"The ultimate villain of the story, who's causing the problem the heroes must solve."
Note that Big Bad is not a catch-all trope for the biggest and ugliest villain of any given story. The Big Bad is the one who turns out to be behind several other seemingly independent threats.
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The Big Bad of .hack// could go one of two ways: Cubia although defeating him doesn't really solve anything other than getting him out of the way, or Morganna, although you never really fight her directly. She simply uses the phases to interact and fight for her. Once Kite "kills" Aura, she is able to come back and defeat the last phase of Morganna, and truly be born
I don't think you can really call Cubia the big bad as he's really sort of the bigger bad that results from the big bad's actions.
The true Big Bad here is probably AIDA: it's the root cause of all the problems that are happening and it is the primary antagonist for 90% of the games. Ovan doesn't really count as he was working against AIDA the whole time, making him a Chess MasterAnti-Villain at worst.
The Man in Glasses from Twelve Thirteen turns out not to be. He's the only person who was actually on your side throughout the entire game, while everyone else — including your apparent "ally" that he kills — were trying to stop you from performing the mission you were created for, believing you were too irretrievably damaged to be successful.
The Kurain Village Arc of the Ace Attorney series eventually revealed that it had a Big Bad of sorts in Morgan Fey, whose schemes to get her daughter Pearl installed as the "Master" of the Kurain Spirit Channeling technique spans two games and strikes the main characters from beyond the grave. She also has her daughter Dahlia as a Dragon of sorts.
Two of the games had their own Big Bad.
In the first game, the Big Bad is Manfred von Karma, who essentially set the entire series into motion with the murder of Edgeworth's father. A murder in the present that was orchestrated by him to get back at Edgeworth ultimately results in his comeuppance.
Damon Gant is revealed as the true criminal of the bonus case in the first Ace Attorney. Gant eventually states that he is responsible for controlling Lana Skye, the High Prosecutor who in turn was responsible for "helping" Edgeworth with cases, which resulted in the rumors of Edgeworth's backhanded deals and forgeries that DIDN'T already come about from Edgeworth's already established relationship with Manfred von Karma.
The third game has Dahlia Hawthorne, who on top of essentially being Morgan's Dragon is a Big Bad in her own right because of all the murders she conducted that had to be cleaned up by the end of the game, resulting in finally facing her spirit in court.
The second game doesn't necessarily have someone as the Big Bad but each of the cases impact at least part of the story. In the fourth case, the Big Bad is at first thought to be Shelly de Killer but when he turns out to be an assassin, his client becomes the Big Bad. And guess who his client is: Matt Engarde, Wright's own client. This sets up the overall theme of the game of what is a defense attorney.
Apollo Justice has its own Big Bad as well in Kristoph Gavin, who uses every trick in the book from forged evidence to outright murder to take down Phoenix Wright and keep everyone quiet about it.
Then Ace Attorney Investigations has Ambassador of Allebhast Quercus Alba, who is the head of an international crime syndicate and is quite possibly the first ever Ace Attorney villain to be the The Man Behind the Man to nearly all the other murderers in the game. With the exception of the criminal of the third case, and it's the criminal's father who has a connection to Alba's syndicate.
'Ace Attorney Investigations 2'' has the distinction of having both a Big Bad and a Bigger Bad. The bigger bad is the Fake President of Zheng Fa and his minions who controlled both Zheng Fa, and the prison and legal systems of Japan/USA. The Big Bad however is Sōta Sarushiro, who killed his former best friend, and the aforementioned president for personal reasons and is the final boss of the game.
Mia Fey is implied to have had her own in Redd White of Blue Corp. He's the second criminal in the first game and he has a role in the story of the first game.
Dual Destinies has a Big Bad for just about everyone but Phoenix in The Phantom, the man who bombed the space center seven years ago and again during the game, among other things brought on by trying to keep these crimes hidden. He's also impersonating your detective after killing him a year before the game, trying to lead the case away from himself.
The overarching plot of the Assassin's Creed series has Abstergo/The Templars, with Warren Vidic being their most prominently villainous member in the main games. Juno was also revealed as a chessmaster villain at the end of III. Each game also has its own Big Bad:
In the regular storyline of Asura's Wrath, Lord Deus and Gohma Vlitra are the primary forces that are plaguing the world that Asura finds himself in. In the Grand Finale DLC, however, it turns out that Chakravartin, the Creator, is the one responsible for the Gohma, and by extension, all the horrible things the earth gods did to try to fight them.
The Joker continues to play a critical role in Batman: Arkham City, but it is Professor Hugo Strange who is responsible for the creation of the mega-prison, the unwarranted arrest of Bruce Wayne and all of the "political prisoners" in Arkham City who either knew too much about the prison's creation or spoke out against it (all without trial, no less), and even supplying the various supervillains with weapons in order to fuel their raging gang wars. At the end, it is revealed that Strange is a disciple of Ra's al Ghul (who promised Strange immortality and his position at the head of the League of Assassins in exchange for his help), and Arkham City's purpose was to gather all of Gotham's criminals in one place so that the two could use the dangerously escalating gang violence as an excuse to cure Gotham City's criminal problemby exterminating all of the prisoners via a huge military airstrike.
BlazBlue has Yuuki Terumi, better known as Hazama, the most proactive and involved of its antagonists, and ReliusClover, his partner in crime ever since the start of the Dark War, 100 years before the start of the first game. But as of Chronophantasma it's revealed that they are pawns to the real Big Bad Izanami the Goddess of Death and is using Saya as a Vessel as well as being Imperator she backstabs them leaving Terumi dead and Relius a broken man
BlazBlue's predecessor, Guilty Gear has That Man, who created the Gears, who in turn have wreaked havoc on the world. He's a pretty ambiguous guy (no one even knows his name) and not much is known about him or what he's planning.
Chrono Trigger has Lavos, whose influence is felt in every time period and who is ultimately responsible for not one, but twoThe End of the World as We Know It events (extinction of the Reptites and start of a long ice age in 65,000,000 B.C., and the destruction of the magical Kingdom of Zeal in 12,000 B.C.). The heroes are trying to prevent a third which will occur in 1999 A.D.
Lavos' actual role as the Big Bad is debatable, as it is not necessarily in control of all the plots; they just tend to happen due to different tribes, such as Zeal, worshiping it or its own natural instincts for world destruction.
City of Heroes has a number of especially powerful and influential bad guys that compete to take over the world.
Uka Uka from Crash Bandicoot. While Dr. Neo Cortex seemingly was behind all the events in the first two Crash games, it was eventually revealed that he did everything under Uka Uka's orders. However, in Crash: Mind over Mutant, Cortex doublecrosses Uka Uka and becomes the Big Bad himself.
It should be noted that in the second "era" of Crash (Wrath of Cortex to Twinsanity), Uka Uka stopped being a major force in the games and acted more as a Bigger Bad, generally leaving someone else in charge. While this person was generally Cortex, Dr. Nefarious Tropy was given a chance in the second GBA game. While in the later game Crash of the Titans he gave Nina the same role, Uka Uka contributed enough to the plot to be the Big Bad.
There are also four/five standalone villains: Nitrous Oxide in Crash Team Racing, the Evil Twins in the main plot of Crash Twinsanity (though they're a Big Bad Duumvirate), N. Tropy (who is under Uka Uka) in the sub-plot of Twinsanity, Emperor Velo XXVII in Crash Nitro Kart, and Willy Wumpacheeks in Crash Tag Team Racing..
In Danganronpa, there is Monobear. He is being controlled by the real Big Bad, Junko Enoshima.
Dark Cloud has the Dark Genie. The sequel, Dark Chronicle, had Emperor Griffon/the Dark Element story wise, though the Dark Genie returns in the final Bonus Dungeon.
Demons SoulsSpiritual SuccessorDark Souls notably doesn't have a real Big Bad. The reason behind everything going wrong is simple entropy. Gwyndolin does try to manipulate you in a bid for power, but he's ultimately a minor player — he's not even a required boss fight.
Forrest Kaysen in Deadly Premonition, who caused most, if not all of, the problems in the story ( the murders that take place in Greenvale, and driving the townspeople insane with purple gas) . It's even to the point he's responsible for horribly mentally scarring of the original personality of the one called York, the original personality being Zach.
The Overtime mode introduces Brock Mason, the second Big Bad of the game.
Dead Rising 2 has TK throughout the entire game, although the true mastermind behind the outbreak is revealed to be Sullivan, or Stacey in the alternate timeline of Off the Record
The Case West DLC seems to reveal the series' Bigger Bad in the form of the Director of Phenotrans.
Dead Space has two, Mercer and Kendra. The situation is unique as you fight neither of them, though you do fight what may or may not be considered as the third Big Bad, the Hive Mind. Well, you do fight Mercer.
As a normal enemy, if you're daft enough to let the Infector get through necromorphing his corpse. Considering it's puppeteering the other Necromorphs and is the final boss, yeah, I'd consider the Hive Mind to be a Big Bad. Mercer even talks about "... the Hive Mind's gift", suggesting he considers himself to be it's servant.
Dead Space 2 has Hans Tiedmann at first, until Nicole/The Golden Marker (12B) reveals herself as the true Big Bad
Diablo, the Lord of Terror, is the Big Bad of the series that bears his name, though in Diablo II, he shares this status with his two brothers, Mephisto and Baal, as the "Prime Evils."
The Donkey Kong Country series uses King K. Rool for the series' main Big Bad. Donkey Kong himself was the Big Bad in the earlier games with him versus Mario. Then Mario takes the role in Donkey Kong Jr, with DK being the victim. Donkey Kong Country Returns has Tiki Tong.
Doom 2's big bad is the Mook Maker, the one who spawned all the enemies in the first place. Considering that it only appears once in the game, and its destruction damages untold miles of Hell's surface, we can assume that the big static face we call the Icon of Sin is the big bad of the game.
In Dragon Age: Origins, Loghain acts as your standard Big Bad for a large portion of the game, until he's upstaged by the Archdemon. The sequel then goes on to deconstruct this trope: in the end, every party involved in the games' climax is partly to blame for how things turn out, whether by design or simply being a bit too close to the fire. Cassandra tries to find out who the Big Bad was, but there is only Greyand Grey Morality and Well-Intentioned Extremist characters.
Dragon Quest VI had Murdaw, also known as Mudo until his defeat which you find out evil still plagues the world. After D(h)uran is defeated, he tells them that he, Murdaw/Mudo, and the other demon lords were just pawns of the true Big Bad, Mortamor (also known as Dethtamoor).
Dragon Quest VII had Orgodemir, the Demon Lord who sealed most of the continents of the world to prevent God from defeating him. in the second disk, he tries to seal the continents again, while posing as God Himself.
While not the actual final fight, Temuorin serves this role in Eien no Aselia. Not the most powerful enemy faced, either. Just the one who was in charge all along.
The Elder Scrolls has a different Big Bad in each game, although they're often in the service of Mehrunes Dagon, the Daedra Lord of Destruction, who serves as a Bigger Bad of the setting.
Arena, had traitorous Imperial Battlemage Jagar Tharn, who was secretly in league with Dagon.
Battlespire, a spin-off game taking place during Arena's time period, had Mehrunes Dagon himself leading the Daedric invasion of the Imperial Battlespire.
Daggerfall has several different faction leaders, but the Underking is the one most directly tied to the main quest line (and also the guy on the front cover of the game). Also, Lord Woodborne is the one who turns out to be behind the murder of the King.
In the end, the game doesn't really have a Big Bad. The Underking turns out to be not all that far from a good guy, and Lord Woodborne, while directly responsible for the King of Daggerfall's death, is not an independent operator...
Redguard, another spin-off game which tells a smaller-scale, more personal story, has Imperial governor Admiral Richton as the main antagonist.
Morrowind has the A God Am I supervillain Dagoth Ur. The first expansion pack, Tribunal, has Almalexia, a different A God Am I persona who acts as one of the three Dunmer gods. The second expansion Bloodmoon has Hircine, the Daedra Lord of the Hunt.
Oblivion has Mythic Dawn cult leader Mankar Camoran, but his master Mehrunes Dagon makes an appearance at the very end. The first expansion, Knights of the Nine, has the resurrected Ayleid lord Umaril the Unfeathered. The second expansion, Shivering Isles, has Jyggalag, Daedra Lord of Order who was transformed by the other daedra lords into Sheogorath, Lord of Madness.
Skyrim has Alduin, the Nordic dragon god of destruction. The first large expansion, Dawnguard, has Lord Harkon, the leader of the vampires of Castle Volkihar. The second large expansion, Dragonborn, will have the very first Dragonborn as the Big Bad.
Era 5: Bolbox. In addition, it turns out the ones accidentally responsible for all of these except King Kuralesache are Martians.
The big bad of Fable is the demon Jack of Blades. Fable II has Lord Lucien. Fable III has The Crawler. It is hinted throughout the series that Theresa may be serving as a Bigger Bad, but this hasn't been outright confirmed by the plot yet.
The spoiler was jossed in Fable: The Journey. Theresa actually manipulated everything in order to save the world from The Corruptor (the Big Bad of the game, and the Bigger Bad of the series as a whole up to that point), so she's the Big Good for all intents and purposes.
Fallout: New Vegas: Caesarnote a little trickier since there's an ending path where you join him, but he's still obviously the central figure in the main conflict, and siding with him merely makes your character a Villain Protagonist, with Lanius as the Dragon-in-Chief. Aside from him the DLC all have their own Big Bads:
Dead Money: Father Elijah.
Honest Hearts: Salt-Upon-Wounds.
Old World Blues: Dr. Mobius, later on revealed to be Dr. Klein.
Lonesome Road: Ulysses, who is also the Bigger Bad of the DLCs.
In FEAR, it's a toss-up between humongously powerful psychic Stringy-Haired Ghost Girl Alma and Corrupt Corporate Executive Genevieve Aristide. While Alma has undeniably been wronged, her revenge is... rather extreme. As for Aristide, she just wants to keep her job, and to hell with anyone who has to die in order for her to do so. Events would never have gotten as hellish as they did if either one of them wasn't in the picture.
The Final Fantasy series is famous for its Big Bads. Some of the most well-known, one in every game:
Soul of Rebirth, the sequel quest released with the Game Boy Advance and PSP remakes, puts an interesting spin on this. It's revealed that after the Emperor was killed the first time, his soul split in two, one half going to Heaven and one half to Hell. The Hell Emperor was the Final Boss of the original game. In this one, the party meets the Heaven Emperor... who is also a Big Bad who has upset the natural order of the afterlife and generally made a mess of things (apparently he planned this.) Yes, the Emperor is so evil that even his good half is evil.
Final Fantasy IV has Golbez, Cecil's brother, until later it was revealed he was under control of the alien Zemus. Zemus is promptly killed by Golbez, and transforms into Zeromus, the game's ultimate Big Bad.
The After Years has the Creator, a nigh-incomprehensible alien being out to resurrect its long-dead race, no matter whose planet it has to step on to do so.
Final Fantasy V had Exdeath, who at first appears like a conventional evil emperor type character, but is actually made up of evil spirits that were trapped into a giant tree, and then said tree manifested itself as a humanoid. The GBA version also reveals Enou, a necromancer who was mentioned in the original game as Exdeath's predecessor, another villain who also tried to control the void, as an optional superboss battle.
Final Fantasy VI starts with Emperor Gestahl until he is usurped by Kefka, a Monster Clown who becomes a god by killing Espers and absorbing their souls.
Said "mommy," by the way, is an Eldritch Abomination called JENOVA who was the Big Bad thousands of years before the beginning of the story. Though potentially dead all along, her legacy is felt through her son eons after her defeat. As for the more immediate backstory, Professor Hojo filled the role until Sephiroth descended into villainy.
Fittingly enough, Jenova and Hojo are Sephiroth's "parents". Hojo in a literal case, and Jenova in a metaphorical case.
Crisis Core has Genesis Rhapsodos, who was indirectly responsible for everything Hojo wasn't.Sephiroth is also the big bad for the game's spin offs
Naturally, given how many of these guys are playing or attempting to play "higher power" to each other, a case can be made for all of them being the Big Bad of the entire Compilation. Or at least being a Big Bad for a exceptional period of time, though Genesis and Fuhito comes off as the weakest of the bunch.
Final Fantasy VIII had Sorceress Edea, the schoolmaster of Galbadia Garden, until it revealed that she was merely a puppet for Ultimecia, a sorceress from the future. It is revealed that the final boss battle leaves Ultimecia in a weakened state, in which she goes back in time, and possesses Edea, meaning the game is a time-loop paradox. Also, Edea was the wife of Balamb Garden's schoolmaster, Cid Kramer, who created a special forces military group whose sole mission is to exterminate sorceresses, meaning his wife.
Final Fantasy IX had Kuja and Garland competing for the position, the winner being Kuja, although Garland, like Professor Hojo from VII, is responsible for nearly everything in the background.
Final Fantasy X had the massive entity Sin until it is revealed Sin contains Yu Yevon, a god-like being with a cycle to reincarnate itself as the creature Sin. Also, the Church of Yevon turns out to be evil, with Maester Mika as the Big Bad who arranged the war with the Al Bhed and sought to keep the truth about Sin's nature from the world.
Final Fantasy X-2 has a similar monstrous entity, Vegnagun, who is actually not a creature but a weapon, piloted by the angry ghost of Shuyin, a hero-like character with a similar appearance to Tidus. It is implied Shuyin was the actual person the Fayths were inspired by when creating Tidus.
Final Fantasy XI had the Shadow Lord, revealed to originally be a Galka soldier who sold his soul to the underworld after being wronged in a love affair, in the original game and acts as the overall Big Bad. Expansion packs also added new villains:
Rise of the Zilart: Eald'narche
Chains of Promathia: Promathia
Treasures of Aht Urhgan: Alexander
Wings of the Goddess: Probably Lilith or Atomos (flashback sequences also feature the Shadow Lord's origins)
A Crystalline Prophecy: The Seed Crystal, creator of the other crystals which have been causing trouble.
Final Fantasy XIII has Primarch Galenth Dysley, who is actually Barthandelus, the fal'Cie creator and leader of Cocoon. He and Orphan, his fellow fal'Cie who powers Cocoon, collaborate together to ensure its destruction.
Final Fantasy XIV has the Garlean Empire and its unseen Emperor, though the plot of the game was never completely finished, as Square Enix decided to scrap the game in favor of a reboot, Final Fantasy XIV: A Realm Reborn. It is unknown if the plot of A Realm Reborn will feature the Garlean Empire as the head villain or not. The closest character the game has to a major villain is Nael van Darnus, one of the leaders of the Garlean invasion, though he is just one of many generals.
Dissidia: Final Fantasy establishes that in the Final Fantasy multiverse, the evil god Chaos is the biggest Big Bad. He bosses around most of the people listed above, and the only ones who try to double-cross him are Emperor Mateus, who plans to outlive Chaos to rule the universe and Golbez who, as he was not the Big Bad of his game decides to help his brother, Cecil, in getting the crystal.
Though Chaos himself actually doesn't Boss or even order anyone around at "all". Most of the orders come from either the Emperor, or oddly enough.... Kefka and Kuja.
Final Fantasy Tactics had Lord Folmarv, who is actually Hashmal, the second-in-command and acting leader of the Lucavi. Ultima, his superior, would be considered a Bigger Bad of sorts as she is completely incapacitated until the final battle.
The Fire Emblem Series is home to quite a few per game.
In the first game and its remake (Shadow Dragon), we have the Big Bad Duumvirate of Earth Dragon Medeus and Demon King Gharnef.
The second game has the dark god Doma though he's actually a pretty okay guy, though he has a cosmic-scale sibling rivalry going on.
Medeus and Gharnef return in the third game.
The fourth game has the evil deity Loptous, though he's a very impersonal opponent, and indeed you never fight him directly, with most of the direct villainy being done by his high priest Manfroy and his human vessel Yurius.
The fifth game, a "midquel" to the two halves of the fourth, has the dark priest Veld, though he's actually Manfroy's second in command.
Fire Emblem: Fuin No Tsurugi, the 6th game, had King Zephiel as the main Big Bad.
Fire Emblem: Rekka No Ken (simply Fire Emblem in the English version), the 7th installment, first focuses on Lundgren, as he's trying to kill Lyn so he can rightfully ascend to the throne of Caelin, but he's just the villain in the prologue. After that, there's a decoy Big Bad in the form of Lord Darin, but the actual wirepuller is the Dark Druid Nergal.
Fire Emblem: The Sacred Stones features The Demon King, Formortiis, as the main enemy. He had been defeated by the five heroes many years ago, but he has been revived due to Lyon's creation of the Dark Stone from Grado's sacred stone. While indirectly responsible for Grado's military ambitions, and all that followed it, he is directly responsible for the appearance of monsters across Magvel.
Fire Emblem: Path of Radiance stars Ashnard, king of Daein, as the primary antagonist. He desires a world in which the strong dominate the weak, and he seeks to use Lehran's Medallion to awaken a Dark God and gain power. He is the final boss, and most of the earlier bosses are working for him. This includes the Four Riders, most notably the Black Knight.
Fire Emblem: Radiant Dawn is divided into four parts, each part having its own big bad. In Part I, the primary antagonist is Jarod, a Begnion general who seeks to supress the Dawn Brigade's uprising in Daein. In Part II, it is Lord Ludveck, who wants to displace Queen Elincia as ruler of Crimea. Part III is unique, in that you alternately play as opposing armies; it could be considered Micaiah, or Ike, but it would better be considered Pelleas' signing of the blood pact. In part IV, the big bad is Goddess Ashera, who seeks to destroy the world, which she has deemed irredeemable, at the urging of Lehran.
All Guild Wars campaigns have Big Bads of some sort, except perhaps Prophecies (which has several evil groups.). The Nightfall campaign also makes Abaddon the big bad of the first three campaigns
Lou the Devil in the Guitar Hero series tries to get aspiring rock-stars to sign his contract so he would get possession of their souls, and also kidnaps the God of Rock in order to get an artifact to drain audiences of their souls.
In Half-Life, and its expansion packs Decay, Blue Shift and Opposing Force the Big Bad would have to be the Nihilanth, the creature that was maintaining the rift all along. In Half-Life 2 and its Episodes, it's Wallace Breen, former administrator of Black Mesa and the human ruler of Earth under the Combine. However, with Breen's death at the end of HL2, it's not certain who the actual Big Bad is, but it's highly likely that the leader(s) of the Combine will surface in Episode 3.
The Halo series had two Big Bads, the Prophet of Truth (the leader of the Covenant), and the Gravemind (the leader/Hivemind of the Flood).
Professor Ort-Meyer in the original Hitman: Codename 47.
Sergei Zavorotko in Silent Assassin.
Inspector Fournier in Contracts, as the one who managed to put 47 in the jeopardy that constitutes the game's Framing Device.
Alexander Leland Cayne, the leader of the Franchise in Blood Money.
Each game in the Homeworld franchise has a pretty clear-cut example:
The Taiidan emperor from Homeworld. Spends most of the game in the shadows, but according to the backstory for Homeworld: Cataclysm, he was a twisted, ruthless mess of a ruler who managed to stay on his throne by cloning himself, and who ordered the destruction of a planet - namely YOURS - mostly as a publicity stunt.
The Beast infection is the primary antagonist Homeworld: Cataclysm, and towards the end of the game it is controlled by The Nagarrok, an ancient alien vessel that picked up the Beast infection in Hyperspace. It even has it's own Dragon in the infected lower half of the Somtaaw Command Ship.
The nomadic Vaygr from Homeworld 2 are led by Makaan in their attempts to conquer the galaxy. Unusually for a Big Bad, he's killed before the end of the game, and you spend the last mission fighting off what's left of his fleet as they try to bomb your planet.
The last episode of Jack French reveals that Vince was the serial killer of that episode, and that he killed Nami from episode 1 as well.
Jade Empire plays with this trope: Death's Hand first appears to be a bad guy acting on his own, and then it is revealed that he has been acting on Emperor Sun Hai's orders all along and the Emperor was the one who set up the death of the Water Dragon and the upsetting of the balance in the first place. Once you defeat the Emperor, your kindly old Master Li wanders in, reveals that this was all part of his Evil Plan to get vengeance on his brother Sun Hai, and kills you, and it turns out that he was actually the mastermind behind the massacre at Dirge, as well as the final boss of the game.
Mizar, a.k.a. Tribal leader Jeff's long-lost brother Barry, in Jet Force Gemini.
The Kingdom Hearts series has the scientist turned madman Xehanort serving as the main Big Bad. While by the first game's timeline he is long gone, aspects of him serve as villains of almost every game in the series. There are others. The list of villains in each game is as follows:
It's up in the air who the Big Bad of 358/2 Days is due to all but the very end playing out like a Villain Episode. Xemnas again appears, but this time he's your boss, so (at least from the player character's perspective) he seems like a Good Is Not NiceBig Good, though by the end of the game it's apparent he doesn't care about his followers and would gladly discard them (fatally) should a more useful one come along. There's also Xemnas' number-two guy, Saix, who appears more and causes you far more trouble. The last candidate is DiZ, leader of the faction opposing your group, except that, while he's incredibly unpleasant, motivated mainly by revenge, and probably going way too far, he's actually trying to save the universe from you, and in KH2, he ends up changing his less-than-admirable ways.
In Coded, the Big Bad turns out to be the data version of Sora's Heartless.
The Last Story presents Zangurak as this, until it's revealed that Dagran is the real villain.
The AI Director itself in Left 4 Dead is the big bad behind every possible bad thing that happens to the players, especially on Expert difficulty where all it does is punish players for doing badly and slaughtering them for trying to be good.
In the Legacy of Kain series, while the morality of all of the characters is somewhat difficult to determine, by the end of Defiance, it seems to be firmly established that the big bads of the series are the Hylden Lord (and his entire race in general) and the Elder God.
Actually, the Hylden Lord and hylden in general were pawns in Elder God's game as well. Elder God is the only Big Bad
The textbook Big Bad for The Legend of Zelda series is Ganon/Ganondorf. Ganon's practically incapable of not being the Big Bad. There are exceptions, however:
MapleStory seems to be angling to have the Black Magician as the Big Bad. He sure fits it. He had several heroes frozen in ice for a while, chased the people from continent to continent, and is willing to do it all twice.
Marathon provides a rare, non-villainous (though certainly antagonistic) example: Durandal. Although he has his own goals and desires like any other being, Durandal was the one that set things up for the first game; he's ultimately responsible for everything that happened to the titular Marathon ship. Sure, he helps you halfway through, but only because it fits with what he was aiming for in the end.
In the second game, T'fear is introduced as the commander in charge of Pfhor Battle Group Seven, but he isn't even encountered, much less killed, and serves more as a Bigger Bad. Later in the game, Tycho is reintroduced, this time allied with the Pfhor, trying to kill Durandal and the humans (he has bad experience with both). Tycho, however, is killed about halfway through, and the rest of the game deals with cleaning up the mess.
The Big Bad in both Marathon Infinity: Blood Tides of Lh'Owon and Pathways Into Darkness is the W'rkn'cacnter, an Eldritch Abomination capable of destroying the universe. In both cases, the Jjaro help you stop it. In Infinity, Tycho thinks that he's the Big Bad, but he doesn't know the universe is being threatened and that he's essentially a wannabe, as the Jjaro are transporting you through space and time (although he does force you to go into another timeline, thanks to his capture of you).
Rogue turian Spectre Saren Arterius serves as the Big Bad in Mass Effect. Only, he's not. The real Big Bad is Sovereign, Saren's flagship, in reality a fully-sentient member of an ancient race of "machine devils" known as the Reapers.
And in Mass Effect 2 we have the Collector General, but, again, it's a fake-out, and the real Big Bad is Harbinger, a Reaper merely useing the General to control the Collectors.
No matter who starts the plot in each original Mega Man game, you can guarantee that Dr. Wily is behind it in some way. Same goes for Sigma in the X games (with three exceptions), and eventually, Dr. Weil in the Zero games. Even Mega Man Battle Network does this, with the villains of the 2nd, 4th, and 5th games being connected to — you guessed it — Dr. Wily.
We find out that prior to the Mega Man X series, then leader of the Maverick Hunters, Sigma, was infected with the Zero Virus after he fought the rampaging Zero, the last creation of — yup — Dr. Wily. Sigma eventually succumbed to the virus and turned maverick himself.
Dr. Weil of Mega Man Zero fame seems to be following in Wily's footsteps. Not only is he the one who caused The End of the World as We Know It, he continues to plague the world, even after his and Omega's exile. Most of the machinations behind the series' first half can be indirectly linked to Weil. And, in Mega Man ZX, it was hinted that it wasn't Serpent, Master Albert, or Master Thomas who was the true Big Bad, but it was actually Model W, which is what remained of Dr. Weil's own consciousness.
Moreover, Weil was closely linked to Omega, who was what Wily's Greatest Creation was supposed to be, thus creating a distinct intellectual link between the two Big Bads.
The Metal Gear series is probably best known for its mind screwiness and Gambit Roulettes, and while the series as a whole appears to go through several Arc Villain Big Bads, culminating in the reveal that there has never been a true Big Bad at all, the confusion is mitigated somewhat by the fact that each individual game has a Big Bad of its own:
Metal Slug has General Morden, although he's constantly upstaged by the Mars People or some other threat. In Metal Slug 6, both Morden and the Mars People are forced into an Enemy Mine situation by the Venusians.
In the Metroid games Ridley is Samus' Arch-Enemy, but he is rarely a Big Bad in his own right; usually, he's The Dragon to Mother Brain or a different villain. Presented chronologically, each game in the series has its own Big Bad:
Ridley aside, Mother Brain is the most recurrent antagonist (and can be considered the series' main antagonist), and the Prime games are all tied by the threat of Phazon, which serves as the trilogy's Bigger Bad.
The Might and Magic series has had a number of Big Bads over its very long run.
Might and Magic 1 to 5: Sheltem, a rogue Planetary Guardian, one of many created by The Ancients, who went a little bonkers and decided the best way to protect his own planet was to destroy all the other ones that were created by the Ancients.
Archibald Ironfist was the Big Bad of Heroes of Might and Magic 2, being the evil contender in the titular Succession War. He seems to be set up as this in Might and Magic 7, after being released in 6, but ultimately is upstaged by his Terran advisors, who themselves fail to reach this level by virtue of not causing most of the problems the heroes must solve.
Might and Magic 6 and Heroes of Might and Magic 3: The Kreegan, the ancient enemies of the Ancients, although their leadership changed quite frequently due to consistently being killed by the games' heroes. M&M 6 had the Kreegan Queen and HMM3 had Xenofex and, after Xenofex gets killed in M&M 7note He is not the Big Bad of that game - no one is, most problems the heroes must solve being actually independent -, but he gets killed in it., Lucifer.
Might and Magic 8: Escaton the Destroyer causes, directly or indirectly, most of the problems the heroes must face. As opposed to Sheltem, however, he is not malfunctioning, just caught between his programming and the realization that the Ancients might have failed to consider this situation or deemed it acceptable losses.
Might and Magic 9 and Heroes of Might and Magic 4: These two games mainly suffered from Canon Discontinuity due to 3DO games crashing and burning at the time they were made.
Monster Girl Quest has Illias, The Creator who seeks to destroy the entire monster race. She even killed off an entire city for coexistence between monsters and humans, and sealed a former Hero for rebelling against her. Her deep-seated hatred for monsters was even made into a religion.
Giegue returns as the Big Bad in the sequel, Mother 2, aka EarthBound, though in the American game he's called Giygas.
Porky Minch, who serves as The Dragon for Giegue/Giygas early in the game, later has a role-reversal when it is revealed that Giygas has lost the ability to make his own thoughts, and Porky winds up pulling the strings at the end, taunting the heroes as they battle a powerful but dumb Giygas.
In Mother 3, Porky Minch, aka the bratty kid from the second game who turns out to be The Dragon to Giygas is revealed to be the Big Bad in the final chapter.
In Heaven's Feel, the Big Bad is Zouken (who is directly or indirectly responsible for everything bad that happens in the entire route) , although both Kotomine and (eventually) Dark Sakura could also be seen as this.
Araya Souren in Kara no Kyoukai. Notably, he was confronted about halfway through the series and never heard from again.
The creator race queen Morag in the original. She seeks to restore the reptiloid dominion over the Sword Coast.
The medusa Huerodis in Shadows of Undrentide. She wants to raise the fallen Netherese city of Undrentide for unknown reasons, and manipulates you into delivering a mythallar to do it with. No word on what the next bit of her plan was.
The archdevil Mephistopheles in Hordes of the Underdark. After being bound on the Prime Material Plane by a powerful drow priestess called the Valsharess, he manipulates you into destroying her armies and attacking her, weakening her enough to break free. He wants to Take Over the World.
The King of Shadows in Neverwinter Nights 2. This is a Pure Magic Being that seeks to uphold the laws and protect the descendants of the ancient empire of Illefarn. Problem is, Illefarn is long gone due in large part to the King of Shadows' origin story, and the King is corrupted by Black Magic.
Akachi the Betrayer in Mask of the Betrayer. Sort of. He was transformed into a curse of elemental hunger that is slowly killing you.
In Storm of Zehir, the yuan-ti House Se'sehen, led by an avatar of Zehir, the yuan-ti god of poison. They want to Take Over the World.
Nine Hours, Nine Persons, Nine Doors plays with this in a surprising way. The Big Bad ends up being Ace as the person who set everything into motion, but the current Notary Game is actually being run by June and Santa, who are trying to punish the four men responsible for the first game and to get Junpei to save June's life. Time travel loops and all that.
The Night Of The Rabbit: It is the Evil Wizard Great Zaroff. Though you get hints about it early in the story, you do not discover the identity of the villain until much later.
Lady Margaret, as the queen of the Magog Cartel, is the Bigger Bad behind Molluck, Brewmaster, and all the other Glukkons, however she hasn't appeared in a game yet.
Lady Margaret's grandmother is the Bigger Bad behind Lady Margaret, and is supposed to appear in Squeek's Oddysee.
It was heavily implied in several interviews that the ones really in control of the industry will not appear until the end of the Quintology.
Beiloune in Okage: Shadow King, who turned out to be surprisingly sinister.
There are three in Ōkami: Orochi, Ninetails and Yami. It's later revealed that all of the main bosses in the game, main villains and minions, come from the same source (not another villain, but rather the source of evil's very existence).
In Ōkamiden, there's Akuro, who may or may not be the core of Master Anura, Bullhead, Sen, Ryo, and King Fury, a part of Yami along with the previously mentioned demons, or the Bigger Bad of the first game, using both Orochi and Yami as vessels. The game contradicts itself a lot, though.
Persona 2 toys with the idea of a Big Bad Duumvirate between Jun Kurosu and Adolf Hitler (we're not kidding), before it's revealed that Nyarlathotep was posing as both Hitler and Jun's father and orchestrated the events of the first game.
Persona 3 elevates Nyx, an Eldritch Abomination, as the primary focus following The Reveal. All other antagonists, including Strega, Ryoji Mochizuki and Shuji Ikutsuki, wish to bring about Nyx's arrival, willingly or otherwise. It's worth noting that Ikutsuki instigated the entire thing in order to cause Nyx's arrival, but he dies shortly after The Reveal, so he counts more as a Disc One Final Boss. Even still, The Answer reveals that Erebus, anotherBigger BadEldritch Abomination, was the one pulling Nyx's strings.
Persona 4 has Tohru Adachi, who influences people like Namatame to do the actual dirty work after the first two murders. In typical Persona fashion, the True Ending reveals that Izanami has been behind everything from the beginning of the game, including Ameno-Sagiri, the thing enveloping Inaba in a poisonous fog.
Although the player's goal in the Pokémon series is to become Champion, the leader of each generation's evil team serves as the Big Bad, as they are the ones responsible for whatever troubles are occurring in each region.
Pokémon Gold and Silver/Crystal: In the originals, there is no nominated leader of the regrouped Team Rocket; the final Team Rocket Executive fought in the Radio Tower is the closest the organization has to one. The remakes gave the Rocket Executives names, and so the aforementioned Executive was finally given an identity: Archer.
Pokémon Ruby and Sapphire/Emerald: Maxie (Team Magma) and/or Archie (Team Aqua), depending on which version you are playing (Magma for Ruby, Aqua for Sapphire). Notably, the other team leader will actually assist you in stopping the Big Bad; however, both leaders are Big Bads in Emerald.
Pokémon Black 2 and White 2: Colress is acting like the Neo Team Plasma boss, although he was acting as the boss only for his own purposes and the Big Bad is actually Ghetsis again.
Then there's the spin-off series, Pokemon Mystery Dungeon Explorers of Time/Darkness/Sky: Darkrai, who wanted to cover the world in darkness and has been manipulating events behind the scenes the whole time, messing with the fabric of time and space as well as appearing in the heroes' dreams to get them to kill themselves. If that doesn't qualify as a Big Bad, I don't know what does.
In another pair of spin-offs, Pokémon Colosseum and Pokémon XD, the villainous organization Cipher is the main antagonistic body (and since Cipher is much more competent than any of the main series' Teams, there is no Gym Challenge or Championship to aspire to; you fight Cipher and that's it.) The leader of Cipher is the Big Bad and differs in each installment; in Colosseum it's Nascour, but Your Princess Is in Another Castle and the realBig Bad is the mayor of Phenac City and in the sequel it's Greevil, who you've known from the beginning as Mr. Verich.
Portal: GLaDOS. Not only does she place Chell in danger numerous times, half-way through the game she tries to kill her by placing her on a platform heading towards a pit of fire and at the end of the game, she almost kills her by flooding the Enrichment Centre with a deadly neurotoxin..
In Portal 2GLaDOS continues the role at first, but eventually, she's overtaken by Wheatley. Finally it turns out that it's the mainframe which causes all the problems.
Iris is the true antagonist, as she arranged for the rebellion to be held against the Empire just For the Evulz of it. She had her father imprison Karl because He Knows Too Much and arranged for Raimund to be brought Back from the Dead. Her agenda is to become the god of the world, and intends to use the power and intellect she got from being reincarnated from Rosenkreuz to do just that.
RuneScape has several, usually at least one in each of the various milti-part storylines:
The Pirate series has Rabid Jack. Like Drakan, we've never actually seen him, but since both of the series's big villains so far, Captain Donnie and Mi-Gor, have been stated to be under his command, there's little doubt who the final foe is.
And finally, the Mahjarrat series, which ties together the Desert, Dagon'hai, Defender of Varrock, Black Knight, etc. storylines into one huge Myth Arc that is probably the closest thing to a main story this very open-ended game has, has Lucien, a particularly impressive example. Once you steal the artifact that created the world, there's really no stopping you. To a lesser degree, the other Zamorak-worshiping Mahjarrat qualify, including Zemouregal, Enakhra, and Hazeel, but it's clear Lucien is really the king here.
Seiken Densetsu 3 puts an interesting twist on this: there are actually three different Big Bads: the Dragon Emperor, the Prince of Darkness, and the Dark Lich. The three fight among each other as well as against you throughout the first half of the game, but at the halfway point, one of the three will annihilate the other two and become the main antagonist for the second half of the story. Which one wins depends on which of the six characters you've selected to be your main character.
In Skies of Arcadia, the Valuan empire is led by Empress Teodora, although her head admiral, Lord Galcian, has his own ulterior motives and serves as the true Big Bad. Incidentally, his Dragon, Ramirez, is the actual final boss, taking over after Galcian is killed, and changing the plan from rule the world to destroy the world.
All Sly Cooper games feature Big Bads though they where not always how they appeared.
Sly 2: Band Of Thieves saw the return of Clockwerk, but in pieces, so it disqualifies him from Big Bad status. Arpeggio was resembling the Clockwerk pieces to reform the mechanical bird and fuse with him to gain immortality, but at the end of the game, Neyla quadruple-crosses him and fuses herself with the frame, dubbing herself Clock-La.
Sly Cooper: Thieves In Time features Cyrille Le Paradox, a museum owner who uses time travel to interfere with the Cooper ancestors so he could have his revenge on Sly's father who indirectly caused Le Paradox's own father to be arrested.
Bruno Dondurma, whose chase after the medallion to awaken Lares is the major conflict of Solatorobo. At first.
Suhadi Sadono is this at the start of Pandora Tomorrow, but by the end he has forged a Big Bad Duumvirate with Norman Soth.
Douglas Shetland in Chaos Theory.
Emile Dufraisne in Double Agent.
Tom Reed in Conviction.
While the original Spyro the Dragon series normally had a stand alone Big Bad each game, the new The Legend of Spyro trilogy had the Dark Master Malefor as it's main villain. His Dragons Dark Cynder and Gaul serving as the main villains in the first two games due to their master being Sealed Evil in a Can they're trying to free at the time, but it's ultimately Malefor manipulating everything from behind the scenes. He's finally let out at the end of The Eternal Night and causes havok and destruction for three years while the heroes are Sealed Good in a Can before serving as the direct villain of Dawn Of The Dragon.
In StarCraft the Overmind filled this role. Kerrigan (and possibly the UED) in Brood War, and in StarCraft II, Amon, a fallen xel'naga and former master of the Overmind.
Star Wars: The Old Republic certainly seemed to set the Sith Emperor up as its Big Bad, but he leaves the galaxy before the game even starts. The jury is still out on it, but it's likely that it'll either be Darth Malgus or someone from the Dark Council.
The Street Fighter franchise has M. Bison as its Big Bad, although in the III series, Gill serves as this, even though he may actually qualify as a Well-Intentioned Extremist. Gill's younger brother, Urien, could somehow be considered the real Big Bad of the III series as he seeks to overthrow his brother and plunge the entire world into a state of chaos and destruction.
Mario & Luigi: Dream Team: Antasma the nightmare monster, who forms a Big Bad Duumvirate with Bowser. Bowser ultimately ends up double-crossing Antasma and replacing him as the main antagonist, which is actually rather surprising given the secondary status he has in most Mario RPGs.
In the Mario Party series, Bowser is usually the final opponent the players must face. The exception is Mario Party 3, where Waluigi defeats Bowser and takes his place.
The Super Robot Wars games tend to have many Big Bads, because they're made up of multiple mecha series in a single game. The result is that said game will (usually) have each and every Big Bad the series included did. Still, they tend to add an extra-big Big Bad unique to that game, often the Final Boss. The greatest example in the series is Keisar Ephes, who turns out to be the Man Behind the Man for every single original villain in the Alpha sub-series, and, by extension, is more or less responsible, at least in part, for many of the Big Bads belonging to the various anime included. It also helps that he presents himself as the anti-Ide, making him an indirect Alternate Universe big bad for Ideon. Not bad for a guy who never shows up until the final battle.
In Super Robot Wars Z, The Edel Bernal is a bit of a twist on this, but not that much of a subversion. We technically see him around occasionally, but he doesn't reveal his nature and part of the plot until, like Keisar Ephes, the final battle. He's just a Psychopathic Manchild with ridiculous levels of power that organized the entire situation for his sick pleasure and let his unwitting Dragon do all the dirty work with a simple utterance of "I love you" once in a while.]]
The Tale of ALLTYNEX trilogy have the titular Master Computer Alltynex OS where almost everything that goes wrong in the series can be traced back to it. Altough in reality it can be traced back to the Senate, the one's that caused Alltynex to turn rogue in the first place.
The Tales Series has its fair share of Big Bads, although in many of them you don't learn that they are the Big Bad until much later in the game.
Tales of Phantasia has Dhaos who is really trying to use the mana of the World Tree to save his homeworld, Derris-Kharlan.
Tales of Symphonia, the distant prequel, has Mithos Yggdrassil, who is trying to use the power of the World Tree to revive his sister Martel and create a world where all people are stripped of free will and therefore are equal.
Tales of Eternia alternates it, initially pointing to Balir, but he was Dead All Along and Shizel is the person behind it. However, she was possessed by a god called Nereid, triggered by Balir's very death, among other factors.
Tales of Graces has Lambda for the main story, along with Fodora Queen in the Future arc.
Tales of Legendia switches it up a bit, with Vaclav as the Disc One Final Boss during the first half. Maurits takes over the spotlight, but he's subordinate to the Nerifes, the real Big Bad. Afterward, the Character Quests' overarching plot involves the black mist, and Schwartz, the one generating it.
Tales of the Abyss has Vandesdelca, aka "The One Who Would Seize Glory" (more commonly known early on as Luke's swordsmanship Master, Van Grants)
Tales of Vesperia has Alexei Dinoia, though the last act of the game involves cleaning up his mess.
Faulkner of Vanguard Bandits. From his very first appearance in the story, to the endgame fight against in every ending. He isn't hesitant to head out to battle himself multiple times earlier on to lay a massive-sized beatdown on any poor fool who gets in his way.
The Viewtiful Joe series has one, mentioned at the end of the second game being responsible for everything... but the third game doesn't seem to be coming out any decade soon.
The Virtua Cop series has international terrorist Joe Fang. In the first two games, he's the leader of a crime syndicate known as the EVL Inc. Then in the arcade only release Virtua Cop 3, he returns as the leader of the ECM terrorist organization.
Sargeras is the ultimate Big Bad of the entire Warcraft universe, but because he's usually on his throne or out of commission, his various minions tend to take over the roles. Out of several characters, Gul'dan and Medivh probably counted as a Big Bad Duumvirate during the First War (or game), while Gul'dan took over the role alone for the Second (since he was using the orcs and fighting the humans). In the expansion, the job got handed off to Ner'zhul. In the Third War, Sargeras's Dragon (well, one of two), Archimonde, filled the role, while the other Dragon Kil'Jaeden and the Lich King both held it in an Evil Versus Evil situation in the Frozen Throne expansion. For World of Warcraft Big Bads, see that entry below.
In the original game, there were multiple story arcs, not all of which tied together and some of which had their own Big Bads, such as VanCleef (the final boss of one of the first dungeons), the Diabolical Mastermind behind the Defias who were behind everything until then in the human quests, right from the kobolds at the beginning. The closest to an overall Big Bad was C'Thun. Everything in Kalimdor was very obviously leading up to the Battle of Kalimdor, with the Silithid being woven in through multiple quest lines, culminating in the Scepter of the Shifting Sands quest chain. C'Thun wasn't quite the final boss before the first expansion.
In Burning Crusade, the initially hyped final boss Illidan didn't really have a lot to do with much of what was going on (after all, it was called "The Burning Crusade", not "Illidan Is a Bit of a Jerk"), but this trope was fulfilled satisfactorily later on when a patch added the new final boss, Kil'jaeden, the acting leader of the Burning Legion who are behind that whole Crusade thing.
In Wrath of the Lich King, as the name implies, it's very clear who the Big Bad is. The Lich King is a typical Evil Overlord bent on world conquest, and makes sure to appear several times along the story (unlike Illidan).
Subverted in Cataclysm; though we know Deathwing is responsible for the rearranging of Azeroth, it is heavily implied that something else is behind the scenes that even Deathwing himself is working for, making Deathwing The Dragon rather than the Big Bad.
In Mists of Pandaria, this trope is zig zagged. While the Sha might seem like the expansion's Big Bad, the only reason they exist is because of all the infighting going on between the various races and factions of Pandaria, which includes the Yaungol, Mantid and Mogu (to name only three of many); and then there's the recent helpful arrival of the Horde and the Alliance, who instantly proceeded to bring their own war to Pandaria, which made the Sha problem even worse...
Xenosaga: The Xenosaga game series (as well as Xenogears) makes particular use of Big Bads, specifically by using bait and switching the big bads multiple times. A routine of the Xenosaga games is that once a Big Bad has been "dethroned" from their role, their connections to the main characters are deepened and explained. This happens with Albedo and Margulis, among others.
The ultimate Big Bad of the Xenosaga series turns out to be Wilhelm, The Chessmasterpar excellance who was manipulating all the previous Big Bads (and every other character as well).