in season 2 when most people thought Katherine was the main villain. It was actually the top vampire Klaus.
Zorro: The 1950s Disney series had The Hero fighting the evil Capitan Monistario - who found himself Hoist by His Own Petard after only 13 episodes, halfway through the first season.
In Mario & Luigi: Superstar Saga, you defeat the Big Bad, Cackletta, halfway through the game. However, Fawful captures her essence, which she then uses to possess Bowser. At the end of the game, you fight Bowletta, but even then you're not done as you then get sucked inside her to fight the real Cackletta INSIDE Bowser's body. And after THAT, you still have to escape the castle before it blows up. If you fail, you have to go through the final boss fight again. Good luck.
Humorously enough, the first fight with Cackletta is also the Disk One Final Boss of the dungeon itself. The real boss is a rematch with Popple and Rookie.
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.
Final Fantasy III. You play through a 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, up comes the Cloud of Darkness, the embodiment of all the dark power in the world, who forces you to go through yet another dungeon, filled with a couple of more bosses that are tough as nails before you can face her down.
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.
Diablo II was divided in four acts. One final boss per act. In act 2 you're expected to kill Baal before he can escape his prison, but run into a giant bug called Duriel instead. Diablo is the final boss of act 4, but the expansion comes and Baal turns out to be the true final boss of the game instead.
And in Diablo III, the first major boss of the game is the Skeleton King, who is faced halfway through the first act and is largely unrelated to the rest of the game's plot (unfortunately for the characters in-game, he's literally barring the way to that plot). Then the player must face Belial and Azmodan before the realBig Bad is finally revealed to be Diablo himself once again.
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 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...only to find that the Demonlord wasn't dead after all...
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.
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 whoever fired the giant beam of death aimed at God is living in his basement.
Dragon Age II 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... a power-mad Knight-Commander Meredith.
Eternal Wings has Geldoblame, who goes insane after infusing himself with Malpercio's power and is killed by Fadroh's soldiers, after you've beaten him.
In a really weird twist, Geldoblame is the last boss you fight, in a manner of speaking—he comes back in the middle of the end-of-game/credits cutscene as a Puzzle Boss who has more HP than the Final Boss but can be instantly killed with the special spirit finishers.
Vesperia has it too, with the second part concluding with an epic battle against The Man Behind the Man, Alexei. In fact, this boss is easily the most evil character in the entire game; in comparison, the final boss is just misguided.
Oddly enough, shows up in Bomber Man 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, Sirius, the guy who has been helping you out, showing up on almost every level and giving you hints, and dropping you the Remote Bomb powerup before every boss, flies in and kills him, then points out that the guys you've been fighting stole the superweapon from him, and you've been unwittingly helping him recover it. After that, all of the hint-givers in the previous levels tell you that you should die because it would be easier. They aren't lying. The hidden final world is WAY harder than anything and everything that came before it.
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.
Anyone who's not Wily in the Mega Man series, except Sungod from Rockman World 5.
Anyone who's not Sigma in the Mega Man X series, except Lumine.
Symphony of the Night: Alucard's final foe appears to be Richter Belmont, 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 is actually being mind-controlled by a weird ball of light; if Alucard focuses his attacks on this, it's revealed to be the evil priest Shaft and the entire second half of the game, the Inverted Castle, is unlocked.
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 enter the mirror in Dario's room and cut Dario off from the fire demon that's fueling his powers. After a long series of events that result from this, he eventually goes to The Very Definitely Final Dungeon and does battle with the manifestation of the mutated and out-of-control powers of Dracula. Or something.
Portrait of Ruin: If Jonathan and Charlotte beat the vampire sisters head-on, Brauner stops them and flees the castle with them, leaving Eric's wish unfulfilled and sending the duo on what would likely be a country-wide hunt for the vampire and his hostages. If Charlotte manages to cast Sanctuary on them, they're cured of their vampiricy and, grateful for the forced Heel-Face Turn, grant access to the second half of the game and the eventual battle with Brauner himself...only for Brauner to be hijacked by Dracula at the very end. And Death. At the same time.
Order of Ecclesia: If Shanoa defeats Albus without having saved all the villagers (one of which is hidden behind a breakable wall), she goes home with all the Dominus glyphs for the ritual ...which ends in her life being sacrificed and her mentor gloating over his plan coming to fruition. If she does manage to save all the villagers, Albus gets a chance to warn her about what's coming up, leading to her calling out her mentor for the Treacherous Advisor he is, resulting in an epic boss battle with him. Which ends when he gives up his life to summon Dracula's castle. Nice try, Shanoa.
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 Dracula's Servant 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 Dracula's Servant, by taking too long to reach the final stage.
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, Kaileena turns out to be the Empress the prince has been seeking and the ensuing 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. Kaileena becomes the final boss in the bad ending if you haven't gotten the water sword.
Legend of Legaia pulls two of these. First, after you beat Zeto and clear the world map, you discover that there is another region (and later a third) to explore. Later, after Prince Cort has been defeated and the Mist has been eradicated, Songi shows up and has Juggernaut eat your town.
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 that he must also defeat 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 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 usingoverwhelmingfirepower.
Done even more convincingly in Ōkamiden. You've got all the brush techniques, all the divine instruments (bar the one you get for New Game+), 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 MechaMoon Rabbit that will destroy Nippon. You beat King Fury, and hey, who's this guy called Akuro? As it turns out, all the previous bosses, including the aforementioned King Fury, were just fragments of Akuro that had taken on their own personalities. So, technically speaking, you were fighting the same guy the whole time.
Jade Empire sets up Emperor Sun Hai as the apparent Big Bad of the game, with hints that his Dragon Death's Hand may actually be the real driving force behind the evil plot. The player character fights and kills the Emperor at the end of the fourth of seven chapters of the game, after which your supposed kindly mentor Sun Li emerges as the true Big Bad.
In BioShock, Jack battles his way to the apartment of Andrew Ryan in order to kill him, only for Ryan to point out Jack's Tomato in the Mirror status. After which Ryan commits Jack-assisted suicide in a cutscene. Only then does poor Jack realize that he's been listening to the real Big Bad all along.
Maleficent is not, in fact, the last boss in Kingdom Hearts I, 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.
Maleficent still wouldn't have been the final boss though, that was going to be Chernabog.
In 358/2 Days, Xion is not the last boss, despite having all thetrappings of one. No, there's still an epilogue chapter, with the true (and less challenging) final boss fight with Riku, as you re-enact the Deep Dive trailer.
In Coded, Sora's Heartless likewise is a Sequential Boss which behaves very much like the final boss. However, the final boss of the game is actually Data-Roxas.
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.
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/Dark Serge and Fate itself, whatever that may be. Turns out it's the computer that's keeping everyone from being killed by the dragons. And it wasn't evil so much as trying to resolve its programming. Er... Well anyway, then you take on the dragons who are planning to destroy the Earth, only they/it aren't/isn't the final boss either because the Time Devourer ate it long ago. 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.
Chrono Trigger: 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.
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, Siegfried, 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, Beatrice, a little girl who had been randomly appearing throughout the game all along, and was manipulating everyone, including Siegfried, to her own ends. Even then, she's not the final boss: her pet planet-organism...thing is.
Wild ARMs 2 does this with Vinsfeld, who is 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. Granted, there is a factor that ties them together, but it's tenuous enough to call them two seperate plots.
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 Mao's dad, but it turns out the real final boss is Super Hero Aurum. 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 Vulcanus, only to find out at the end there's still one more battle...and, Vyers/Mid Boss is a parody of this.
Parodied even harder in Disgaea 4: A Promise Unforgotten, where Desco actually has the title "Supposed Final Boss". Then there's DES X, with the title of "Final Boss"...who's also actually this trope. Finally, there's Nemo, with the (accurate) title "True Final Boss".
In Prototype, the game is not over when you kill Elizabeth Greene. To be sure, the infection slackens off considerably when you do, but there's still Blackwatch to deal with. And The Starscream.
In The World Ends with You, everything in the game seems to build up to it being done when you defeat Higashizawa. After all, it's The 7th day, when the Reaper's Game is supposed to be done. However, after defeating him, Neku wakes up on the first day...of a new Reaper's Game. 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 nuclear, annihilating the Evil Chancellor 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 Lyndis. Every chapter builds him up to villain status, including Kick the Dog moments, 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 Begnion Occupation Army led by Jarod, the second part has Crimean Rebels led by Ludveck, the third part alternates by mission between the Begnion Empire and the Laguz Alliance, and the fourth part has the goddess Ashera and her minions.
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 the Disc One Final Boss and Final Boss of Red and Blue.
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 Anti-Climax Boss more than anything.
Pokémon Black and White plays with this as well. By this point, players should be used to the villainous plot being thwarted before the eighth gym, so the fact that nothing's changed and you're headed to the Pokémon League should be a sign something's up, but having Team Plasma interrupt your Pokémon League challenge? And then it's played perfectly straight when Ghetsis turns out to be the main villain instead of N. Also, technically this means that like Gold/Silver, the true "final boss" comes in the postgame, since you still haven't actually beaten the Champion when you first see the credits.
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, Ashtar is set up as the Big Bad, but the story doesn't end with his defeat. After facing a familiar monster in the next stage, Ryu goes through the final lair and discover that the real mastermind is Jaquio, the villain from the previous game. Ashtar was merely a pawn whose death allowed Jaquio to be reborn. Then in III, Foster is presented as the main antagonist, but then Clancy, who initially helps Ryu take on Foster, reveals that he was merely using Ryu in his plot to reclaim a doomsday weapon from Foster. Unlike the previous examples given, Ryu never gets to fight Foster, as Foster is killed by Clancy instead.
In Arcanum: Of Steamworks & 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. Psyche! Another one of the evil villains banished to the Void defeated Arronax centuries ago and stuck him in a magic bubble. It's not the evil elf wanting to enslave Arcanum you've got to worry about, it's the First Necromancer coming back to wipe out all life on the planet
The first three sectors of Iji set you up to find Krotera, who you fight as soon as you see. That's all to set up the arrival of the Komato.
Persona 4 has a variation on this trope, in that the game's story is a murder mystery, so it's less a case of a fake final boss and more a case of a fake culprit. The murder case seems to wrap up once you apprehend Mitsuo and he confesses to the murders. But the player can easily figure out there must be a twist in store, since you're only in the middle of the summer, and catching the killer would mean the game is, well, over. Sure enough, after a couple of in-game weeks of peace, our heroes discover that Mitsuo is just a copycat, and the real killer is still at large.
Later on, there's a Disc Two Final Boss, in the form of Taro Namatame. This time, however, everybody's too pissed off to realize that he's also not the real killer and, if you agree to kill him, you get the bad ending. Let him live, and the game goes on for another month.
When you do find and take out Adachi, the real killer, the game is still not over — the fog and the threat of Shadows are still out there, and there's still one final Big Bad behind the scenes that you have to take down to get the True Ending.
The Updated Re-Release, The golden, does this a third time with Marie, who if you level up her social link all the way before the new winter month events exclusive to The Golden, pulls a Disc Three Final Boss by turning out to be another part of the Real big bad, yet takes the powers of both Taro Namatame and Adachi's powers and the fog they create inter herself to become Kusumi no Ookami, and is the Final Boss without the True ending. Also played with in that you have to beat her to get the True Ending's new Epilogue.
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 BlazBlue 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. Later on, "Chronophantasma" reveals that the Big Bad Duumvirate Relius Clover and Hazama/Yuuki Terumi are not the real Big Bad as they were revealed to be an unwitting pawn to the "true" Big Bad Izanami the Goddess of Death and using Saya as a vessel being the Imperator of the NOL.She later abandons the duo after their defeats leaving Terumi Killed Off for Real and Relius a Broken man.
A 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. 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.
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 (And anything in quite a while, for that matter), The Fight of the Courageous Ones plays in the background and your Original Generation main character gets an Eleventh HourCombining Mecha to help defeat him. However, some series haven't got finished (Or started, for that matter) yet, and if you watched GaoGaiGar, 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).
From the same game, Pasder can be considered a Disc 0.5 Final Boss, for very similar reasons.
Fassad from Mother 3. You encounter him near beginning of the game, as in before the Time Skip, witness him as he sadistically torture an innocent monkey while he's trying to corrupt your hometown by introducing money to the villagers. 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. Fassad does come back as a cyborg you fight later on, but it's still obvious that he's just a minion to the real Big Bad Porky Minch.
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, Kerrigan plays this role. She even fights your forces personally in the final mission (although you can't kill her; she'll teleport back to her base when her HP is low). The end strongly hints that she's going through a Heel-Face Turn, and there's a Bigger Bad looming in the horizon. She is. Mengsk is the Disc Two Final Boss, meanwhile
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.
In Phantasy Star Online 2, the story gradually builds up to a confrontation with Dark Falz Elder. However, he simply escapes after being defeated, and it's then revealed that he's just one of four incarnations of Dark Falz that are running rampant...
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. In fact, if you choose to go for the NCR or the Legion, you don't even have to deal with him.
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, Coldman dies 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.
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!
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.
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 your former team leader, Molov.
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 II: 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, and they don't even get to kill him until the final dungeon.
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 Killbane, seemingly a dumb thug in a wrestler's mask and cheap suit before, takes over as the Big Bad of the game with Matt Miller as his second-in-command. In Saints Row IV, Loren is brought back as the boss of Johnny Gat's loyalty mission by Matt (now an ally) since he notes that you never got to personally deal with him.
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.
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 HER ON THE SECOND LEVEL IN THE GAME. Medusa, on the other hand, plays this trope entirely straight.
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. The final boss of part one, that is. Cue the second part of the game, where you get to meet Nero, Blanck and Baion. They're worse.
Happens in Persona 3. After beating the final Arcana Shadow, 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're right. The Dark Hour happens, but with the added twist of a main supporting character being a villain. And you still haven't found out who the Big Bad is yet. That new classmate of yours is The Dragon to the real Big Bad, Nyx.
In Kirby 64: The Crystal Shards, the game ends after beating Miracle Matter, except that weird sequel bait pulled when the head fairy seems to be evil still. If you collect all of the shards and beat Miracle Matter again, you go to the final level and face the real Big Bad, Zero-Two, who is not happy about what you did to him last time.
The demon Mal'ganis is this in Warcraft III. He appears to be the man behind the Zombie Apocalypse and his death is the objective of the final mission of he first campaign, but he's actually far from it. Ner'zhul and Archimonde are the true Big Bads, the latter being the Final Boss.
Subverted by the huge golden mecha from Dogyuun. It appears in the intro where he kills the protagonists' friend, then flies off in stage 1 (and the start of stage 2). However, instead of a mid-game boss, it's only the stage 2 boss.
In Max Payne 2, the story is mostly about Max trying save Mona Sax and help protect his mafia friend, Vladimir Lem, from Vinnie Gognitti and his men. However, it isn't until later that you find out that Vladimir Lem is the real Big Bad and was using Max, while at the same time, setting him up to get killed throughout the game.
The fight with Luca Blight in Suikoden II. He had been played up as the main villain up to that point and the characters talk as if his defeat will end the war. The fight itself is much harder than anything up to that point, even split up into three teams and is capped off with a duel between Luca and Riou. And yet, with his defeat you're maybe two-thirds done the game.
In Dishonored, your goal is obviously to rescue the kidnapped future Empress and then get revenge on the Lord Regent who had the previous Empress assassinated and framed you for her death. After doing this, you might think the game is over... but you'd be wrong. You get betrayed again by the leaders of the resistance group that was helping you get your revenge, opening another chapter in the storyline.
In Asura's Wrath there are two examples. First, is Deus, the one who instigates one of the main plot points of the game, kidnapping Asura's daughter for more power. Vlitra, who's the other big bad, Re awakens and you fight him after defeating Deus. Played with here in that it's out right stated Vlitra was ready to return by the time Deus is defeated by other characters. Played straight with Vlitra, that, if you Download the DLC, the True Final Boss of the game, the golden Spider, whose real name is Chakravartin, turns out to be the true bad guy behind the plot.
Crash Bandicoot 2: N-Tranced is an odd case in that the Big Bad of the game is clearly Dr. N. Tropy taking orders from Uka Uka, and N. Trance is The Dragon despite being billed as the main antagonist. Once N. Trance is defeated, you're sent to collect Plot Coupons to unlock three hard extra levels, after which you fight N. Tropy.
Donkey Kong Jungle Beat has the Cactus King, who appears after the first 12 kingdoms have been completed. This appears to be the final boss at first, especially after the ending ceremony plays and the credits start rolling. However, during said credits, you will see footage from levels you haven't been to yet. After the credits roll, you'll unlock a new kingdom barrel, containing 4 new kingdoms. Once those are completed, you can fight the real final boss, the Ghastly King.
In Bio Menace, once you beat Dr. Mangle, he reveals that the actual person behind the infestation is Mr. Cain. You have thte next two episodes to kill him.
NeoQuest II has Ramtor, who you fight twice (he runs off the first time). Beat him, and you get a hero's welcome. And also several more chapters of the game.
Messiah does this with Father Prime, who is the main villain initially and is reached and killed quickly, but once you defeat him, it turns out you've merely allowed a greater bad guy to take over.
An unusual example - in Carmen Sandiego Great Chase through Time, you appear to catch all the criminals and are told to take a rest after catching Jane Reaction in the 15th Century. However... insert Disc 2, and Carmen breaks out all the criminals and gives you new cases to work on.
Ceadeus in Monster Hunter 3 Ultimate. It helps that it was the True Final Boss of the Wii version, as the later one contains a slew of new missions and chapters afterwards.
The PS3 version of Ni No Kuni does the same thing with Shadar, who was the actual final boss in the DS version, and whos defeat sparks a cutscene that could easily be the end of the game. Like some examples above, cutscenes are shown to make it clear to the player from the beginning that the White Witch is the real Big Bad and Shadar is just The Dragon. The real point is how the characters react when they find out.
In Dragon's Dogma, once you defeat the Dragon, the world is changed for the worse (the sky is always dark and the monsters are given a massive boost in power) and the Everfall opens up. Once you collect 20 Wakestones you then deal with The Seneschal and take his place.
Literal example from The Legend of Dragoon: Emperor Doel is presented as the main antagonist throughout disc 1, and the main focus of the story at that point is to end the Seridan War by reaching the Imperial Capital and slaying Doel. Of course, his defeat at the end is only the beginning of the story.
In Grand Theft Auto: Vice City, your goal from the start of the game is to get revenge on those who ambushed the deal at the beginning. A few missions later, it is revealed that Ricardo Diaz was the one behind the ambush, but when you finally kill him and look at the in-game stats, you see you're only about 30% into the game. The final bosses are actually the man you're working for the entire game, Sonny Forelli, and your own sidekick, Lance Vance.
In a way Grand Theft Auto Libery City Stories counts as this as well. Being loyal to Salvatore and the Leone Family, Toni's goal is to help wipe out the other rival mafia families, the Sindaccos and the Forellis, from Liberty City so that the Leone's will be unchallenged. Shortly after you kill the Sindacco don and wipe out their family, as well as weakening the Forellis beyond recovery, the real antagonist of the game is actually the Sicilian Mafia, that has been planning for the three mafia families of Liberty (Leone, Sindacco and Forelli) to wipe each other out in the mist of gang warfare, and then claim their territories after the carnage. Thus, they have been pulling the strings, making deals with their business rivals in the area, which have caused friction and rivalry between the mafia families in the first place.
Terraria has the Wall of Flesh, an Eldritch Abomination that could very well be a final boss. By the time you're ready to fight it, you've very likely already defeated the Eye of Cthulhu, Eater of Worlds, and Skeletron, and obtained what seems like the highest tiers of weapons and armor possible. However, that doesn't mean it's the final boss. It simply means that all the really good items aren't unlocked until "Hardmode", a permanent change to your world that makes it much more dangerous, is activated.....which occurs as soon as the WoF is defeated.
In Higurashi: When They Cry, it seems that the curse of Oyashiro-sama is to blame for the main characters going crazy and the bloodshed that follows...Surprise! Oyashiro is one of the good guys! It's actually a disease that causes the insanity.
Played more straight in Umineko: When They Cry. Beatrice spends the first half of the story as a dog-kicking sadistic Troll who wants to make Battler surrender to her, and she is defeated in an awesome and fancy final battle. In Chiru, it turns out it was all an act: she loved Battler and wanted him to discover the truth, which he wasn't even close to solving in the "final battle". When he does reach it, she's already dead. Bernkastel takes the position of the Big Bad from that point on.
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 Archer 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 Lio Shirazumi as Araya's final pawn and the last threat to Shiki.
Ace Attorney Investigations: Miles Edgeworth sets up Case 5 as though you are going after The Yatagarasu, which in and of itself features several game-ending-worthy reveals, but count your evidence: there's more to go and there will be a very long, standing room only conversation in a hallway before this game is over.
In the fourth case of the first Ace Attorney game, you manage to expose the true murderer of Robert Hammond, Yanni Yogi, and when everything seems to be over, Edgeworth claims responsibility for the DL-6 incident, on the last day before the Statute of Limitations expires, and you have to find the true murderer from that incident. The port also adds a fifth case. But not until after rolling the credits as normal at the end of case 4.
In Danganronpa, Monobear turns out to be a proxy for the real mastermind behind the events of the game, Junko Enoshima.
In Homestuck, Jack Noir is the primary villain for most of the series. John in particular thought he was the Big Bad. He is pretty shocked when Vriska tells him that there's a far more powerful and evil villain out there—the time-traveling nigh-omnipotent cherub Caliborn, AKA Lord English—who is responsible for starting the entire mess they are facing. She even says that Jack isn't really evil enough to be the Big Bad. He's "just" a murderousasshole.
Although in another sense, Jack didn't even become the Big Bad until after he offed the Black King and Queen. These two were the Big Bad duo for almost all other sessions of the game, yet turned out to be astronomically small potatoes in comparison to Jack and then Lord English.
In fact, Homestuck is full of separate instances where characters think one person is the final boss, only to find out another is. The Black Kingdom royal family, Jack Noir, Doc Scratch, Her Imperious Condescension... Thankfully, at least so far, it's pretty obvious that Lord English is, for real this time, the actual Big Bad. We mean it. Unless he's not. Wouldn't put anything past Andrew Hussie.
In Legion Of Superheroes 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 he is usurped by Brainiac.
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.
Alvin the Treacherous in Dragons: Riders of Berk acts as a recurring antagonist in season 1 and looks like he'll be a larger threat in Defenders of Berk, then in the second half of "A View to a Skrill" he's attacked and nearly killed by Hiccup's Evil Counterpart Dagur the Deranged, who then takes control of the Outcasts in Alvin's stead and looks like he'll be the main villain from then on. Meanwhile, Alvin returns to Berk in the finale and allies with Hiccup and company to defeat Dagur.