Warning: Beware of unmarked spoilers!!
- Attack on Titan has several that have been revealed through the course of the story:
- The Royal Government of humanity, who are behind an Ancient Conspiracy for keeping the status quo, and hide a dark secret. That secret, being the fact that the Royal Government is nothing more than a puppet regime of the Reiss family, direct descendants of the First King of the Walls and wielders of the Founding Titan. However, they refuse to unleash the Founding Titan's power against opposing forces, as whomever of royal blood possess it is confined to the First King's will, believing all Eldians deserved to be destroyed as a form of atonement for their past actions.
- The conclusion of the Return to Shinganshina reveals the Kingdom of Marley: the nation behind every major event that started the plot. Case-in-point, they are the ones who stole seven of the Nine Titan Powers from Eldians a century ago, and are the true reasons the Eldian people fled to the Island of Paradis to seclude themselves behind the three Walls. Coming into the events of the main storyline, they are the ones who keep sending the mindless man-eating Titans, and they are the force behind the Beast Titan and the other Titan Shifters who breached Wall Maria at the beginning of the story. All because they want to seize the rich fossil fuel deposits of the island.
- Willy Tybur, being the patriarch of the Tybur family, is revealed to be the de-facto ruler of Marley itself, though he (and the rest of the Tyburs) leave governmental matters to the Marleyean military (led by General Calvi, and later Theo Magath). However, the failure of the Paradis Island Operation and the reveal of Eren Yeager being the current wielder of the Founding Titan has him stepping out of the shadows and rallying the rest of the world in declaring war against Paradis Island, being the last straw that results in Eren putting everything in motion to unlock the Founding Titan's true power and instigating the Rumbling.
- Karl Fritz, the 145th King and a bearer of the Founding Titan. As revealed by Willy Tybur, he was the one responsible for Eldia's downfall and seclusion to Paradis Island, leading to Marley's rise in power and abuse of Eldians. He was wracked with guilt from the war crimes committed by his ancestors, so he decided to punish his own subjects to atone for those sins, wishing for the extinction of the Subjects of Ymir. So, during the great Titan War, Fritz abandoned the majority of his people on the mainland, to suffer a cruel fate from other ethnicities. Then he took those who followed him to the island of Paradis where he sealed them within three Walls, isolating them from the world and erasing their memories. Not only that, he ensured that his successors would uphold his will by means of Vow of Renunciation. That means that his successors will never be able to use the Founding Titan to its true potential and would never kill the Mindless Titans marauding across the island. Fritz's plan would have succeeded, but he underestimated the Attack Titan which disrupted his designs and conquered the Founding Titan.
- The flashbacks of Ymir Fritz from the War for Paradis arc introduces one of the two Greatest Scope Villains of the entire series: the ancient Eldian King Fritz from 2,000 years ago. He gleefully exploited Ymir's powers to conquer Marley and had his daughters devour her corpse to inherit her Titan powers. His vision was for Eldia to enslave the entire world using the power of the Titans. It was therefore King Fritz who in some senses is ultimately responsible for the chain of events and the misery that the main characters experience. He unleashed the Titans as a powerful weapon against Eldia's opponents and created the Eldian Empire, eventually provoking the Titan civil wars, King Karl Fritz's guilt, the Great Titan War and Eldia's fall (and ongoing conflicts with Marley) in the plot's present.
- The Source of Organic Matter (the other Greatest Scope Villain) also counts as this, as it is the anomaly that granted Ymir Fritz the first Titan Power that resulted in all the horrors for two millennia. It continues to latch on to every wielder of the Founding Titan, the last being Eren Yeager. That being said, it's unclear if it has a purpose beyond that of granting a Founding Titan wielder the potential to fully use its power, and it's ambiguous as to whether or not it has any malicious intentions unlike the aforementioned King Fritz.
- There's also a hidden Greater-Scope Villain influencing the entire plot, not revealed till Chapter 121: Eren Yeager himself. He used the past and future sighting ability to peer into the history of the Attack Titans to manipulate them into reaching their current state. He was the one who influenced Kruger to give Grisha the Titan, hinted to him about Mikasa and Armin. He compelled Grisha to butcher the Reiss family to prevent the Will of the First King interfering with his plans for salvation, then commanded Grisha to feed himself to his younger self. It is revealed he was pulling the strings all along since the moment he kissed Historia's hand (which showed Eren what he needed to do), and then he steps up to be the Big Bad (alongside the Source of Organic Matter) once he lets Ymir unleash the Wall Titans and orders them to raze the nations outside Paradis.
- In Arpeggio of Blue Steel the Fleet of Fog claim to answer to a mysterious Admiralty Code, though what that actually is remains unclear.
- In Berserk, that would be the Idea of Evil. Conjured into existence by humans' collective wish to explain their suffering, it keeps the world a miserable place, enabling characters like Griffith and the rest of the Godhand to run rampant over humanity. It has no actual, independent will though and that's where the Godhand comes to play. They can be and do as they wish, because every fiber of their being and actions represent and embody It.
- Black Clover:
- Zagred, the Word Devil, is this in the first saga. He’s the one who deceived the humans into committing genocide against the elves and cast the forbidden Reincarnation Magic, leading Patry to become the main villain of the story. Patry, unaware of Zagred's role, follows his plan of reincarnating the elves, gathering the magic stones, and summoning the Shadow Palace. This leads to Zagred gaining body in the living world, his goal all this time, so he can spread chaos and destruction to fulfill his sadistic desires.
- Morris the Shadow Dictator and Mad Scientist of the Diamond Kingdom, is responsible for one of the operations of the Diamond Kingdom and he was the one who threw out Fana after he found her useless. He doesn’t fully appear until the second saga and even forms a Big Bad Duumvirate with the Dark Triad to bring demons into the human world.
- Lucifero is this in the second saga (and also the first, due to Zagred being his subordinate). He’s the most powerful devil in the series, the devil who serves Dante and is also the source of his Gravity Magic, with Dante acting on Lucifero's behalf to form the Qliphoth tree and bring Lucifero to the living world.
- Megicula is another one in the second saga. She is responsible for placing the curses on the House Silva and the princess of the Heart Kingdom.
- The greatest Greater Scope Villain of the series is none other than Lucius Zogratis, the original identity of Julius Novachrono, he’s had this role as both the Big Good and the Greater-Scope Villain the entire time, being the oldest of his siblings who groomed them to become devil hosts with the goal of forming the Qliphoth to steal Lucifero's power, granting him enough power to lead a self-proclaimed holy war that he calls "Judgment Day". When he finally reveals himself after their defeats Lucius steps into the Big Bad role.
- Black Fox has Brad Ingram, mayor of Brad City and president of Gradsheim, and is the other man responsible for killing Rikka's family, and further up the corporate totem pole than Lauren.
- Bleach: Prior to his proper introduction, Yhwach has had an influence on the world, with events going back as far as the earliest parts of the series being a result of his mere existence. He is the progenitor of the Quincies, the Emperor of the Vandenreich, the creator of the Sternritter; even the creation of the Gotei 13 is implied to be connected to him. Many centuries before the start of the series, a war broke out between the Soul Reapers and the Quincy, in which Yhwach was believed to be killed. In truth, he survived and would return 1,000 years later. He's responsible for the Echt culture that brought Ryuken and Masaki together and killed off both Masaki and Kanae. The Quincy bloodline that he is the progenitor of attracted Aizen's Hollowfication experiment White and provided a means of stabilizing the Visoreds. Neither Ichigo nor Uryu would exist, or even be the kind of people that they are, without Yhwach's influence.
- In Chainsaw Man, the story's Big Bad Ensemble is the Horsemen of the Apocalypse, but the first three were simply the prelude to Death who is Nostradamus' "Great King of Terror" prophesized to end the world and make Devils the dominant race.
- Claymore: The Organization which has used the island Claymore is set in as a giant-sized research lab for the whole time as a means to produce controllable Awakened beings. They created the Yoma and every single nasty thing that inhabits Claymore's Crapsack World ultimately exists only because of them, Abyssal ones and Priscilla included.
- 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.
- Skull and Van Vogt from Cyborg 009 serve this role in Cyborg 009 vs. Devilman, as they're the ones who authorized and backed up Dr. Adams Teufel's High-Teen Number Cyborgs and "Cyborg Demon" research. The ending of the OVA also features The Cameo from the Demon Statue, the Greater-Scope Villain of the entire Cyborg 009 manga.
- Danganronpa has the Hope's Peak Steering Committee, who only properly appear in Danganronpa 3: The End of Hope's Peak High School (which is why they're in this section), but their actions are behind the whole Hope's Peak saga. Junko may have been the one to directly instigate the Tragedy, but she never would have gotten as far as she did if they hadn't bent over backward to admit her and cover up her crimes, thinking that they could control her and use her talent for Izuru.
- In Daimos, had Olban never murdered Leon in his pursuit to be King of Planet Baam, the Baam-Earth war would have never started.
- Death Note:
- Ryuk is the Greater Scope Villain 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.
- Digimon
- Apocalymon in Digimon Adventure. His existence was an anomaly which created the Dark Masters, who in turn were responsible for almost everything the children endured in the Digital World.
- Millenniumon and Myotismon in Digimon Adventure 02. Milleniumon infected Ken with the original dark seed that led to his corruption. Myotismon was responsible for everything else, even the villains who used Ken were unaware they were helping him revive himself. There is also Dagomon, a Lovecraftian creature of darkness that lives in the Dark Ocean and is never actually fought.
- The D-Reaper in Digimon Tamers is responsible for Calumon coming to real world, Zhuqiaomon's Devas attacking the humans and all of the chaos the Digital World suffers, yet the kids don't know of its existence nor does it harm the human world until the final third of the series.
- Digimon Frontier: Lucemon was this before he was revived. Until they defeated Cherubimon, the kids thought Lucemon was already gone. But they soon find he corrupted Cherubimon into unintentionally giving him the strength to return.
- Digimon Data Squad: Kurata is responsible for Merukimon's hatred of humans by invading the digital world and murdering several innocent Digimon permanently, and, even after his death, he ultimately caused the conflicts of the final arc: His actions lead King Drasil to try to destroy the human world, and his final act, though not his intention, was to set both worlds to collide, which would have destroyed them if it wasn't stopped in the final episode. Although, one could say SaberLeomon's unprovoked attack set Kurata on his genocidal plans, but by the present day, Kurata is a megalomaniac who intends to take over both worlds and only destroy the digital world when he gets bored of it.
- Digimon Adventure: (2020) does this recursively, with each Big Bad acting to set up a new villain who operates on a larger scale. The evil Digimon operating across the Cloud Continent such as Soundbirdmon, Eyesmon, and Ogremon are led by Devimon. Devimon in turn is just one of many minions across the greater Digital World feeding data to Millenniumon.
- Dissolving Classroom: The devil, who never takes a direct hand in the manga's events but is Yuuma's apparent object of admiration and worship, appears to be allowing Yuuma to channel his power through Yuuma's apologies, and who possessed (or is at least inside) the reporter who brings Keiko to the press conference in the final chapter.
- Dragon Ball:
- King Piccolo is responsible for many sagas before and after his time as the Big Bad in his arc. His rampage in the past spurs his good counterpart Kami to create the Dragon Balls, thus prompting the Pilaf gang and the Red Ribbon Army to seek them for their own ends; his evil caused the Crane Hermit to turn corrupt, leading to him acting as the Big Bad for the 22nd Tenkaichi Budokai arc; and Piccolo Jr is born post-mortem as the Big Bad of the 23rd Tenkaichi Budokai arc.
- 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. Despite never coming into contact with the protagonists until much later in the story, his transformation of the Saiyan race into genocidal killers-for-hire and his decision to ultimately destroy their planet, Vegeta, ultimately sets the entire Dragon Ball series into motion. The biggest being that he's the reason why Goku was sent to Earth. Even after his demise, his influence is still felt. The Super Saiyans exist directly because of him, he lives on in a sense in Cell (who takes on most of his personality traits), he is the reason why the Namekian Dragon Balls can now revive several people at once (used to be one per wish), and his defeat leads Beerus to Earth seeking a Super Saiyan God.
- Dr. Gero is the Greater-Scope Villain of the Android Saga. When he appears properly, he's a Big Bad Wannabe who the Z-fighters think is one of the androids Future Trunks warned them about (apparently the Butterfly of Doom meant that he decided to turn himself into an android instead of releasing the two much stronger androids who were responsible for the Bad Future), but he's the one who created Androids 17 and 18 (by kidnapping two runaway teens and turning them into cyborgs against their will), Cell, Super 17 (in GT), Androids 13, 14, and 15 (in the movies), and Android 21 in Dragon Ball Fighter Z by turning his own freaking wife into an android monster with Horror Hunger who causes the plot of the game.
- Majin Buu was originally unleashed by the evil wizard Bibidi (though Shin thought he created Buu), destroying all but one of the Supreme Kais and who knows how many planets, before Shin (the Sole Survivor Supreme Kai) confronted him and killed him. He left behind two things: Buu sealed away on Earth, and a doppelganger named Babidi who wished to continue his plans. The heroes sans Shin never meet Bibidi, and Babidi doesn't last too long himself, but he's the reason the Majin Buu arc happened. Super implies that it's one reason for Universe 7's low mortal level, as Shin was the youngest and least experienced Supreme Kai, but the deaths/absorption of all his superiors left him to manage the universe on his own, a task he was extremely underprepared for. He didn't even know that the Potara earrings could be used for fusion until Old Kai told him, and had only heard rumors of Beerus' existence, despite the Supreme Kai and God of Destruction being supposed to work together.
- Near the end of Dragon Ball Z: Battle of Gods, Lord Beerus states that there are eleven other universes out there, and that each one has their own God of Destruction, and each of them has their own attendant like Whis. The English dub hints that some of them may be even more powerful than Beerus and Whis themselves. Dragon Ball Super introduces the rest, and they're varying degrees of villainous; Quitela (from Universe 4), for example, is downright nasty, while Champa (Universe 6) acts like a more boorish version of Beerus (they're brothers), but most of them are generally well-intentioned if a bit sociopathic (comes with the job), and some like Arak (Universe 5) and Belmond (Universe 11) are downright benevolent. The movie also reveals that Beerus encouraged Frieza to destroy Planet Vegeta, which pretty much caused the entire series.
- A Dog of Flanders (1975): Hans, because he blamed Nello for the fire (when it was actually his own fault) to save a quick buck, and it led to Alois' father kicking Nello being out on the streets on Christmas day. All the villagers are disgusted that Alois' father would so something so cruel to a child, and even though he implores to them that he'll change and make it up to Nello by adopting him and raising him as his own son, it does little to change their opinion....and then Nello is found dead.
- Dr. STONE has the mysterious voice they refer to as the "Why Man", after his first appearance consisted entirely of a morse code message repeating "Why?" He reappears later on with the clear intention of re-petrifying the world, and has adopted protagonist Senku's voice. They realize from this that the Why Man isn't human, and is also on the moon, leading to the main goal of rebuilding society to get to the moon.
- Fairy Tail:
- Zeref, the Black Wizard. It's been 400 years since his presumed death, and people are still fighting against demons and other evil artifacts he made back then. Hades, the closest thing the series has to a Big Bad at that point, is one of the few who realizes he's Not Quite Dead, and aims to unleash his sealed power on the world. However, it turns out Zeref was doing nothing not because he was sealed, but because he simply didn't want anything to do with the world's destruction. In fact, it's that kind of presumptuous thinking that spurs Zeref into taking up the role as Big Bad.
- Acnologia, the Black Dragon of the Apocalypse, is one of the most terrifying forces of destruction known to man, and the only being Zeref himself fears. It turns out getting rid of Acnologia is on Zeref's agenda (though at the expense of the rest of mankind), and once Zeref is defeated, he ends up being the sole remaining enemy Fairy Tail needs to defeat.
- For the Tartaros arc, we have an unusual zig-zagged exemple. Mard Geer serves as the Arc Villain/Dragon-in-Chief to E.N.D., the master of Tartaros, who is sealed away in his book while the former intends to free him. While it's eventually revealed that E.N.D. was merely a Decoy Leader for Mard Geer to rally the rest of Tartaros around, what he doesn't realize is that E.N.D. is actually Natsu, the main character. It's not just him, either; the entire Tartaros guild does what they do in the name of Zeref and E.N.D, and eventually wiped out in large part thanks to Natsu, all without knowing that their "master" and their biggest enemy are one and the same.
- Fruits Basket: Ren Sohma, Akito's abusive mother. She is introduced very late to the story and never interacts with Tohru. But she is ultimately the reason why the story happens in the first place: it was her idea to allow Tohru to live in the Sohma estate, while the relentless psychological torture that she subjected on her daughter turned her into a Psychopathic Manchild who violently keeps the Sohma men from straying away from her side.
- In Future Robot Daltanious, the Heliosian Empire was paranoid about losing their power, so they bred their own Clone Army to function as spare organs/puppet rulers and constantly abused them until one clone had enough, escaped and led an army that annihilated them. Even Harlin feels moved by his tragedy, despite the fact that said clone murdered his entire family and also tried to murder his last remaining son.
- Lord Tamamo in Ga-Rei, master of the original Kyuubi and Mitogawa's superior.
- In Gintama, The Tendoushuu. They are an organization founded by rich Amanto centuries ago as an independent third party to monitor Altana usage in the universe (caused by a devastating war that lead to the Amanto in deciding have someone outside of any government control). They instead became a power unto themselves and used their granted influence to control other planets and taking the Altana as a means of studying it. They are indirectly responsible for making Earth, especially Japan, be invaded by the Amanto, leading to the Joui Wars and the resulting aftereffects within the series.
- In Guilty Crown, GHQ is secretly being assisted by Da'ath, an ancient organization existing since human evolution and which is responsible for the Apocalypse Virus' creation for their Adam and Eve Plot.
- Mamo at the end of the Gravestone of Daisuke Jigen is implied to have been watching over (and possibly controlling) the events of the film. This may just be a Shout-Out, but the sequel Goemon Ishikawa's Spray of Blood suggests there is a hidden figure who wants the main characters dead. This could be Mamo or someone completely different.
- In High School D×D, Trihexa, the Beast of Apocalypse, is this to the story. When it is unsealed, it will wreak havoc on all the mythological realms, and the universe itself.
- In Higurashi: When They Cry, Nomura and her employers at Tokyo just used the Big Bad and their goals to further their own plans.
- Hoshin Engi: Dakki is the Big Bad, but late in the story she's revealed to be working for Joka, an extremely ancient and powerful being who has been secretly manipulating the course of history for millennia, in the hope of turning Earth into a replica of her destroyed homeworld. Few people were even aware of her existence, and Dakki was her dragon (with an agenda, of course).
- 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.
- Kars from Part 2 of JoJo's Bizarre Adventure. He is the creator of the Stone Masks and the reason why Pillar Men are seen as evil (as his species is naturally a subterranean, nocturnal race and prefer to live away from humans). Because of his creation of the masks, Kars is indirectly responsible for the tragedies both the Joestars and Zeppelis face early on as well as serving in Dio's ascension and giving him his powers. This leads to the Joestars being intertwined in a fate in which each JoJo must do battle with evil.
- Dio Brando, the starter Big Bad of the series, is this for the rest of the series, affecting the plot whenever he doesn't take up the Big Bad role directly, especially in Part 6.
- It's eventually revealed in Part 5 that Diavolo was the one who initially discovered the Stand Arrows and distributed them, making him a Greater Scope Villain for Parts 3 and onward.
- Kichikujima: Zanta Maria, who inspired the family and Hitomi who gave them their powers and taught them magic.
- In Kill la Kill, Ragyo Kiryuin is ruler of the world, and Satsuki’s boss, but is mainly a background threat until later. The real example is the Original Life Fiber, the source of all life fibers, who manipulated the evolution of mankind since its arrival on Earth and eventually seeks to assimilate all humans and consume and destroy the planet to launch its spawn into space to reproduce Lavos-style. Ragyo is merely a servant to the Original Life Fiber.
- Kirby: Right Back at Ya!: The evil Lord Nightmare. He's the creator of the Demon Beasts which he used to terrorize the universe, prompting the foundation of the Star Warriors, which Meta-Knight and Kirby are part of (among some other characters, original or not, survivors or related by proxy) and that were nearly wiped out, which set the fate that a young Star Warrior (Kirby) would defeat them. King Dedede purchasing those monsters (and getting huge debts out of them) to try to defeat Kirby is one of the driving forces of the plot. Corrupting some denizens of Dream Land into Demon Beasts is also his doing.
- In La Seine No Hoshi, Madame Catherine was angry that Marie Antoinette had a more pretty dress than her (yes, really), so she killed the main character's parents as they supplied the flowers for it. This motivated her to become the titular vigilante heroine.
- Lucky Star: Although there are no antagonists proper, the characters do sometimes hear and talk about terrible things that happen, involving other girls being kidnapped and enslaved. Kagami's very first line in the show is "Such a bad boy...", about someone she reads about in the news before bringing it up with Tsukasa and Konata while they walk down the street.
- 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.
- The Zabi family and Gihren Zabi in particular become this in the various sidestories set during Mobile Suit Gundam's One Year War. Mobile Suit Gundam: The 08th MS Team, Mobile Suit Gundam 0080: War in the Pocket and The Plot to Assassinate Gihren are all examples of this, featuring Zeon officers all acting with the consent of or on order from Gihren Zabi.
- Jamitov Hymen and Bask Om from Mobile Suit Zeta Gundam serve as this for Mobile Suit Gundam 0083: Stardust Memory. Much of what happens in the OVA, including Operation Stardust's success itself could traced in one way or another to them, ultimately leading to the Titans taking power. All the while Haman Khan lurks in the background.
- Duke Dermail in Mobile Suit Gundam Wing. He's the string-puller behind OZ and connected to most of the large political shakeups in the series, though he mainly lurks in the background while Treize and other villains move things forward. In the end, he's offed before the finale, leaving a Big Bad Ensemble with plans all unrelated to what he was aiming for.
- Mobile Suit Gundam Wing: Endless Waltz reveals another one acting in the shadows - Dekim Barton. He was the one who funded the creation of the Gundams in the first place and devised the original Operation Meteor, which the White Fang later appropriated for their own use. While the conflict in the series was going on, Barton was building up his own private army for his own bid to conquer the Earth Sphere.
- 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.
- My Hero Academia has All For One, All Might's Evil Counterpart and Arch-Nemesis, and the man who crippled him and killed his predecessor several years prior to the story's start. He's the one who nurtured the main Big Bad Tomura Shigaraki into a villain in the first place, and spends most of the first part of the series supporting him from the shadows before finally revealing himself during the Hideout Raid Arc after Tomura is boxed into a corner. Tomura becomes the Big Bad after All For One's defeat and imprisonment by All Might... that is until he has All For One's original Quirk implanted in him. All For One returns to become the Big Bad when he uses his original Quirk to hijack Tomura's body and use him as a puppet to steal One For All.
- Naruto:
- The Akatsuki were the Greater Scope Villains for Part I. We're told that they're out there, and that Sasuke's brother, Itachi Uchiha, is a member, and that current Big Bad, Orochimaru, is motivated in part by fear of them. Two of their agents (Kisame Hoshigaki and the aforementioned Itachi) put in a brief importance and inflict horrible damage on the town, but then they pass right back out of the story, and Orochimaru becomes the focus again. In Part 2, the Akatsuki take center stage, and their leader, Tobi, becomes the series' new Big Bad.
- Danzo Shimura is another one for Part 1. Every non-Uchiha Big Bad is connected to him, including Orochimaru. If it includes the Uchiha, he’s responsible, indirectly or otherwise, for the Start of Darkness or action of no less than four villains (Pain, Itachi, Sasuke and Kabuto).
- Another is the Ten-Tails, the original Tailed Beast, of whom the other nine are pieces of its chakra divided. Tobi aka Obito Uchiha wants to reform the Ten-Tails and become its Jinchuriki, so he can enslave everyone with the Infinite Tsukuyomi and complete the Eye of the Moon plan.
- Madara Uchiha began the Infinite Tsukuyomi plan along with manipulating and twisting Obito into his successor. Madara is indirectly responsible for almost every bad deed to happen within the context of the Akatsuki's actions and also being responsible for the Uchiha Clan having a tarnished reputation, indirectly fueling his descendants' future.
- The series' final arc revealed that the greatest Greater Scope Villain of all is Kaguya Ōtsutsuki, the first chakra user, the true identity of the Ten-Tailed Beast/Gedo Statue, and a Physical Goddess more powerful than any other enemy the heroes had fought and Black Zetsu, who is revealed to have been responsible for setting the entire generational conflict that began with Hagoromo's sons, jumped to Hashirama and Madara, and then Naruto and Sasuke. Every conflict and casualty from the warring clans era to the modern village wars and the Akatsuki can be traced back to his constant manipulation of the world.
- Momoshiki and Kinshiki Ōtsutsuki from Boruto: Naruto the Movie. It turns out they were a threat to even Kaguya, as they were the reason why Kaguya used Infinite Tsukuyomi to make a Zetsu army in the first place.
- Some extra scenes and dialogue in Boruto imply that even the two aforementioned characters answer to a certain clan above them.
- In One Piece:
- The Five Elders, a cabal of five Celestial Dragons who appear as the highest rank in the World Government, are ultimately the ones who pull the reins of most of the organizations which cause most of the events in the story: they control the Marines (which Akainu is now in command as the Fleet Admiral) and executing Gold Roger and trying to defeat Whitebeard indirectly gave them the means to ignite two Pirate Eras, which in turn caused the pirate boom in all the seas; employ the Seven Warlords of the Sea (which Blackbeard wanted to be part of as a means of recruiting several Impel Down prisoners and ultimately sparking the War of the Best to kill Whitebeard) and mostly pay no attention to them (which allowed Crocodile and Donquixote Doflamingo to act with impunity for long, as seen in their respective arcs); try to cover-up the Void Century even if it means to put several innocents on trial and execute them (how the Cipher Pol 9 tried to deal with Nico Robin), and completely ignore the crimes the Celestial Dragons do (such as slavery, which caused the incidents in Sabaody). It takes well over one thousand chapters before they meet the main characters face to face.
- Blackbeard is an example of this through the Drum Island Arc, since his pillaging of the country is what causes Arc Villain King Wapol to leave the country and stumble into the Straw Hats. Blackbeard himself is not present in said arc at all, except for a brief mention early on, and in fact only gets introduced nearly a 100 chapters later in the Jaya Arc.
- Doflamingo is the greater-scope villain of the Jaya (as the boss of Arc Villain Bellamy) and Sabaody Archipelago Arcs (being the original owner of the slave auction house that the Straw Hats thrash, leading to the World Nobles calling in an Admiral attack on the island). His presence in both arcs is minimal, having little to no stakes in their ongoings, but his influence can be felt. He only becomes a proper Arc Villain when the Punk Hazard and Dressrosa Arcs come by.
- The character named Imu. They are the one the Five Elders (the above mentioned Greater Scope Villains) bow down to, and the true ruler of the world of One Piece. Their existence is mostly a secret from even other top officials, like Sakazuki and Kong, partly for obvious reasons and mostly because their very place is a complete betrayal of the World Government's deepest principle, instated by its founders: that there will not be a single king everyone shall bow to.
- The Emperors Kaido and Big Mom for the Punk Hazard, Dressrosa and Zou arcs. Kaido is the one buying the artificial Devil Fruits that Doflamingo and Caesar Clown are producing in order to create a Zoan-based army, and Big Mom is the one behind Caesar's gigantification experiments. They later lose this status as they take center stage as the Big Bad Ensemble for over two hundred chapters, before they're finally brought down at the climax of the Wano Country arc.
- Kaido becomes the Greater-Scope villain of the Thriller Bark arc in hindsight, once it's revealed that he's the one who killed Moria's former crew, traumatizing the Warlord into an obsessive scheme to amass a crew of undead soldiers exactly so he wouldn't have to worry about their lives ever again.
- He's also the reason Shanks showed up so late to Marineford. Kaido attempted to attack Whitebeard while Whitebeard was leaving the New World to rescue Ace, and Shanks intercepted him in order to let Whitebeard and his fleet travel unmolested. Because of that, however, Shanks was unable to intervene with the war and deescalate the situation before Ace and Whitebeard were killed.
- Rocks D. Xebec was the captain of the Rocks Pirates, which included not only the above-mentioned Kaido and Big Mom as his subordinates, but also Whitebeard, the Big Good of the Marineford War, and they all attempted to overthrow the World Government in order to elevate Rocks as the "King of the World'' 38 years before present time. This makes Rocks this trope by default since those three subordinates of his went on to become legendary figures of their own, whereas Rocks ended up being forgotten by history thanks to an aggressive campaign from the World Government to erase his overthrowing attempt (thus an interesting case of two Greater Scope Villains directly opposing each other). What little is known about Rocks himself is that he was the most powerful pirate in the world before Gold Roger unseated him, and there are some intriguing hints that the aforementioned Blackbeard considers himself Rocks' successor, as Luffy is to Roger.
- In Outlaw Star, the Big Bad is a Kei Pirate named Hazanko who seeks to overthrow the Tendo King, an unseen Greater Scope Villain. But there is an even greater villain 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.
- The Overdevil in Overman King Gainer.
- Pokémon: The Series:
- Giovanni and Team Rocket (the organization) in Pokémon: The First Movie as they were the ones that commissioned the creation of Mewtwo and caused him to turn on humanity with their mistreatment of him.
- Madame Boss, Giovanni's mother and the head of Team Rocket before him. Giovanni himself is this in the anime, since getting on his good side is the main reason the Team Rocket trio constantly try capturing Pokemon, namely Pikachu. In fact, he barely pays any attention to them and is only involved during major situations. In fact, at the time of this writing, he's only battled against Ash once and won.
- Team Magma for Pokémon: Jirachi: Wish Maker, as Butler used to work for them and tried to create a Groudon for Team Magma using a machine utilizing a piece from the Pokémon, but failed and was admonished for it, making him want to seek out Jirachi and use its power to bring forth Groudon that way.
- Team Plasma in Pokémon: Genesect and the Legend Awakened, as they were the ones responsible for the creation of the Genesect Army.
- Primal Dialga in the anime adaptation of Pokémon Mystery Dungeon: Explorers. Granted, as he wasn't even the villain of the game.
- In Pokémon Adventures, Team Rocket is responsible for the events of the Diamond and Pearl and Platinum chapters, as the Rocket Generals managed to capture Arceus during the HeartGold and SoulSilver chapter and use its power to create Dialga, Palkia, and Giratina, which after the events of the chapter were sought out by Team Galactic for their own goals.
- Pretty Cure:
- 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.
- Suite Pretty Cure ♪ has Noise as the Bigger Bad behind the Minor Land villains. He eventually becomes the Big Bad after his existence has been revealed.
- Doki Doki! PreCure: Proto-Jikochuu was unsealed by the King of the Trump Kingdom, who wanted to save the life of his daughter Marie-Ange with the Eternal Golden Crown, which kept Proto-Jikochuu sealed inside a crystal fountain. After Princess Marie-Ange was saved, Proto-Jikochuu corrupted the King and turned him into King Jikochuu while residing inside him. However, Proto-Jikochuu was never in control of King Jikochuu and only corrupted his heart. King Jikochuu always acted on his own accord and was motivated by his own selfishness. Once King Jikochuu was purified in the penultimative episode, Proto-Jikochuu is consumed by Bel, who in turn is consumed by Proto-Jikochuu instead. As a result, Proto-Jikochuu becomes the Monster of the Week in the final episode.
- Puella Magi Madoka Magica:
- The Big Bad Ensemble of the original anime and manga is the powerful witch Walpurgisnacht and Kyubey/Incubator, but an even more powerful threat exists in Madoka's Witch form, the omnipotent Kriemhild Gretchen, who only appears in several onscreen timelines in Episode 10 and being the True Final Boss defeated in Episode 12. Homura's main goal is to prevent Madoka from becoming a Magical Girl in the first place, specifically because of this fate that she seals by making a contract with Kyubey. Originally, she only wanted to protect Madoka in return for the kindness only she had shown her.
- The villains in the original story, Walpurgisnacht and Kyubey, take a backseat in most spinoff manga, where the main characters deal mainly with other characters with which they have little or no on-page involvement. Though Kyubey often turns out to be behind the plot.
- Puella Magi Tart Magica, being set during the Hundred Years' War, also has King Edward III of England, who started the war back in 1337, along with each descendant of his who kept it going, down to Henry VI in its present day. The Big Bad, Queen Isabeau, is cooperating with them in exchange for power.
- In a rather unique example, the ultimate cause of all problems in the series is not a character, but forces of nature — the second law of thermodynamics
, entropy, and the impending heat death of the universe are what Kyubey is trying to fight against.
- Rave Master: Shakuma Raregroove, the father of King and grandfather of Lucia, was the one who first used the Sinclair, kickstarting the conflict of the entire series and made sure his family would continue his war to destroy the world.
- Kardis, the goddess of destruction in Record of Lodoss War.
- Revolutionary Girl Utena has the Swords of Hate, a swarm of living swords that are metaphorically behind Akio/Dios’s insanity and Anthy’s role as the Rose Bride. It is representation of the world’s physical, social, and emotional assault on those not living to its expectations no matter how unjust they are. In this case, it targets those who do not live to complete altruism as the Prince and those accept being The Scapegoat.
- Chaos in Sailor Moon, with all the Big Bads of each arc revealed to be incarnations of it.
- Samurai Champloo: The Tokugawa Shogunate's efforts to consolidate its power, while it isn't discussed much, puts into motion the driving force behind the series. The Tokugawa clan's attempts to drive the Christians (of whom Fuu's father is the leader) out of Japan, forcefully incorporate the formerly independent Kingdom of Ryukyu (where Mugen is from), and suppress any potential or actual rivals attempts at seizing power, including the Takeda and Hojo clans, of whom Jin is possibly a member of the former based on the heraldic symbols (or mon) being on his attire in one way or another effects the lives of the protagonists. In a somewhat more direct manner, the Tokugawa Shogunate also hired some assassins to kill the two swordsmen Mugen and Jin and follow Fuu in order to kill her father.
- The Demon King in The Seven Deadly Sins is the master to Fraudrin, Meliodas's brothers, and all the other Commandments; struck a deal with the Supreme Goddess in order to "punish" their children Meliodas and Elizabeth for their "sins" by cursing them for 3,000 years; and his reasoning for leading the Demon Clan to take over Britannia is to have one of his sons to absorb all the Commandments and use him as a vessel outside of Purgatory. But even when the seal to the Demon Clan's prison has been broken, he decides to stay on the sidelines for most of the story and let his minions handle matters because he has yet to regain his full strength and the seal has only been broken enough to let demons weaker than him through.
- D in So I'm a Spider, So What? is not directly responsible for the world being in danger. She even offered a solution to solve the problem long ago, but it clearly doomed to failure from the start and only something she offered because the way it worked amused her: The world was drained of energy and on the brink of collapse, so the System she suggested to oversee the world's repair drew energy from people's souls by forcing them to basically live inside a combat RPG. If they fail to repair the world in a timely manner, the gradual damage to their souls will cause them to break apart. For her own amusement, she also continues to sabotage anything that seems like it would resolve the situation. Unfortunately, the idea of actually confronting her and making her pay for her crimes is laughable: She's nigh on omnipotent and capable of squishing gods like they were little baby spiders. You have to play by her rules.
- Spy X Family has a greater-scope villain during the Cuirse Arc in Leonardo Hapoon. He's an arms dealer that makes money off of pro-war extremists and usurped the Gretcher family's organization, having the previous leaders killed. Hapoon also hired Snoops and several highly-skilled assassins to head onto the cruise ship to finish the job by killing Olka and her son, the last remaining members of the Gretcher family. Hapoon doesn't even physically appear, but his actions cause the arc to occur.
- Sword Art Online's first main villain is Kayaba Akihiko, the creator of the Aincrad VRMMO, a game that helped influence some later villains in some way. One of them is his rival who used his game as a template for his own, the other was an Aincrad survivor who wasn't quite done with his fun, and a third is a Mad Scientist who attempts to use his augmented reality technology to try and revive his daughter who died in SAO. He also invented a lot of technology associated with virtual reality, or at least had a hand in them, and made the first VRMMORPG, so almost everything the later arcs make plot points out of, from World Seeds to Medicuboids, can be tied back to him.
- A smaller, though more serious example would be Laughing Coffin, an infamous player-killing guild. They started off as a secondary group of antagonists, only being featured in a few episodes of the original arc. Then the game ends and the remnants of the guild end up securing a poisonous chemical which they use to cause the events of two separate arcs: Phantom Bullet (where the poison is used to make an Urban Legend about a deadly gun) and Alicization (where said poison puts Kirito into the arc's situation in the first place). And because they were made this way because of Sword Art Online's permadeath system, they too are tied back to Kayaba.
- The Anti-Spiral in Tengen Toppa Gurren Lagann. Its existence wasn't brought up until LordGenome the Spiral King gave a vague warning of its coming. Its war on all Spiral lifeforms led to humans being forced underground. Assuming it has any sentience and not just an event, the Spiral Nemesis is the bigger threat, as its capability to destroy the universe is why the Anti-Spiral turned against all life in the first place.
- Toriko several times reveals that the Big Bad is just a pawn or a servant to a much bigger bad. However, both the villainous NEO organization and the Blue Nitro's goals revolve around Acacia's Gourmet Demon — which makes him the main reason of everything that happened.
- Knives in the anime adaptation of Trigun. Unlike in the manga, he remains crippled from Vash's attack at July until the very end of the series, forcing him to work indirectly through Legato and the Gung-ho Guns.
- While Osamu Tezuka's Unico has Baron Ghost and Lord Kuruku as two of the biggest threats the titular character has ever faced, the Greater-Scope Villain in the series is Venus, the Goddess of Love and Beauty, which the little unicorn has hardly interacted with. In the manga's prologue, she originally wanted to regain her status as "The most beautiful person" by summoning the West Wind to separate Unico from Psyche (Goddess of Soul) out of intense jealousy in the hope of making Psyche unhappy forever. When she returns in the final chapter, Venus is enraged that her original plan didn't work and discovering that the West Wind actually cared for Unico. Despite being "The Goddess of Love and Beauty", Venus' behavior and actions towards others is the complete opposite of her title.
- The Sacred Ancestor in Vampire Hunter D is the vampire progenitor, the most powerful and ancient of the Nobility and responsible for the current state of the world — a post-apocalyptic hellhole where vampires used to be the dominant species and humans were their playthings (though, things are slowly changing). He is heavily implied to be Dracula himself and as well as the titular protagonist's father, who has made his life goal to find and destroy him. However, the Ancestor is never seen in the story (except for the first OVA where we see his portrait where he resembles D very closely, while in the manga and illustrations, he is always covered in darkness) and D takes on individual villains on separate installments.
- Voltes V has two: the Stupid Evil Emperor Zambajil, who set up the entire conflict by enslaving his cousin in in his desire to become Emperor, and the ancient Boazanians that created the Fantastic Caste System which allowed Zambajil to seize power.
- In Yo-kai Watch: Shadowside, Shutendoji's initial goal was to gather the Youseiken so "The Princess" would awaken and take the human and Yo-kai Worlds... until it's ultimately revealed all of Shutendoji's efforts were to use the Youseiken to awaken The Overseer. A far greater destructive force, Soranaki almost drove the Yo-kai race into extinction, and was part of the Big Bad Ensemble of Yo-kai Watch: Forever Friends, corrupted Shien and was fought by Enma and three Yo-kai Gods; and 90 years later, did the same with Fukurou, Douketsu and several other Shadowside Yokai.
- Yu-Gi-Oh!
- The original manga and anime 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. Dark Bakura is a villain in other stories, and since Zorc Necrophades becomes the background villain in those as well.
- Much of the conflict during the Battle City arc can be traced back to Marik Ishtar's abusive father, an extremist who only saw his son as an extension of the Ishtar family's role as Tomb Guardians and never loved him as a person. The intense pain Marik was forced to endure during the Tombkeeper's Initiation at the hands of his own father is what gave birth to his Superpowered Evil Side.
- The manga-only spin-off Yu-Gi-Oh! R has two: Dark Bakura, since he kills Pegasus in the Duelist Kingdom arc, which fuels the motivation of the villain of the spin-off, Pegasus' adopted son Yako Tenma, to resurrect him. At the same time, however, there's the Wicked Avatar, a card that was meant as an Evil Counterpart to all three Egyptian God Cards, but Pegasus never published it. Yako published it after Pegasus' death and it corrupted him, and the corruption drives Yako to get revenge for his death.
- Yu-Gi-Oh!: Capsule Monsters has Yami Bakura, who inhabited the Millennium Ring, corrupted Alexander's soul, and led him on the path to darkness. He's not mentioned by name at all, but the Ring and its effects tie into the backstory as well as present day events.
- Dark Bakura also has a significant role in the backstory of Aigami, who is the Big Bad of Yu-Gi-Oh! The Dark Side of Dimensions, and the evil essence of the Millennium Ring corrupts Aigami, making Dark Bakura the Greater-Scope Villain for that movie as well.
- The Light of Ruin in Yu-Gi-Oh! GX. Season 2's villain was serving it, and the third season's villain turned evil because of it.
- The King of the Underworld in the Dark Signers arc of Yu-Gi-Oh! 5Ds, 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 the Crimson Dragon, is being played like a violin by Rex Goodwin. Z-One however, is a straighter example, as not only is he The Man Behind the Man for Paradox from Yu-Gi-Oh!: Bonds Beyond Time and the Yliaster organization, he is also the one responsible for the Zero Reverse disaster.
- Yu-Gi-Oh! ZEXAL has an evil deity called Don Thousand, the true ruler of the Barian World.
- Yu-Gi-Oh! ARC-V:
- First, there's Zarc, a power-hungry duelist from the utopian Original Dimension, as it is now called. Corrupted by the four Dragons now used by The Chosen Many, he became cruel, destructive and insane, and might have caused The End of the World as We Know It had his former friend Ray not tried to stop him. To say the least, she failed, despite defeating him. The dimension was split into four separate ones (Fusion, Synchro, Xyz, and Standard). Zarc's body was destroyed and his soul itself was sundered, a part of it now within Yuya, Yuri, Yuto, and Yugo. Zarc's malignant personality still lives inside all four, and through the Dragons, constantly tries to consume them for the sake of his revival. Ray still lives and still opposes him, her own soul having fragmented and now residing within Lulu, Zuzu, Celina and Rin.
- Of course, that also means the Dragons themselves could qualify, especially since Zarc seemed able to hear the voices of Duel Spirits.
- YuYu Hakusho has the Black Book Club, a cabal of wealthy human businesspeople and crime bosses who learned of the Demon World and decided to use their wealth to pillage it and torture and kill its inhabitants. The second season's Big Bad, Sakyo, is a member, the third season's villain Sensui turned to evil upon witnessing their atrocities firsthand, and it's through thwarting Sensui's scheme that the heroes catch the interest of the Three Demon Kings, kicking off the final season. The only members to directly oppose the heroes are Sakyo and first season Arc Villain Tarukane; the other members are unceremoniously slaughtered by either Sensui as payback or Sakyo due to not needing them anymore.
