As the page description for Big Bad notes, that character may be the one who is directly responsible for the plot, but is not necessarily the most powerful or significant evil presence in the setting. That's where this trope comes in — the setting has a villainous presence that is more significant than the Big Badin the setting as a whole, but isn't causing the conflict of the story (and may have little to do with it at all). Perhaps, it is an important Sealed Evil in a Can that never gets released, is simply unconcerned with current events, or is a mindless force that can't by any realistic stretch of the imagination be considered a character. Sometimes, the real Big Bad will seek to exploit or make use of it, or may pay lip service to it, though this doesn't always happen. If the Big Bad tries to harness the Bigger Bad for their own gain, they'll likely learn the painful (sometimes fatal) lesson that Evil Is Not a Toy.
Note that despite the name, this is not a subtrope of Big Bad. A Bigger Bad is a more threatening force of evil in the setting and overshadows it, but due to mindlessness, imprisonment, lack of interest, or other factors, it is disconnected on a personal level from the main plot, which is caused by the Big Bad. A being can be a Big Bad in one story and later be Kicked Upstairs to Bigger Bad (or the reverse).
Also not to be confused with The Man Behind the Man, where a villain directly tied into the story is revealed to be controlling or manipulating the apparent Big Bad. In this case, The Man Behind the Man is the actual hidden Big Bad (not a Bigger Bad), and the character previously assumed to be the Big Bad is stripped of their "Big Bad" status and Demoted to Dragon or even Disc One Final Boss status. Don't take this to mean that the Bigger Bad needs to be completely physically absent from the story. They can certainly appear or even be indirectly behind the Big Bad, but the important distinction is that unlike The Man Behind the Man, they are never in direct conflict with the heroes.
A being who fits this trope is likely a demon lord, archdevil, God of Evil or Eldritch Abomination with a Religion of Evil and/or Path of Inspiration built around them. They are probably Made of Evil and will probably exist As Long as There Is Evil. Overlap with Ultimate Evil is also likely. The plot role can also overlap with MacGuffin, though this is less common. In more mundane cases, this role can be taken by a distant dictator who, like the supernatural version, overshadows a work but doesn't enter it directly. Sometimes is a Diabolus Ex Nihilo or (in video games) a Giant Space Flea from Nowhere. In either case, likes to hijack the plot.
In any work where Those Wacky Nazis are the antagonists, it's a virtual given that their marching orders ultimately come from Adolf Hitler, even if he doesn't physically appear. In any Christian allegory, Christianity-inspired work or vaguely-spiritual work written by a Christian, there will usually be some implication that Satan exists, somewhere, and is probably ultimately responsible for the evils of the Big Bad on account of being the originator of sin, but either can't or won't take much of an active role in the plot.
As a general rule of thumb, if you're uncertain whether a character counts as Big Bad or Bigger Bad—if you can remove the character from the story or replace them with an impersonal force without dramatically affecting the plot, they're probably this trope. However, note that the Bigger Bad may be part of why the villain became the Big Bad in the first place.
Compare Villainous Legacy, where a villain serves this type of role long after their defeat and/or death. May also overlap with Predecessor Villain, if the predecessor was significantly worse than the current Big Bad and still exists in some form.
Frieza is this to Vegeta during the Saiyan arc before becoming the Big Bad himself in the Namek/Frieza arcs. Same for his father King Cold, before showing up himself at the beginning of the Androids arc.
Dr. Gero created the Androids and Cell, causing everything in their respective arcs as well as Trunk's Bad Future, but is killed very early in the Androids arc while the threat of his creations continues.
Ryuk is the Bigger Bad to Light, since he's responsible for all of the events while Light simply uses the weapon Ryuk gave him, and eventually kills Light.
Overshadowing Ryuk is The Shinigami King. Although never seen in person, he casts a shadow over the entire world of Death Note, having created the MacGuffins in the first place. Indeed he was the one who gave Ryuk another notebook that allowed him to kick off the entire story to begin with.
The Death Note itself can be considered a Bigger Bad. Light noted how the Death Note tempts the people to try it, and how its mere presence in the human world has a huge impact on it. So did Near, when he spoke about how the power of the notebook corrupted Light.
The Ten-Tailed Beast, the original tailed beast, of whom the other nine are pieces of its chakra divided.Big Bad Tobi wants to reform the Ten-Tails and become its Jinchuriki, so he can enslave everyone with his Mangyeko Sharingan.
The Akatsuki were the Bigger Bads for Part I.
The series' final arc revealed the biggest Bigger Bad of all is Black Zetsu. He is revealed to have been responsible for setting in motion the entirety of history since the Ten-Tails defeat, and into the present all for the sake of reviving Kaguya, the true bad. He is essentially responsible for the entire series, and beyond, manipulating EVERYONE to set in motion the Infinite Tsukuyomi.
Chaos in Sailor Moon, with all the Big Bads of each arc revealed to be incarnations of it.
Lord Tamamo in Ga-Rei, master of the original Kyuubi and Mitogawa's superior.
The Emperor of Darkness from Mazinger Z and Great Mazinger fits the bill. The Humongous Mecha previous Big Bad Dr. Hell found were ancient -and severely outdated- weapons of his army. During the first series he did not directly interfere with the plot, and he remained in his underground empire, watching the war between Kouji Kabuto and Dr. Hell as one of his underlings schemed to bring both of them down. After causing the end of Dr. Hell's army and Mazinger-Z he became Big Bad of the next series. And again, together with the rest of the Mycean Empire in Shin Mazinger.
In Outlaw Star, the Big Bad is a Kei Pirate named Hazanko who seeks to overthrow the Tendo King, an unseen Bigger Bad. But there is an even bigger bad above the Tendo King called the Tenpa Emperor, who is only mentioned once. The identity, powers, and position of these characters is never explained, but the fact that Hazanko had to use the Leyline in order to become a Physical God to beat them, means they're terrifyingly strong.
In Berserk, that would be The Idea Of Evil which also doubles as the story's actual Big Bad in a way.
Zeref the black mage in Fairy Tail. It's been 400 years since his death, and people are still fighting against demons and other evil artifacts he made back then. And it turns out he's still alive, but dormant. It's later revealed that there's a being that even Zeref fears, Acnologia: The Black Dragon of the Apocalypse.
In Code Geass R1, Cornelia is the one making decisions about how Britannians in Area 11 will deal with Japanese rebels, while The Emperor of Britannia is far away and sets national policies but gives his children some free rein (within certain boundaries) in how they govern their territories. (This leeway is to see which child can achieve results and prove their worthiness to succeed him.) There are only two scenes in the entire R1 series in which The Emperor has more than a cameo-like appearance — one of them is a speech he gave, and the other is a Back Story flashback.
In a similar function to Sailor Moon's Chaos, Black Hole of Pretty Cure All Stars DX 3 was this for not only the separate villains, but for those who showed up in even the team up movies. It only applied for the All-Stars movie series.
In InuYasha, Magatsuhi, the spirit of evil in the Shikon Jewel. Does nothing for 90 percent of the show, then shows up and causes trouble. Dangerous, evil, ancient, but it's still Naraku driving the Evil Plan.
Jesei is spoken of in the third to last episode of Inukami! and only after that does he affect the plot directly. The rest of the time he was just an observer and instigator of an unknown part of another character's backstory.
The first series and the manga have Zorc Necrophades, the demonic being originally defeated by the Pharaoh. He's both Made of Evil and The Corruption, and was born of slaughter and genocide. Dark Bakura is trying to release him, and at the very end of the final arc Zorc finally takes center stage as a Big Bad in his own right.
Though he never appears, Dark Bakura is technically this due to killing Pegasus in the Duelist Kingdom arc, which fuels the motivation of the Big Bad of the spin-off, Yako Tenma, to resurrect Pegasus, since Yako was his adopted son.
At the same time however, Yako was corrupted by the Wicked Avatar, a card that was meant as an Evil Counterpart to all three Egyptian God Cards, but Pegasus never published the Wicked Avatar. Yako published it after Pegasus' death and it corrupted him, and the corruption drives Yako to resurrect Pegasus and get revenge for his death.
The Light of Ruin in Yu-Gi-Oh! GX. Season 2's Big Bad was serving it, and the third season's Big Bad turned to evil because of it.
The King of the Underworld in the Dark Signers arc of Yu-Gi-Oh! 5Ds, being the force behind the Earthbound Gods and the reason that the Dark Signers can make a Deal with the Devil and return Back from the Dead. This one may not qualify, though, as there's no indication it's even sentient and it, along with its Good Counterpart the Crimson Dragon, is being played like a violin by the straight Big Bad, Rex Godwin.
Yu Gi Oh ZEXAL has an evil deity called Don Thousand, the true ruler of the Barian World.
Blue Cosmos leader Muruta Azrael, and his successor, Lord Djibril, take on this role in Mobile Suit Gundam SEED Destiny's sidestory, CE 73: Stargazer. As the heads of Blue Cosmos, and the powers behind the Atlantic Federation, all of Sven Cal Bayan's actions can be traced to them, as can the Earth Forces' eventual assault on the Stargazer satellite. Despite this Azrael makes only two, non-speaking, appearances, and Djibril, while mentioned, is never seen.
Except for Part 2, which deals with the creators of the stone mask that gave Dio his powers, Dio Brando is this for JoJo's Bizarre Adventure, affecting the plot whenever he doesn't take up the Big Bad role directly, especially in Part 6.
The Five Celestial Serpents or World Nobles from One Piece are the ones who hold the reigns of the military, using them as playthings and sentencing innocents to death to cover up the world's lost age, while also gleefully owning and abusing slaves of every race and doing literally everything they condemn because they're above the law. Currently Sukazaki/Akainu and Blackbeard are fighting for the position of Big Bad, but the World Nobles are always in the shadows telling Akainu what to do.
Sword Art Online's first Big Bad, Kayaba Akihito, is the source for the next two Big Bads, as his game helped influence them in some say. One of them is his rival who used his game as a template for his own and the other was a survivor of Akihito's game.
The "Here Comes Tomorrow" story arc of Grant Morrison's New X-Men gave us the original character John Sublime, who was introduced with the strong suggestion that he may be the greatest overarching threat permeating the X-mythos. A sentient colony of bacteria almost as old as the Earth itself, Sublime was revealed to have orchestrated many major events in the X-Men's past, including the creation of the Weapon X program, all in a bid to wipe the mutant race from the Earth (as they are the only species immune to his mind control). It's implied that he may have even manipulated humanity to create the very idea of anti-mutant prejudice in the first place, thus making him the one villain who has managed to consistently keep the heat up on the X-Men since Day 1.
Due to the chaotic nature of creative teams on the books at the time, the comics of the '90s featured a lot of these, with a writer introducing a mysterious mastermind character of some sort, then abruptly leaving or being kicked off the book shortly afterward, with the next creative team deciding not to follow up on the plotlines of the previous and aborting the entire arc. Typically these characters are never so much as mentioned again, although Peter David got to revisit one he created, the Isolationist/Armageddon, nearly twenty years after the fact.
The Marvel Universe has the cosmic beings Death and Oblivion, who are incredibly powerful and exactly what they sound like. They tend to empower mortals to achieve their goals for them; Thanos and Maelstrom, respectively, are their favorite "heralds," each of whom is a universe-threatening Big Bad in his own right. The two cosmic beings have each been around for (in our time) decades, and have been directly battled only a handful of times.
Sonic the Hedgehog: One could make an argument that MammothMogul is this. Thousands of years ago, he founded the Order of Ixis, which eventually led to the creation of Ixis Naugus, whose actions, which may include starting the Great War, in turn led to Dr. Robotnik's rise to power, who's death ultimately led to nearly every villain in the book today, with Naugus responsible for the ones that aren't Mogul. Naugus and Robotnik are still quite active (and are, in fact, the current top two villains of the series), whereas Mogul has semi-retired from active villainy, running a casino and deciding to use his immortality to outlive the heroes and make his move then.
As revealed during Fear Itself, the Marvel Universe's realSatan. The other demon lords hold meetings around his throne sometimes, but it's stated that all of them, including, apparently, cosmically-powered ones like Shuma-Gorath and the aforementioned Dormammu, are terrified of even trying to sit on it. He's been gone from this plane of existence so long that even among the demons themselves it's a common belief that he doesn't actually exist.
Green Lantern baddie Krona may well be the Bigger Bad responsible for almost everything wrong with The DCU. While he's not the most powerful villain in the setting (though he's close; in a crossover with the Marvel Universe he curbstomped Galactus), he's the man behindParallax, the Manhunters, and, indirectly, the Anti-Monitor, as his experiment was the thing that fractured the original Monitor probe in two. In turn, he thus unintentionally caused virtually every Crisis Crossover the DC heroes have ever faced. In his early appearances, it was actually stated that his experiment created evil itself, though this has since fallen by the wayside and may be Canon Discontinuity.
The trope can easily become a problem when a bunch of writers work in a shared universe, especially one where the characters are in speaking distance of each other. For example, Marvel kept doing multibook crossovers over the course of the two years Lucifer was, or at least six hundred and sixteen fragments of him were, running wild and free on Earth. With the possible exception of Annihilation, nothing that inspired the crossover events was a bad a problem as this but Ghost Rider was the only one who seemed to care about it.
Similarly, Christopher Priest lamented the idea of trying to get Black Panther mainstream attention because even when he had the character, mentally degenerating from a brain aneurysm, come dangerously close to annexing Canada, none of the other writers felt the need to address it in their books.
In Grant Morrison's Batman, Dr. Hurt is the main Big Bad, but is revealed to have a Bigger Bad controlling him, who he thinks is the demon Barbatos, but is actually a weapon Darkseid sent back to the dawn of man when Batman was hit by the Omega Effect in Final Crisis.
Death Of The Family: Batman confides to Alfred that the main reason he grants Joker Immunity is because he sincerely believes killing the Joker wouldn't make things any better. Gotham would just send someone worse, or bring the Joker back from the dead, or something. To Bruce, the Joker is just one facet of the true Big Bad of his story: Gotham City itself.
The early Conan the Barbarian comics from Marvel often had the royal family from the Kingdom of Turan as this trope.
Shockwave. While Megatron or Scorponok or any other Decepticon are always front and center as the Big Bad, Shockwave has always worked behind the scenes with his regenesis project, which is a number of energies which bond to planets and create different Ore. This kicks off the earth conflict, which he is absent for, as the empowering Ore is there and everyone is fighting over it. It kicks off Spotlight Kup, which he is also absent for, because it drives Kup crazy. It is the reason behind the Syndromica arc, which he has very little to do with. In addition his projects have been behind the destruction of numerous civilizations, which he was also absent for because the Dynobots got to him before he could stabilize them. As of Transformers Dark Cybertron he has subverted the Trope, and stepped up as the major threat, requiring all the Transformers to unite against him.
The Dead Universe and alternate universe that seeks to consume the one present and mind controls anyone it can reach, even controlling the Decepticons to do its bidding. Later we learn that Shockwave is responsible for its existence.
Senator Roark and Mob Boss Wallenquist in Sin City. The former is an immensely powerful and unashamedly Corrupt Politician who can get away with anything while the latter is an immensely powerful crime lord controlling most of the organized crime in the city. While both men are responsible for the greatest evils in Basin City and perpetuate the Crapsack World itself, neither would really qualify as the main villain in any of the stories. Their organizations and influence are so vast that they're usually concerned with larger matters than direct confrontation with the (Anti-)heroes.
Discord in the second and third parts, while he was the Big Bad proper in the first part. While Loneliness and then Princess Gaia/Nightmare Whisper are the Big Bads for the second and third parts, Discord's actions in the first part (and the actual show) are the reason one, possibly both, of them even exists at all and everything in the entire fic can be traced back to Discord, even though he's been Sealed Evil in a Can the entire time. He is set free and becomes the Big Bad for the final arc.
Discord's father Havoc fits for the series as a whole. After all, he created Discord in the first place, plus he's more or less directly responsible for Discord's original reign over Equestria, as he fed Discord his own brother and Havoc's avatar in order to increase his power, then sent him to Equestria. Though that was actually his Avatar, which had gone Drunk on the Dark Side to the point it was considered insane even by Draconequus standards.
Subverted in the Shining Armor Arc. Father Deer is set up as the supreme leader of the Hooviet Empire, above even General-Admiral Makarov, but not only is Makarov revealed to be playing his superiors, but it turns out Father Deer doesn't really exist.
New Dawn revealed the real villain of the first book was not the cat's paw Nebiros, but rather the insidious New Order, at first seemingly spearheaded by Chris, but in reality controlled by an even bigger bad: Sharon Tate Roman. And to add to the intrigue, it is unknown if Nebiros or Chris even knew she existed.
Satan is this in The Prayer Warriors, since he is said to have created the false gods and had a hand in the rise of communism in Russia, but hardly ever appears.
Queen Chrysalis in The Nuptialverse, as everything wrong in-universe is more or less related to the emotional fallout caused by her invasion in "A Canterlot Wedding", from the strain on Twilight's friendships to fuel for Olive Branch's anti-Celestia tirade. Not to mention she's still at large while everypony else deals with their own problems. That said, Discord is an even Bigger Bad, seeing how he made Chrysalis what she is in the first place.
Chrysalis plays a similar role in Cadence In A Minor. She never actually appears in person, but raping a brainwashed Shining Armor while taking the place of his bride is the root cause of most of the fic's conflict.
Discord again in Secrets and Lies. Twilight's fear that he is attempting to escape once more, and that he provoked her into killing another pony in order to weaken the Elements of Harmony, kick off the events of the story, and Topsy Turvy, said other pony, in fact planned it in order to sow enough chaos to release him.
Moriarty was there was an essay published by Doyle's Fandom trying to upgrade Moriarty from Break Out Villain to true Big Bad status for the Sherlock Holmes book series by doing a Revision about Holmes cases and arguing that Moriarty was there as a Bigger Bad for various BigBads cases: after all, canon has established him as a Diabolical Mastermind, with vast criminal resources that can be exploited by minor criminals by a fee. For example, the essay proposes that the criminal of the very first novel, A Study in Scarlet, after losing his Memento MacGuffin and recognizing he is Lured Into a Trap by whoever put the ad in the paper to recover it (Holmes), then consulted Moriarty, who commissioned a Master of Disguise to pose as an elderly woman to get it (it worked!).
Justice League of Equestria would appear to have Darkseid for the series as a whole, judging by Athena's comments about the War in Heaven against his forces. Mare of Steelends with him opening a boomtube to Equestria, setting him up to be the Big Bad of the main Justice League of Equestria story.
The Cadanceverse has Nemesis, the entity/force that corrupted Celestia and Luna, and is still free and on the loose even after they're purified by the Elements of Harmony.
In The Lion King Adventures, the Ultimate Evil of the entire series is the Writer, an Author Avatar of ThatPersonYouMightKnow's dark side. He created the entire universe and all the characters in it, as a means of having his own world in which to create chaos and destruction.
In the Medaka Box fanfic World As Myth, Ihiko Shishime seems to be this, as his existence is heavily implied to be the reason for the Big Bad's plans.
Tales of the Oppressed has King Sombra. He's the one responsible for everything bad that happened in the story, but 38 chapters in and he's only had one major appearance.
The War of Megazords Vs. Gundams has two Bigger Bads: Patrick Zala and Mykan Yuki. They fueled each other's hatred towards Naturals and Coordinators receptively and are what sparked their respective wars. In short, Mobile Suit Gundam SEED had Zala the Big Bad and Mykan its Bigger Bad, while Megazords vs. Gundams had the reverse.
In Memories, Discord's mother is this. It was because of her that Discord took over Equestria, because of her that Discord "Discorded" the Mane Six, and because of her that Serenity had to die. (she got better) She appears to be becoming the Big Bad in the sequel, though.
Somber Ties has two. The first, as one might expect from a story that takes place in the Chrystal Empire, is King Sombra. The second (and bigger) one is Blackheart, as the evil force behind his rise to power.
Atlantis: The Lost Empire has the Leviathan, a rouge Atlantian robot who's only role in the movie is to completely destroy the Ulysses submarine and kill off the majority of the crew on the expedition.
Treasure Planet has Captain Nathaniel Flint, based on the original Captain Flint from Treasure Island. While he is long dead by the main story, it is his treasure that drives the plot not to mention he set the planet to explode when the treasure was found.
In The Princess and the Frog, the friends on the other side appear to be the dragons for the Big Bad, but ultimately his evil scheme was to sacrifice souls to them in order to get out of a deal he made with them before the film.
Wreck-It Ralph has the Cy-Bugs from the game Hero's Duty, who are powerful and a great threat as a whole, while just being a threat in Ralph's quest and having nothing to do with the situation at Sugar Rush. However, they come back in the climax, when they begin to destroy Sugar Rush, and the Big Bad even fuses with one of them!
In Frozen, Prince Hans' twelve brothers could qualify because their abuse on their brother is what made him a Jerkass.
In Anastasia, there's the Dark Forces that Rasputin sold his soul to and gained most of his powers from to get revenge on the Romanov family. The deal he made with them spectacularly backfires; first he's reduced to a decaying zombie stuck in limbo after he drowns and stuck like that until the last Romanov dies, and when his reliquary is destroyed they immediately claim him, and he dies a rather horrific death.
In The LEGO Movie, "The Man Upstairs" was the template that the Big Bad was based on. On top of that "the Kraggle" is merely one of his many bottles of Krazy Glue used to glue his pieces together.
In James Bond, this crops up a few times, usually in the early films but it's returned for the Craig movies. Generally the Bigger Bad is either a Nebulous Evil Organization like SPECTRE (e.g. Thunderball) or Quantum (e.g. Casino Royale) or some unnamed client country that is generally implied to be Red China (e.g. Goldfinger). Dr. No has both, as No works for SPECTRE but it's implied they were hired by China. You Only Live Twice has SPECTRE and its chief Blofeld acting as the Big Bad while working for this Bigger Bad (though, as he blatantly extorts money from them at one point under their protest, this might be more of a Big Bad Duumvirate).
The Mandarin in the Iron Man films. He is the leader of the Ten Rings, the terrorist organization who held Tony Stark hostage in Iron Man 1, and he personally appears as the Big Bad in Iron Man 3. In actuality, he is an actor named Trevor Slattery who was drugged and hired by the real Big Bad of the movie, Aldrich Killian, as a cover for his failed Extremis experiments. Marvel One-Shot: All Hail the King reveals the existence of the true Mandarin, whom Trevor's portrayal of him was loosely based on him.
In John Carpenter's Prince of Darkness Satan, the Big Bad in this dimension, turns out to be just The Dragon for his father: the Anti-God, who is in a mirror-universe waiting to be summoned.
In Scream 3, the Big Bad, Roman Bridger, is revealed to have told Billy Loomis, the Big Bad of the first movie, about his fathers affair with Laureen Prescott, and is thus indirectly responsible for the events of the first movie, and even more indirectly, the Roaring Rampage of Revenge of Mrs. Loomis in the second one. Billy Loomis himself is the Bigger Bad of the rest of the movies, posthumously.
The dream demons in A Nightmare on Elm Street, who gave Freddy Krueger his powers. They do make an appearance by way of flashback in Freddy's Dead, but they are never directly involved in the plot.
In the Hellraiser films, there is Leviathan, the god of hell. The films' Big Bad Pinhead is the leader of the Cenobites, who are Leviathan's foot soldiers, but Leviathan itself only appears in the second movie. It has a slightly more active role in the comic spin-offs.
In Halloween we have the man in black, who is really Dr. Terrence Wynn the leader of the cult of Throne, who placed the curse on Michael in the first place. They wish to aid or possibly control Michael. He is only directly involved in the fifth and sixth film.
The Jigsaw Killer is the Big Bad in the first three Saw movies. After he dies at the end of the third one, he becomes a Bigger Bad posthumously, as his remaining legacy hovers over and still drives the actions of his various apprentices nominally trying to continue his work: Amanda (who dies before Jigsaw himself), Detective Hoffman, and Doctor Gordon. Plans he deliberately set into motion before his death still have far-reaching effects long after he died.
Assuming Prometheus is in continuity with the rest of the franchise, the Engineer race serves as this to the Alien series, having created the Xenomorphs to begin with.
In the Starship Troopers films, Behemecoatyl is retroactively the Bigger Bad of the first two films. It is the absolute leader of the Bugs, but is never seen in the previous ones, in which the humans only fought its minions.
The unseen King George III in The Patriot, ruler of the British Empire. He's only ever referred to in passing, but Cornwallis and the other Generals ultimately answer to him.
G'mork: I am the servant of the power behind the Nothing.
The main villain in Ghost Ship implies he is working for Satan, or at least Hell. He says he needs to find enough souls to make "management" happy, and he needs the current salvage crew to fix the Graza for him to accomplish that mission.
President Patel, the leader of Elysium. While he personally disapproves of Delacourt's methods for enforcing the status quo, he sits at the very top of a tyrannical system that can only be sustained through the continuous exploitation of Earth's inhabitants.
In Smiley Smiley himself is this. It turns out he is a Red Herring for the events of the film, which turn out to be an elaborate prank on the protagonist based on the legend of Smiley. However, just when we think Smiley himself never existed in the first place, he shows up in the last ten seconds of the movie.
Daryll Lee Callum is this in Copycat. Peter Foley, the actual copycat of the title, is a fan of serial killer Callum who is committing his killings in an attempt to impress the imprisoned Callum.
Lockdown's employers in Transformers: Age of Extinction. They're the ones who sent Lockdown to hunt down Optimus Prime and it's revealed that they were the creators of the Transformers.
The writers behind the Marvel Cinematic Universe seem to be setting up Thanos as the Bigger Bad of the universe as a whole. So far, he has served as The Man Behind the Man to two different Big Bads in two separate movies, being the true commander of the Chitauri army in The Avengers and Ronan the Accuser's benefactor in Guardians of the Galaxy. The heroes never even get to meet him face-to-face in either film. Being a genocidal galactic emperor with vast armies at his command, he may well be the most powerful villain so far unveiled in the series.
In The Karate Kid, Kreese could be seen this way, being the cruel sensei who helped turn Johnny into what he is but is never directly confronted during the movie.
In Kung Pow! Enter the Fist, Master Pain (later "Master Betty") is the delegate of the mysterious Evil Council, who seem to be set up as one side of a larger conflict. ("Behold, the symbols: One... over here. The other... over there.") All the audience knows about them by the end, including their long-term goals, is that they're aliens... and French. It makes just enough sense to be weird that we don't learn more and seem like material for a sequel.
Morgoth was always the ultimate evil presence in Middle-Earth, but after his defeat and imprisonment at the end of The Silmarillion, Sauron took over the role of the active Big Bad, overlapping with Dragon Ascendant. Morgoth was not destroyed, however, and Tolkien's writings indicate he will free himself in time to command the forces of darkness once again at the Last Battle.
Sauron himself as the Necromancer during The Hobbit - he definitely exists and will later be revealed as the canonical ultimate evil, but has no direct role in the story's plot, except as a device to give Gandalf a reason to leave the group for chapters at a time to go get information on him.
In the Chronicles of the Kencyrath, the ultimate enemy is Perimal Darkling (think The Corruption on a cosmic scale), which appears to be largely mindless and is in no sense a "person", nor does it seem to have desires beyond consuming the whole universe. Master Gerridon, nominally The Dragon, generally serves as the primary antagonist.
The Lords of Norsunder are the ultimate malevolent force in the Inda books, but during the timeline of the series are largely uninterested in human affairs. Erkric, the Big Bad, came up with his schemes on his own but bargained with one of them for his powers, but when he failed to live up to his end she killed him and then departed.
Several of Tad Williams' works feature an entity called Unbeing or Old Night, which is the representation of entropy and ultimate decay. It's never any of the Big Bads, but is portrayed as being tied to their actions, and at least one (Hellebore of The War of the Flowers) planned to deliberately unleash it.
In The Belgariad and The Malloreon, the King of Hell is mentioned several times as a demon god Sealed Evil in a Can who controls the single nastiest faction in existence, but because he isn't part of the conflict between the Light and Dark Prophecies, he to all practical intents and purposes sits the series out. A couple of his top minions do show up in supporting villain roles, but were likely acting independently.
The Council of Thirteen are the political heads of the Yeerk Empire, but only appear in one book, a Villain Episode where they're more focused on judging Vissers One and Three than the conquest of Earth per se. Visser Three is the commander of operations on Earth and consequently functions as the Big Bad. The main plotline ends with his defeat.
Crayak is a Sufficiently Advanced Alien who plays The Chessmaster throughout the galaxy to encourage mass genocides of entire species for no reason; in a series full of shades of grey he's one of only a handful of characters who qualify as pure evil. However, he only becomes directly involved in the story a handful of times and isn't terribly invested in it. The implication is that he and his Good Counterpart, the Ellimist will continue their long "game" millennia after the Animorphs' series has ended.
The Black Thing in A Wrinkle in Time. IT is the Big Bad, and the Man with the Red Eyes may be ITs Dragon. The Movie states that the Black Thing was created by IT, making IT the biggest villain of that adaptation.
Azathoth in the whole of Cthulhu Mythos, a manifestation of perfect amoral chaos who creates and destroys, kept asleep by the Lesser Outer Gods with 'pipes and drums' so his awakening doesn't destroy the universe, but never does anything except listening to music. Most of the other powerful Eldritch Abominations (Shub-Niggurath, Yog-Sothoth) also take a very distant role in most of Lovecraft's stories, a notable exception being "The Call of Cthulhu". Nyarlathotep is a bit more hands-on, and August Derleth's Mythos stories frequently feature the likes of Cthulhu and Yog-Sothoth about to personally emerge everywhere before being halted by a Deus ex Machina or explosives.
The Crimson King was presented as the central evil in Stephen King's metaverse; however, in an example of The Devil Is a Loser, when he's finally confronted in the Grand Finale of The Dark Tower series he's revealed to be nothing more than an insane old man armed with nothing except suspiciouslyfamiliar flying grenades, who is promptly defeated in one of the most ignoble manners possible. It's later revealed he had relied on ancient technology to give him most of his seemingly multiverse-spanning omnipotent powers, and when he lost that through the efforts of various heroes on various realities he was reduced to the pathetic wretch confronted by Roland.
The Rift War Cycle: Nalar, Raymond E. Feist's God of Evil, is slowly revealed to fill this role, and being imprisoned in another dimension, can do little more than be the influence for the various Big Bads in his books and the trueBig Bad, the Dread, has nothing to do with him. Leso Varen, his minion, fills this role as well (making Nalar an Even Bigger Bad).
Ian Fleming's James Bond novels often have the Soviet Union sponsoring some or all the activities of a novel's main villain.
In Gone, Caine is the Big Bad, the counterpart to the hero, and the one who usually drives the plot. The Gaiaphage is an Eldritch Abomination that arrived via meteorite, crashed into a nuclear power plant, Mind Rapes several main characters including Caine, and looks at the whole situation as a game, but rarely shows up and is usually just a vague threat in the background.
Arawn Death-Lord who played the role of the Big Bad for The Book of Three and The Black Cauldron, is this for The Castle of Llyr and Taran Wanderer. By The High King, he's the Big Bad again.
There's also Gwyn the Hunter's unnamed lord. Even Gwydion doesn't know his name or identity, but believes that he's greater in power than Arawn - although not necessarily evil, since Gwyn's function (basically a Grim Reaper figure) is a necessary one.
The Bellon-Tockland Institute in Dean Koontz's False Memory, a semi-fascistic psychology think tank. The main villain of the book, Mark Ahriman, is a psychologist who develops a form of mind control and employs it both on behalf of the Institute and for his own deviant amusement; the trouble he causes for the main characters stems from his grudge against the stepfather of two of them, another academic who spammed Amazon with with negative reviews of Ahriman's work, as well as a previous affair with the wife/mother which ended badly. Although we do see Ahriman manipulate a patient into biting off the nose of the U.S. President as a "message", and the Institute's connections are used in the Back Story to explain how he has escaped any accountability for his murderous pastime, the Institute's plans have no direct bearing on the novel's events and they are ultimately clearedof any connection to Ahriman after the protagonists break his control on them and another one of his unstable pawns randomly kills him.
The Otherness from the Repairman Jack series, a vast, impersonal cosmic force locked in an endless war to conquer the multiverse. In our world, its goals are carried out by the immortal Rasalom and his disciples.
In Warrior Cats, the Dark Forest serve this role during the Power of Three arc. They are recruiting an army to destroy the Clans, and are made up of the most powerful villains the heroes have ever faced. However, this is mostly going on in the background, as the main driving point of the arc is uncovering the secrets of the past and defeating the villain Sol, who is trying to make the Clans destroy each other.
Big Brother from 1984...maybe. He never actually enters the story, and the major Party officials (like O'Brien) do most of the villainy. George Orwell intentionally leaves lots of questions about Big Brother unanswered. How much power and influence does BB have? Has there only been one BB, or has the title been passed on from person to person over time? Does he even exist, or is he just the Party's fictional mascot?
The Nameless in the Coldfire Trilogy. He/she/it/they (it's complicated) is far and away the most powerful evil in the series, but while it features prominently in the backstory of Gerald Tarrant, the bad guy actually responsible for the conflict is Calesta. The Nameless's only real role in the present-day story is to punish Tarrant for apparently backing out on the Deal with the Devil they made.
The first six books of the Galaxy of Fear series have Borborygmus Gog as the Big Bad. He's got a very long leash and a lot of discretion, but ultimately is employed by The Emperor. Palpatine only appears once, in a call to the scientist.
He [Gog] could order the deaths of hundreds if he wished. With his terrible knowledge he could engineer nightmares. But as powerful as the scientist was, the Emperor could snuff him out with little more than a thought.
All the villains of the Hand of Thrawn duology have motivations that revolve around Thrawn, who has been dead for over a decade.
In the Fever series by Karen Marie Moning, the Unseelie King is the ultimate evil force but makes no obvious appearance until the end of book five where he saves the day. Seemingly still evil since he is still technically the originator of all the evil things going on because he created all the Unseelie..
The planet Mesa and Manpower Inc. was eventually revealed in the Honor Harrington series to be ultimately responsible for the long and bloody war between Manticore and Haven. When their role was revealed, then it was discovered they were merely a front for the secretive Mesan Alignment organization.
The Brethren, by John Grisham, makes reference early on to one Natli Chenkov, a Russian politician and Communist hardliner who is suspected of planning to stage a coup and start a war the director of the CIA doubts America can win. The main action of the book involves three former judges (the titular Brethren) who run a blackmail scheme from prison and unwittingly hook the congressman whom said CIA director hopes to install as President to beef up the military and block Chenkov's ambitions, bringing down the CIA's wrath on them. Whether this makes Teddy Maynard (the CIA director) the Big Bad (albeit a Well-Intentioned Extremist) or the Brethren Villain Protagonists (albeit sympathetic ones) is arguable, but Chenkov is hardly mentioned after the initial explanation.
Similar to King's The Dark Tower, all the horror novelist Brian Keene's works are connected by the Labyrinth, in which dwell the Thirteen, Eldritch Abominations that existed in the Primordial Chaos before the birth of the universe. Among them, the Thirteenth is the most powerful and feared.
Legacy of the Dragokin: Kthonia is the most powerful villain in this story but she is neither involved, aware of, or inclinded to assist with Jihadain's Evil Plan. When Kalak kills Jihadain, however, she becomes the True Final Boss.
Harry Potter and the Chamber of Secrets. If you consider each Horcrux as a separate person, the main portion of Voldemort's soul (residing in the disembodied Voldemort himself) was a Bigger Bad in this book. Tom Riddle was more a manifestation of Voldemort's will, and in any way acted independent from him (although in his interests).
Harry Potter and the Half-Blood Prince doesn't feature Voldemort at all, and all his actions take place outside the main events of the plot. The Big Bad of the book eventually turns out to be Severus Snape, who kills Dumbledore and set most of the events in motion to further himself in Voldemort's eyes. Although the next book reveals that Snape was actually a deep-cover double agent for the good guys.
In The Chathrand Voyages, it's established early on that Arunis (most dangerous individual member of The Big Bad Shuffle the series has going on) worships entities called the Night Gods. These gods later turn out to be very real, and Arunis doesn't just worship them, he wants to be one. They've set him a task to complete before they'll accept him into their ranks- namely, scouring Alifros, the world where the books are set, of life- but otherwise take no direct part and Arunis (and the other villains) stand and fall by their own merits.
In Fred Saberhagen's Empire of the East, the eponymous evil empire is ruled by mortal men, particularly by Emperor John Ominor, the Big Bad. It was founded, however, by Orcus, the king of all demons, whom Ominor overthrew in a coup and imprisoned. It will probably not surprise anyone to learn that Orcus eventually escapes.
Dale Brown's books have portrayed the Chinese presidents and high commands that tacitly condone the generals' and admirals' actions as this, in contrast to the Russian presidents who have directly been Big Bads.
Chancellor Paige from The Maze Runner Trilogy, the head of all the mess that is WICKED. Eventually, though, the cruelty of that position gets to her and she decides to cut their losses and stop torturing people for a cure that might never come.
In "Prisoner of the Daleks" Dalek X (the Dalek Inquisitor-General) serves as the main villain. However it is mentioned he answers to the Supreme Dalek.
In the Nightrunner series, the God of Evil Seriamaius seems to encourage his followers, especially necromancers, (and others) in villainous actions, but never appears as an actual character except in prophetic dreams. Granted, none of the more benign gods put in personal appearances either.
Angel: From seasons 1 to 3 and much of 4, the law firm of Wolfram & Hart play the role of Big Bad; however the unseen Senior Partners are always portrayed as the Bigger Bad. Angel spends the whole show and all his strength trying to grind their operation to a halt, even for a moment, by destroying their means of influencing Earth. Optimistically, he was just successful enough to make them focus their attention upon him. The downside would be that he now has their attention. As of Season 9, they've been branching out in the Bigger Bad department; their machinations are now starting to affect Buffy and the Scoobies too.
Arrow: The episode "Broken Dolls" implies that Ra's al-Ghul was the one behind season 1's Big BadMalcolm Merlyn.
Breaking Bad: Don Eladio, the head of the Juárez Cartel. His actions drove Gus Fring to the be man he is in the show and his cartel causes problems for Walter and Jesse for three-and-a-half seasons. Despite all this, he only appears twice in season 4 and is killed off in his second appearance.
The True Demons were Eldritch Abominations that ruled the Earth before humans, and all the monsters and "demons" that the heroes fight are nothing but remnants of them that they left behind as one final "screw you" before leaving/being kicked out.
In Season 9, Whistler is revealed to have been behind Twilight in season 8 and seems to be the new Big Bad.
Firefly: It is implied that the Blue Sun Corporation was going to end up like this, being responsible for River's ordeal at Academy (note how she freaked out whenever she saw the company logo), sending the Hands of Blue after her, and being the ones to which all the nastier members of the Alliance answered. Cancellation of the series, however, left things at just implications.
Freddy's Nightmares: Freddy Krueger. He was only directly involved in the plot of eight episodes, though a few implied he was pulling the strings behind the scenes.
Goosebumps TV series: There's the implication that it's actually R.L. Stine himself (the author of the books) who's behind everything in all the stories (in a meta sense he is, of course) and the ultimate evil of the series, even though he doesn't appear in any of them. In the intro, a man in black walks up to a town, and his briefcase (clearly marked with his name) flies open. The papers fly out and morph into the Goosebumps logo, which proceeds to spread misery around the town until it reaches a creepy mansion, which then shows clips of some of the stories.
Kamen Rider Gaim has the Helheim Forest. While it's the central reason why the Riders are fighting Inves and each other and later on the Overlords, it takes a backseat to the overall conflicts. Case in point, even when Takatora reveals its true nature and why Yggdrasil is fighting it, Kouta still finds a reason to oppose Yggdrasil more than Helheim.
Nikita: For the first season-and-a-half, Oversight was this to Division, officially giving Percy his orders even as he was recognized as series Big Bad. As time went on, and Percy started overstepping his boundaries, Oversight grew more wary of him, and by the time Season 2 started, they had Percy locked up and replaced by Amanda. And now, as of the midway point of the season, Oversight is defunct, the Guardians having killed most of them in a (successful) plot to free Percy; this has resulted not only in Amanda taking Division rogue, but in the last remaining Oversight member to join forces with Team Nikita.
Rumpelstiltskin for the whole series, as he is The Chessmaster who sets everything in motion.
Cora is this for Regina the Evil Queen, as she is Regina's mother and the one who shaped her into the Big Bad she is now and her influence remains on her even though she's been out of the picture for a long, long time now. In Season 2, Cora appears personally, ditching this status and becoming the full-on Big Bad.
The Big Bad Duumvirate of the last third of Season 2 take their orders from a mysterious boss whom even they have never met. His name? Peter Pan, who is later revealed to be the even Bigger Bad to the original Bigger Bad Rumpelstiltskin!
Power Rangers Turbo: The finale reveals Dark Specter, the Bigger Bad behind Zedd, Rita, the Machine Empire, and Divatox. In Power Rangers in Space he gathered together all the Big Bads of the franchise to that point under him, and sicced newcomer Astronema on the Rangers, but seldom directly intervened. In the end, he was done in by The Starscream and never faced the Rangers directly.
Revenge has the Americon Initiative, the domestic terrorist group who the Graysons laundered money for (which they then framed David Clarke for). Initially just a part of the backstory, they later started influencing the story again in late season 1 via their assassin the White Haired Man, and in season 2 seem to be stepping down to knock the Graysons out of the Big Bad position.
The first season finale reveals two things: the first thing being that Randall was working for an even Bigger Bad called the American Government and President of the United States all along, and the other thing being that the blackout was not an accident and that someone deliberately caused the nanites to go out of control.
The Big Bad in Sharpe is usually a French commander with wide powers, but responsible to his superiors and ultimately Napoleon.
Smallville: In the fifth season, Brainiac is the Big Bad. He's behind every nasty thing that goes down that season, and is one of the greatest threats Clark ever encounters. His goal, however, is to release General Zod, a Bigger Bad who was trapped in the Phantom Zone on Jor-El's orders. Zod can't do anything, and in fact is unable to even communicate with Braniac. General Zod's status as the series' Bigger Bad is further emphasized due to him being the ultimate source of the Big Bads from almost all later seasons; his son Doomsday and his younger clone Major Zod. The General is able to come out and play on exactly one occasion.
Ra was the first Goa'uld to find Earth and use a human as a host, which gave him and other Goa'uld a massive supply of hosts, soldiers and slaves and allowed them to spread all across the galaxy, with Ra as the top System Lord for over ten thousand years. He's killed off in the original film before the series, but his legacy poses the main threat for most of the series.
In seasons nine and ten, the Ori are the Bigger Bad, since they're ascended beings and thus more of a concept rather than actual characters. Their Dark Messiah Adria takes on the Big Bad mantle for season ten.
Supernatural: For the first 4 seasons the primary villains have been working on the imprisoned Lucifer's orders to bring about the Apocalypse and prepare Sam Winchester as the archangel's earthly vessel. He is freed in season 5, and steps down to Big Bad as he again walks the Earth and plans humanity's extinction.
24's seventh season has African warlord Benjamin Juma. While Juma is behind the story's core conflict, his underling Iké Dubaku serves as the direct Big Bad in the season's first ten episodes. Subverted when, after Dubaku's capture, Juma finally appears onscreen and becomes a proper Big Bad himself.
Loki in Norse Mythology, who spawned or is otherwise responsible for many of the monsters that threaten the gods. He takes up the Big Bad mantle in time for Ragnarok.
In the Big Finish Doctor Who Divergent Universe arc the Kro'ka controls where the Doctor, Charley, and C'rizz go but is working for the Divergence. In Caerdroia he is revealed to be working for Rassilon, who meets the Doctor in the next story.
The best examples may be the Obyriths and their partner Tharizdun. The former are beings that predate mortal life and even gods. The latter is a god seduced by the Obyriths into evil and madness who shares their desire to destroy everything. Tharizdun used a shard of evil to create the Abyss (and by extension all demons), making him responsible for the existence of the greatest evils in the setting.
Vecna, one of the most notorious evil gods in the history of the game, who is known for his dreaded Eye and Hand, claims to have gained his power from a being he calls simply the Serpent, but the exact nature of this being (which is possibly his only ally) is unknown.
The Dark Powers in the Ravenloft setting can play this role depending on what type of game the DM is running. Just as many people say that the Dark Powers are not evil at all, but may actually be good. After all, each domain is an Ironic Hell for its ruler, who is an eternal prisoner of it, making Ravenloft a prison of the damned. Seeing as the Dark Powers punish evildoers, it is very possible that they are good.
The Deathlords of Exalted are Omnicidal Maniac ghosts granted power by the Neverborn in the name of destroying Creation. The Neverborn themselves, however, aren't much a threat; they're busier spending time coping with the pain of being eternally-dying-but-never-truly-dead and sending strange messages to their servants.
The Exarchs, who stormed the Supernal realms and broke reality in the time of Atlantis. Together all eleven of them form the main villains of the setting, responsible for both the Abyss and the depressing state of the world.
The Chaos Gods rarely pay any attention to mortal affairs, spending the vast majority of their time fighting each other, but the powers that are available to mortals because of their very existence (and the corruption and madness that results from them) are the cause of multiple evil factions in both settings.
40K has the even Bigger Bad of the C'tan, who created the Necrons, indirectly created Chaos with their war against the Old Ones (which in turn allowed the Chaos Gods to be born later), and indirectly led to the creation of the Orks and Eldar (as the Old Ones created them to fight against the C'tan). Originally they served as part of the Big Bad Ensemble, but then the 5th Edition Retcon had them be shattered into pieces millions of years ago.
Blue Rose has the seven Exarchs of Shadow, though it's never stated explicitly whether they actually exist or are just a myth.
Kazavon in Pathfinder's Curse of the Crimson Throne campaign. A monstrous Blue Dragon and Psycho for Hire who once served as Zon-Kuthon's Champion, Kazavon was killed long before the story began. His evil persists however, in the form of seven Artifacts Of Doom made out of his bones, which are so contaminated by the pure evil of his soul that they corrupt all they touch, exacerbating the evil that is already there in the human soul. Queen Illeosa, The Big Bad of the setting, is wearing the Crown of Fangs carved out of his teeth; with her defeat the story is over, but the possibility of someone else picking up the Crown (or one of the other six items) remains a very real threat.
The Eldrazi, until Rise of the Eldrazi when they actually show up.
Yawgmoth, who had a similar treatment. For most of the original storyline, the various Evincars of Rath were the setting's primary antagonists, especially Volrath. Rath and its Evincars were essentially satellites to Phyrexia and Yawgmoth, it's ruler. While Phyrexia turned up quite a bit throughout the game's history (going at least as far back as Gate to Phyrexia in Antiquities), Yawgmoth Himself didn't take center stage until the Urza's Block and then not again until Invasion.
In Margin for Error, Adolf Hitler is obviously the power behind the German Consul, but his presence in the play is limited to a bronze bust and an obnoxious radio speech.
Quest for Glory is very fond of this trope, particularly the Sealed Evil in a Can variety. Every plot from the second game onwards revolves around the chief villain attempting to summon one of these, with various levels of success.
The Patriots in the Metal Gear saga. A faceless, all-powerful group of power brokers that rule America from the shadows, the Patriots are the biggest overarching threat pervading the series, though Snake doesn't directly come into conflict with them until the final game. Ironically, most of the Big Bads that he faces before then are actually battling the Patriots themselves for their own reasons. The Patriots simply stay in the shadows and don't get involved personally. The label becomes a lot more appropriate when you learn that they're not even human: they're a nebulous system of AIs that are far beyond any one person's control, even the one who gave them their programming and unknowingly caused everything to happen: Major Zero, who's a Bigger Bad himself.
Ganon in Zelda II: The Adventure of Link is the force motivating all the other bad guys rather than an actual character in the game, but he didn't actually tell anyone to do anything. Who the Big Bad in Zelda II is, is up for debate.
Ganon is this in the first part of A Link To The Past, until Agahnim succeeds in unsealing him and leaves the spotlight to him (Agahnim isn't mentioned again until encountered in the final dungeon). Ganon comes out of Agahnim's body after this battle, and Ganon calls Agahnim his "alter-ego", meaning Agahnim was either a disguise used by Ganon or a person possessed by him.
Sargeras — the Fallen Titan and founder of the universe-consuming Burning Legion — is a Bigger Bad through most of the lore, with exception of the War of the Ancients (where he is Big Bad, though never fought directly) and the events leading up to the first RTS game, where he possesses the mage Medivh, and uses him to open the Dark Portal, leading to the invasion of the Orcs. After Medivh's first death he is MIA as far as the story has progressed (all of the actual gameplay except for two dungeons, which takes place in the past), and leaves the work to his Co-Dragons, Kil'jaeden and Archimonde.
the Old Gods are the primordial elemental beings who ruled the world before the Titans came. Even when they are not actively pulling the strings (they mostly are), one can always find signs of them in the world. This is especially true in the Mists of Pandaria expansion, where Word of God states they are not pulling the strings actively, but VERY prevalent Sha energy is the aftermath of one who died in the war against Titans during the creation of Azeroth.
The One Being in the Mortal Kombat series. Although Onaga, the original ruler of Outworld, and Shinnok, the former Elder God, would also count.
In Kirby's Dream Land 2, all Zero did was send Dark Matter out to Pop Star. Zero never appeared until Dreamland 3, which was where Dark Matter was changed from a single entity to a species mostly controlled by Zero. In Dreamland 2 however, Dark Matter is the Big Bad while Zero is the Bigger Bad. However, considering Zero never shows up until the end, Zero can be considered the Bigger Bad of the entire Dark Matter trilogy, with the Dark Matter in Dreamland 2, the Dark Matter possessing Dedede in Dreamland 3, and Miracle Matter in Kirby 64: The Crystal Shards being the Big Bads of their respective games.
Word of God confirms that Sephiroth is in control, but all of his powers and motivation, most of Shinra's military might, and the reason for the WEAPONs' creation is Jenova. She might have been the secret Chessmaster, but she doesn't actually seem to be anything more than a vegetable during the game proper. Considering Ifalna's report, she was basically kicked upstairs from the role of Big Bad.
Hojo, the Mad Scientist responsible for Sephiroth's existence, and for Sephiroth gaining enough power to enact his Evil Plan, and who is also the single most vile entity in existence.
In the Baldur's Gate series, as revealed near the end of the first game, the dead god Bhaal pushed the plot into movement in the backstory, but being dead, takes no active part in the story of the games other than as semi-impersonal power scattered among his mortal children. All the three Big Bads in the series are after this power in some way or another.
Phantasy Star has The Profound Darkness. The series protagonist's struggle against the Dark Force/Falz, the recurring Big Bad, amounts to Fighting a Shadow of a fraction of the Profound Darkness' own evil and hatred. DF himself is a threat to the entire universe, so nobody wants to find out what the Profound Darkness can do if left unchecked.
Gerald Robotnik from Sonic Adventure 2. The main conflict of the story is against Eggman, but it was Gerald's actions 50 years in the past that caused many of the problems in the game. However, he is only a Posthumous Character and has a rather indirect effect on the story in general. The story doesn't revolve around stopping him and his machinations are only revealed after Eggman accidentally sets off the Colony Drop at the end.
In Starcraft I and II, the Big Bads are the Zerg Overmind, Sarah Kerrigan and (in Wings of Liberty) Arcturus Mengsk. The Zeratul side missions (starting in Brood War and continuing in Wings of Liberty) reveal a nebulous Bigger Bad looming in the horizon: Amon.
In Resident Evil, Ozwell E. Spencer is one of the founders of the Umbrella Corporation, who murdered his rivals to gain total control. He was also into world domination. However, he never interacts with or even takes notice of the protagonists, and the various biohazards of the games are instigated by underlings with their own motives.
Kalibaar's Master from IV is set up to be this. But it's never really explained what happened to him.
The Creators served as this between I and V, but might have been retconned out by VI - in the early games, they were an enemy race to the Ancients, stated to be evil and of fairly equal power to the Ancients (who created both the Big Bad, the Big Good, and the worlds the games take place on), but with absolutely no relation to the games whatsoever except possibly the war with them being the reasons the Ancients doesn't put more effort into correcting the Sheltem situation. The exposition of the backstory in VI contradicts their existence, or at least the war with them, however.
The Kreegan were sort-of this in VII - as far as the game is concerned, the Kreegan are just hanging out in the Land of the Giants, being a threat greater than the ones that comes closest to being the Big Bads for the game and keeping someone they kidnapped before VI with them. Their king gets killed, but before and after that he has no relation to the plot of the game, and Armageddon's Blade showed his death did little to slow the Kreegans.
Dracula also plays this role in Curse of Darkness, with most the game being about his resurrection.
In the Lords of Shadow continuity, Satan is the bigger bad of the games, working through the lords of shadow in the first and his bastard children, the acolytes, in the second. Amusingly, the only reason he's in the background for Lords of Shadow 2 is because he's absolutely terrified of Dracula because his power visibly surpasses his own (let that sink in for a second) and doesn't wish to fight him again because Dracula as a human killed him the last time.
In Sly Cooper and the Thievius Raccoonus game, the Big Bad is a mechanical owl named Clockwerk. But in the second game Clockwerk becomes the Bigger Bad because he is now destroyed, shut down, and separated into several pieces, but still a very dangerous potential threat if he were to be rebuilt. Most of the bad guys are just using pieces of Clockwerk for their own small-time schemes, until it becomes clear that Arpeggio intends to fully rebuild Clockwerk to take Clockwerk's body for himself so that he can be immortal. Then his protege Neyla backstabs him and takes Clockwerk's body for herself.
Dragon Age: Origins has the Archdemon as the Big Bad; Dragon Age II has Meredith. Side quests for Morrigan and the downloadable content Witch Hunt suggest that Flemeth may be the Bigger Bad of the setting as a whole.
The first Archdemon, Dumat, may also fit. Corypheus revealed that Dumat promised him and the other Magisters the Golden City, but was "betrayed" and returned as one of the first Darkspawn. Furthermore Corypheus frequently commands "Dumat, grant me your powers!" during battle to which a power is always granted. The quest Altar of Dumat can result in an amulet if sacrifices are made. Both of these events suggest that Dumat still has some form of presence in the world despite being slain.
In Bully, Mr. Harrington, the father of DerbyHarrington, fills a role like this. He doesn't make a personal appearance in the story and is only referenced in a few lines of dialogue, but his money and meddling in school affairs are one of the root causes of a lot of the corruption at Bullworth Academy.
Ace Attorney Investigations 2 has Teikun_Ō, who not only took the identity of the president of Zheng-Fa but also had powerful associates in the Prison and Legal systems of Japan/the USA. However, his actions also lead to his death at the hands of the Big Bad: Sōta Sarushiro
The return of the Shadowlord, the Big Bad of the game's original story arc, was orchestrated by the Zilart princesKam'lanaut and Eald'narche. They become the Big Bads of the first expansion Rise of the Zilart, but their plans unwittingly (though perhaps they were influenced by him) to allow the Big Bad from the second expansion Chains of Promathia back into the world.
Ultimately, all of the troubles that happened in the game stemmed from the pact made by the Shadowlord with the Celestial Avatar Odin. Odin gave Raogrimm the power to get revenge for his murder in exchange for releasing Odin from his slumber, this revenge and its consequences nearly lead to the destruction of Vana'diel at least half a dozen times since then, but none of that was ever part of Odin's goal. Odin is also not too bad of a guy if you get to know him.
Myth has the Leveler, a malevolent force that is responsible for turning a hero to darkness every thousand years.
As told by Tekken 6's Scenario Campaign mode, Jin Kazama is the one who set the world into chaos (and thus the actual antagonist) but only did so in order to awaken the monster Azazel. This is most apparent in the story mode, where Azazel is taken out almost casually a short while before the true final battle against Jin.
The next game introduces Dr. Weil, who created the Dark Elf and shows up with his own ultra-Nigh Invulnerable version of Zero: Omega. Weil rebuilds Copy X and uses him as an Unwitting Pawn, along with the children of the Dark Elf, Crea and Prea, who never intentionally did anything evil because they're mere infants.
Solatorobo has Baion, who sees no need to learn to control Lares (since Nero and Blanck can do that for him already) or chase the protagonists as Bruno did; instead, he just wants to summon Tartaros and bring about The End of the World as We Know It.
For the first and second games The Reapers are in dark space, and the goal of the Big Bads of those games (each an individual Reaper) is to facilitate their return. In the third game, the Reapers have arrived, and serve as the Big Bad this time.
Leviathan reveals the eponymous creatures, which created the being that created the Reapers. They're rather miffed about this, as it wasn't their intention at all.
Portal and Portal 2 have Cave Johnson, the deranged, corruptandnon-wheelchair-friendly CEO of Aperture Science, despite being long dead by the time of the games. He's responsible for the company's horrific (and counterproductive) policies, as well indirectly responsible for creating GLaDOS and putting her in charge of the facility.
Easily Yami from Ōkami, who's existence creates all of the evil beings you face in the game, being the root of all evil and all. Doesn't appear till the very final battle and is barely hinted at before, also doesn't seem to be a very intelligent being either since it doesn't talk.
In Ōkamiden, one of the two possible origins of the Big Bad, Akuro, is that he was the true Bigger Bad of Okami and was controlling Yami.
Assassin's Creed III reveals that the true villain is, and always has been, Juno. Juno's machinations were a major reason the Assassins and Templars were never able to put aside their differences and work together to make a better world. All so that Desmond would have no way to save the world from the solar flare that didn't also allow her to escape.
In the Twoson and Fourside arcs of Earthbound/Mother 2, the main threats are Mr. Carpainter and Monotoli, respectively. However, they get their power from the Mani Mani Statue, which eludes the party until Fourside, when the party can enter an illusion version of it named Moonside and destroy the statue, which breaks Monotoli's power considerably.
A number of villains belonged to the mysterious Black Cloak Society, making them a potential Bigger Bad for the whole series. Unfortunately, the series died before anything could come of it, though they return in Fan SequelThe Silver Lining in a more direct role.
The AGD Interactive remake of II added The Father, a member of, and possibly the leader of the Black Cloak Society, who's the villain behind Hagitha, the main villain of the game. At the end of the game, he also curses Graham, which causes the events of the next two games.
Storm of Zehir has Zehir, the yuan-ti god of poison.
The fan campaign The Maimed God's Saga has Malar, the Faerűnian god of savagery.
Skullgirls has The Trinity, the supposed creator of Double, who is the antagonist for many of the characters.
The Grotesqueries Queen could be considered the true big bad in the backstory of Nier since it was because of her that the Gestalts and Replicants were created to allow humanity to outlast the White Chlorination Syndrome caused by the Queen's remains.
The Garlean Emperor in Final Fantasy XIV, the unseen superior to Big Bad Nael van Darnus, who commands his invasion force. However, later content patches imply that Garlemald is currently undergoing a brutal war of succession, implying the emperor died before we ever even saw him. Once the Garleans are gone, the next bigger bad is Zodiark, the god worshipped by the Ascians. To a lesser extent, the Ascians themselves step down after Lahabrea is defeated and instead focus on teaching the beast tribes ways to summon their primals stronger than ever before. While they'll be a threat eventually, for the time they're content to just sit back and help the already dying world kill itself faster.
God is indirectly responsible for the awful cycles of war in Duel Savior Destiny with the constant resurgence of the army of Ruin, but he's not pulling the strings. Nor is the Big Bad his minion. In the final route you can finally fight God and actually completely resolve the story, but until then he's just not really present.
Fallout 3: It's heavily implied that the aliens from Mothership Zeta have been watching humanity for years, and it's also heavily implied that it was they who launched the nuclear weapons that started the Great War and ravaged the planet, just to see what would happen.
Fallout: New Vegas and its DLCs feature a really weird version. The Big Bad Ensemble that occurs if you have all DLC installed- Caesar, Elijah, Klein, and Ulysses- are all to a degree responsible for the conflicts of the game, and each other's plans. By the end, they all seem to be the Bigger Bad to one another.
Caesar (AKA Edward Sallow), the Big Bad of the vanilla game, was the one who led the Legion when it conquered Ulysses's tribe, thus giving him his motivation in Lonesome Road. He's also the one who ordered the White Legs to destroy New Canaan, the one who gave them intelligence, attack dogs, and other aid, and the one who sent Ulysses to help them. This, along with the fact that Salt-Upon-Wounds, the leader of the White Legs, considers himself a soldier for Caesar, makes him the Bigger Bad of Honest Hearts.
Father Elijah, the Big Bad of Dead Money, has a plan that dwarfs the other's plans in monstrosity and sheerscale. It was also he who soloed the Big MT, where he acquired a lot of advanced technology that would help him enact his plan in Dead Money. The way he completely ownedthe Think Tank, led by Klein, also partly caused them to want to break out of Big MT to spread chaos into the rest of the world using their advanced pre-war technology- and he gave them a way to do it, considering he battered the walls down by ramming a train into them.
Doctor Klein and the Think-Tank, the Big Bad of Old World Blues, were responsible for the creation of the Cloud, the Ghost People, and the invincible laser-shooting holograms of the Sierra Madre. This caused the Sierra Madre to transform into a Death World, thus setting up the events of Dead Money. Elijah's plan also revolved around exploiting said poisonous gas and holograms to make himself emperor of post-war America, and he would've never been able to do that if the Think-Tank didn't so thoroughly screw up the Sierra Madre.
Finally, Ulysses, the Big Bad of Lonesome Road. He told Father Elijah about the location of the Sierra Madre, and is thus indirectly responsible for aiding Elijah's plan. He also asked the Think-Tank an Armor-Piercing Question which, along with Elijah's rampage, caused them to want to break out of the Big MT and screw up the rest of the world like they did with the Sierra Madre. He was also sent by Caesar to train the White Legs in modern warfare, letting them become the main antagonists in Honest Hearts, and found caches of machine guns for them to use, giving them the ability to wipe out many civilizations in Utah, where guns were rare except among the New Canaanites. He went rogue soon after to enact his plan in Lonesome Road. In terms of the main plot and the conflict between NCR and the Legion, he's also the one who initially reported the location of Hoover Dam to Caesar.
Ajunta Pall, the founder of the Sith Order and thus the Bigger Bad behind the vast majority of Star Wars media. Among Bigger Bads he's fairly unique in that many of his successors are much worse than he was, and indeed it's possible within the game to help his tortured spirit find redemption.
Revan reveals that the Sith Emperor was responsible for Revan and Malak's fall, and thus the events of the KOTOR games. He takes the Big Bad role for Star Wars: The Old Republic.
Several Yu-Gi-Oh! video games feature the mysterious Egyptian demon Nitemare, the original creator of the Shadow Games and thus the Biggest Bad of the entire setting. While due to numerous contradictions the games in which he appears are not canon to the greater series, it remains somewhat unclear whether Nitemare himself and his role in the Backstory are, as he was created, though never used, by Kazuki Takahashi himself.
Ray Bulgarin from Grand Theft Auto IV. He is an antagonist much more influential in the Niko Bellic's life than Dimitri.
Phazon from the Metroid Prime trilogy. A mysterious toxic mutagen that destroyed the Chozo civilization on Tallon IV, ripped open a dimensional hole on Aether, and is being used to create biological weapons by the Space Pirates. Initially thought a passive corrupting force, there are hints throughout the first two games that Phazon is actually Sentient Phlebotinum, which is confirmed in the third. Each game has its own Big Bad, and Phazon is always why they're a threat in the first place.
The Big Bad of Iji is General Tor, but as he explains he is utterly subservient to his military leaders, who are themselves subservient to the Komato race as a whole, because of their powerful herd mentality combined with millennia of cultural jingoism. The idea is that war is bigger than one person, and is ultimately a symptom of a severely messed-up society.
In the original Half-Life, the Big Bad was the Nihilanth, a powerful alien leading the Xen invasion forces. However, Valve revealed that the Nihilanth and his forces were invading earth in order to flee from the Combine. Sure enough in Half-Life 2, the Combine are the main antagonists. In fact, while Dr. Breen is the Big Bad of the sequel, he is subservient to another Bigger Bad, the Advisors, who not only take direct control over the remaining Combine's forces in Episodes One and Two following Breen's death, but who also implied to be the leaders of the Combine overall.
In the Dragonborn DLC for Skyrim, the main antagonist is Miraak, a former Dragon Priest and the first Dragonborn. It's later revealed that he's subservient to Hermaeus Mora, the Daedric Prince of Knowledge, who he's plotting to overthrow. Turns out, Hermaeus Mora was letting Miraak build up his power, knowing he'd eventually target the last Dragonborn and lure them to Solstheim, where Mora could recruit them. He then used their conflict to steal the secrets of the Skaal, before killing Miraak and informing the Dragonborn they've inherited his position. Overall, quote an impressive display of a Bigger Bad and Manipulative Bastard at work.
Mehrunes Dagon was this in Arena to Jagar Tharn. Then a really obscure text revealed that Alduin was the Bigger Bad to him in Battlespire and Oblivion.
In Warframe, much of the game's mess can be laid at the feet of the leaders of the Grineer and the Corpus, none of whom you get to strike directly at.
In Harvester, the entire game is merely a simulation to create serial killers, making the programmers behind the simulation fit this trope.
In Mario & Luigi: Partners in Time, the Big Bad is Princess Shroob, the Shroob leader. Except she's only been the main leader since the beginning of the game; Peach sealed her older sister away offscreen at the very beginning of the game, making the younger Princess Shroob the Big Bad and the older one the Bigger Bad.
In Suikoden III, Hikusaak, Emperor of Harmonia, plans to gather the 27 True Runes to create a world of perfect order - a soulless dystopia. The actual villains of the game are the people trying to stop him, because their plan to do so will kill millions of people.
While the Big Bad in Persona 3 is Itsuki, for trying to bring about The Fall by causing Nyx to descend to Earth and turn everyone into braindead zombies, it's easy to assume that, by extension, the Bigger Bad is Nyx. However, it's eventually revealed that Nyx is more of a force of nature than an actual entity, and doesn't really wish to bring about The Fall. No, the real Bigger Bad is Erebus, the manifestation of mankind's will to die, who actively does want to bring about The Fall and can do so by coming into contact with Nyx.
While the real killer and mastermind behind the killings and abductions in Inaba in Persona 4 is Adachi, the path to the True Ending reveals that there's someone behind even them: Izanami, who gave the protagonist, Adachi and Nametame the power to enter the TV World in order to test humanity.
Persona 4 Arena reveals another Bigger Bad: The Malevolent Entity, who is heavily implied to be Nyarlathotep.
Nyarlathotep has this role in Persona 2: Eternal Punishment. In Innocent Sin, The Reveal about him showed he was actually involved directly for a decent chunk of the game, but in Eternal Punishment, while his existence is revealed early, he's mostly only referenced when bringing up Innocent Sin's events and that his power caused The Plan to bring about The End of the World as We Know It, but it's mostly his pawns that interact with characters, and he himself doesn't actually appear until the very end of the game.
One has been vaguely hinted as existing in the main Shin Megami Tensei continuity, as well. Exact nature is unclear, but there have been various opaque references to YHVH not always being the tyrant he is now, meaning the root cause of the Order Versus ChaosForever War is something else. Its exact nature is a point of debate among fans, as is whether or not it's likely to be "officially" revealed at all. YHVH and Lucifer themselves are also skilled at playing Bigger Bad when the situation calls for it.
Ares in God of War: Ascension, the Big Bad of the first game, plays this role due to Ascension being a prequel detailing the consequences of Kratos breaking his oath to serve, with Ares himself not playing any direct role.
The Legend of Spyro trilogy has it's main villain Malefor in this role in the first two games, with whatever servant he has acting as The Dragon in each game, Cynder in the first and Gual in the second, as the Big Bad plotting his return, before taking over as the Big Bad in the third and final game.
In Saints Row: The Third, Monica Hughes is this for Cyrus Temple, as she is the one who spearheaded the STAG initiative.
The TouhouStory Arc consisting of games 10 through 13 is generally referred to as the "Moriya arc", because the events of each game are caused by a character who debuted in the previous game, despite not appearing in the game in question, starting with the Moriya Shrine members. Subterranean Animism was caused by Kanako giving Utsuho the tremendous powerthat gave her ideas of megalomania. Undefined Fantastic Object was caused by a geyser that Utsuho created launching the Palanquin Ship into the sky. And Ten Desires was caused by Byakuren landing the Palanquin Ship on Miko's mausoleum, giving her the boost she needed to resurrect.
Manus, Father of the Abyss, is this to the world of Dark Souls. He is only encountered in Downloadable Content and long dead in the present day thanks to the Chosen Undead defeating him in the past, but he is ultimately responsible for the Vicious Cycle plaguing the world. One of the reasons the First Flame needs to stay lit is to keep the Abyss (the unfettered form of the Dark Soul) that Manus unleashed sealed away. Without the First Flame keeping the Dark Soul in check, all humans would likely become monsters like Manus. In the sequel, the Big Bad is a fragment of Manus' soul granted human form. The smallest fragment no less.
In Psychonauts, The Butcher is the primary reason his son, Coach Oleander is as screwed up as he is, and why he embraces the whole Take Over the World schtick. In a weird variation, defeating the former (or rather a mental projection of him) is key to defeating the latter.
The Galactic Federation in Phoenotopia. They're the greatest immediate threat to humanity present (other than Billy), but they're not directly responsible for any major plot points; they simply prompt the abductions, spur Gale to bring Billy to the Phoenix Weapons, and give Billy a chance to take over Earth.
Fate/stay night gradually reveals over the three routes that the source of the Grail's corruption is Angra Mainyu, who will be reborn if any of the Big Bads succeed in their plans.
The Snarl, a God-killing Eldritch Abomination, is the most powerful and malevolent presence in the series, and the whole reason everything is happening, but appears to have no real mind or personality of its own; there are some hints as of this comic (major spoilers ahoy) that this might not be the case.
The IFCC Directors are three fiends who are rather, wereThe Man Behind the Man to the Linear Guild, but they themselves refer to more powerful fiends ("the Lower Downs") from whom they are attempting to gain support for their venture, using their corruption of Vaarsuvius as proof of concept.
Lord English from Homestuck is the most powerful character in the setting, but remained The Unseen until after Act 5, despite a great impact (mostly in the form of his chief servant, Doc Scratch) on the plot. The Big Bad was initially thought to be Jack Noir, stab-happy treacherous Archagent, who the protagonists have much more motivation to destroy but he has since lost focus in the story as Lord English's machinations become more and more obvious as well as his possible origin.
Chaos of 8-Bit Theater is an evil Eldritch Abomination and embodiment of decay that is the whole reason behind the Light Warriors' quest. Although he does desire to end (and eternally torment, however that works) existence for no real reason, he does not come into play until the real Big Bad, Sarda, accidentally brings him about. Who was himself indirectly created by Black Mage.
In Sluggy Freelance the Demon King of the Dimension of Pain generally plays this part in Dimension of Pain arcs. The demon lord Horribus serves as Big Bad. Presumably Psykosis will be replacing him in future Dimension of Pain appearances.
Malefor in The Legend of SpyroZonoya's Revenge. Not only was he responsible for everything that happened in the games, he brainwashed Cynder into slashing out the eye of Zonoya, her best friend, which was Zonoya's Start of Darkness. Zonoya was also in love with him, leading to many of her actions in addition to her revenge plot, making him responsible for most of the plot..
The Lord Vyce story arc of Atop the Fourth Wall has the Multiversal Conqueror Lord Vyce the Big Bad, but his goal in conquering is to in fact protect dimensions from, and eventually track down and kill an Eldritch Abomination that he simply refers to as "The Entity", which devours entire planets, and eventually universes. Later it turns the Entity came to our universe as Batman Gambit in hopes Linkara would defeat Lord Vyce, since it considered fighting him to be too inconvenient.
In The Gamers Alliance, the Nameless Evil, which later took over the god Dreamweaver's body and became known as Death, has been behind all atrocities which have taken place in various eras, subtly influencing events to its liking.
The Director is this, as most of the things that happened to the Blood Gulch Crew and Freelancers were caused by him and his plans.
Flashbacks in Season 10 show that the A.I. Sigma qualifies for the Recollection Trilogy as a whole; he's technically the Big Bad of Reconstruction, but he is killed after those events. However, his influence on the Meta still remains in Recreation and Revelation.
In Seasons 11 and 12, Locus and Felix are working for the Big Bad, Control, to manipulate a Civil War on the planet Chorus. However, Felix's word choice ("employers") implies that Control is not the Biggest Bad in the third party that wants the alien technology from Chorus.
Cipher serves as one for the entire RP in general, often acting through proxies instead of fighting the J-Team directly, having a hand in the backstories of several characters, and even created 'M which antagonized the J-Team during the Unova arc. For Orre they end up becoming the Big Bad of the arc.
OLD MAN's nemesis, the Magikarp Salesman, a powerful demon who doesn't really concern himself with the J-Team's antics at all.
The Seven Jerk Dragons serve as this for the PMD-R arc. While they don't make a direct appearance, their actions are directly responsible for the state of PMD-B when J-Team members visit it.
Eddy's Brother from Ed, Edd n Eddy is responsible for Eddy being the selfish, greedy Jerkass that he is, and thus for all of the schemes that drive almost every episode.
In the Dungeons & Dragons animated series, one episode featured Big Bad Venger's master, an insanely powerful Eldritch Abomination that appears and starts destroying the entire realm. Even at the end, when it's banished with the combined efforts of Dungeon Master, Venger, and the Heroes, DM still remarks that what they've accomplished is but a temporary victory.
Horde Prime, mainly in She-Ra: Princess of Power since the Horde was her primary enemy. The master of both Hordak and Skeletor, Prime almost never played a direct role, but would occasionally appear to berate Hordak for his constant failures.
Hordak himself is the Bigger Bad in He-Man and the Masters of the Universe (2002). He plays a prominent role in the backstory as the Arch-Enemy to King Greyskull (and oddly enough to fellow archvillain King Hiss as well) and the one who transformed the dying Keldor into Skeletor. In the series proper he is a Sealed Evil in a Can who only briefly appears as gigantic cloudlike apparition during an attempt to release him only to fade away once the attempt is foiled. Had the series continued Hordak would have been freed and become the Big Bad proper for a season before being defeated by Skeletor. Also, Hordak is the one who divided that series' version of Eternia into the Light Hemisphere and the Dark Hemisphere.
Bravestarr used the exact same format, with Big Bad Tex Hex answering to an entity called Stampede.
On Invader Zim, Zim could probably be seen as the Big Bad focusing on Earth, with the Irken Empire itself (including the Tallests and Control Brains) as the Bigger Bad out to conquer the rest of the universe, especially since technically Zim conquering Earth wasn't even part of the Empire's plans.
The Big Bad Mumm-Ra of ThunderCats (both the original and 2011 reboot) is a servant of the Ancient Spirits of Evil, who grant him his power in exchange.
The Legend of Korra season 2 reveals Vaatu to be the canonical ultimate evil of the entire Avatar universe, as he is the embodiment of darkness, chaos and destruction. He was the reason the Avatar came into existence. It's not until Korra's time that he takes center stage for that season.
American Dragon Jake Long: While the Huntsclan is still Jake's primary enemy, they're ranked as only the number 4 threat to the Magical Community. Instead, the Dark Dragon serves as the most powerful enemy in the series, and thus only gets personally involved in two episodes.
The Three Ancestral Witches are this in Winx Club, especially in seasons 1 and 3. Being responsible for the destruction of Domino, they are the cause of many of the series's problems. The Trix, their descendants, take over their role to conquer the magical universe, and Valtor was their creation and servant. At the end of season 3, they attempt to directly control Valtor to their will, but he's killed before he can do anything. They become more involved in the movies.
While League of Super Evil centers around the schemes of the League, Skullossus is the most threatening villain to the world at large.
The Simpsons has Wainwright Montgomery Burns, grandfather of Mr. Charles Montgomery Burns. He's the reason why Mr. Burns became a malicious and greedy old man, since Wainwright took Charles away from his parents and raised him to be selfish.
According to Word of God, Chris McLean will always possibly be the true villain of the Total Drama series, even though a certain contestant causes trouble in each season, Just in case he isn't.
Darkseid was revealed to be this in the finale of Young Justice, being the secret collaborator with The Light, and the show ended before he could take a direct role.
Grojband has Mayor Mellow, despite not being a villain.
Lauren Faust apparently had an idea for something like this to feature in My Little Pony: Friendship Is Magic. According to her, something turned Luna into Nightmare Moon, and something freed Discord from his stone imprisonment. There are no allusions to this entity in the show itself, and as Lauren no longer works on the show, it's unlikely this will ever be picked up on. The former was picked up in the IDW comics, where Nightmare Moon is a separate entity that merged with Luna upon sensing her envy and resentment towards Celestia. It serves as the Big Bad of the second arc. Whether this story is in canon with the show is another matter.
Scooby-Doo! Mystery Incorporated featured a slew of villains, from Professor Pericles, to Mr. E, to Mayor Jones, and yet all were unaware that they were pawns corrupted by the influence of The Evil Entity that was encased in a crystal sarcophagus, waiting for someone to to set it free.
Batman: The Animated Series: Salvatore Valestra, a mobster who forced Andrea, one of Bruce's love interests, to leave the country. Without her, Batman ended up alone and took the cowl to become Batman. Ordering the death of Andrea's father led to the events of Batman: Mask of the Phantasm, the man he hired also led to a fair share events in the present; the man would become the Joker.