Season 1: Alexander Pierce, as the leader of HYDRA controlling S.H.I.E.L.D., with Big Bad John Garret's Project Centipede being a branch of HYDRA.
Season 2: Baron Wolfgang von Strucker, as the largest leader in HYDRA, being referenced by Big Bad Daniel Whitehall, but not making any appearances. During the second half, Dr. List, The Dragon to von Strucker, is promoted to this as Daniel Whitehall and the other HYDRA leaders are dead, despite him only appearing in three episodes and having nothing to do with Big Bad Jiaying and the other Inhumans.
Season 3: "It", the Inhuman banished to the mysterious planet that Simmons was sent to that is worshipped by HYDRA. However, it escapes in Ward's body in the mid-season finale and become the Big Bad for the rest of the season.
Season 5: Thanos. Despite not appearing in the series, his impending arrival to Earth is what prompts the Confederacy to strike a deal with General Hale to protect the Earth in exchange for gravitonium and Inhuman soldiers, even though they have no intention on fulfilling their end of the bargain. It's revealed that General Talbot's attempts to make himself strong enough to face Thanos is what ends up destroying the Earth in the Bad Future seen at the beginning of the season.
Alias begins with Sydney Bristow discovering that instead of being part of the CIA, her SD-6 operation is one of the Alliance of Twelve, an international terrorist group. The opening of the second episode has Sydney meeting with handler Vaughn for the first time, detailing some of her operations with SD-6. She insists she wants to get it out as in six months, it can be taken down and she can get on with her life. "Six months?" Vaughn asks and then realizes Sydney is serious. He has her jot down a chart of what she knows of SD-6 and she puts down a diagram fitting onto a regular notepad with the main office and a half-dozen different branches. Giving her a look of pity, Vaughn takes down and unfolds a massive sheet of paper, showing a stunned Sydney that SD-6 is at least ten times larger and complex than she thought it was. And it's only one of the 12 cells of the Allliance, making Sydney realize this is going to take a long time.
Vaughn: We started this map five years ago. And all it's done in this time is grow. If all we wanted to do was shut down the Los Angeles cell, we'd have done that three years ago. This is not cutting off an arm of the monster, it's killing the monster.
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 Greater Scope Villain. 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 Greater Scope Villain department; their machinations are now starting to affect Buffy and the Scoobies too.
Ra's Al-Ghul is this for the first two seasons, with Season 2 revealing that he was the one who trained Season 1 Big Bad Malcolm Merlyn, and his presence being felt throughout the second season via his League of Assassins minions, all without ever showing up. Come Season 3, however, he finally does appear, stepping down into the main Big Bad role.
In a similar way to the above Damien Darhk and his organisation H.I.V.E. despite not physically appearing in the first three seasons are responsible for a few episodic plots, the supposed death of Diggle's brother Andy, and Darhk's rivalry with Ra's being one of the main reasons for the League's attempted destruction of Star City in season 3. And, much like Ra's, Darhk finally steps down from this position and become the Big Bad of season 4.
Cayden James appears to be the Big Bad of season 6, except it eventually becomes clear that someone else is manipulating him. It's eventually revealed that a (supposedly) low-level drug dealer named Ricardo Diaz has been orchestrating these events in order to put himself into the position of Star City's crime lord. Diaz remains a threat even after his downfall, although we eventually learn that he's been forced to make a deal with an international criminal financier even Diaz is afraid to cross - Dante.
Eobard Thawne haunts the second, third, and fourth seasons of The Flash (2014) after his death in the first one. His destruction via Ret Gone created the breaches that Zoom and his cronies enter from Earth-2. When a younger version of himself creates the post-Flashpoint timeline at Barry's behest, he causes a ripple that creates the next Big Bad, Savitar. In Season Four, it's revealed that his particle accelerator explosion granted Super Intelligence to yet another Big Bad, Clifford DeVoe.
Supergirl (2015): Yuda Kal was an malevolent Kryptonian deity whose equivalent in our world would have been the biblical Lilith. Her cult was eventually replaced by Rao worship and basically forgotten except for an coven of dark witches that plotted to unleash their goddess' wrath upon the universe by creating the Worldkillers, magically-embued Kryptonian warriors that would serve as main antagonists for Season 3. Yuda Kal herself never appears, though in one episode they attempt to summon her and possess her follower' body, while the goddess high priestess Jindah Kol Rozz, who is directly responsible for creating the Worldkillers, appears behind bars and never fights Supergirl either due to being disposed by one of the villains before getting the chance.
In the Crisis CrossoverElseworlds, the Monitor is responsible for giving John Deegan the Book of Destiny, which causes all the trouble during the crossover. However, he claims that he's actually testing the heroes in order to make sure that they'll be capable of resisting a coming crisis which threatens the whole multiverse, brought about by a being even more powerful than himself (implied to be the Anti-Monitor).
Ash vs. Evil Dead: In the Season 1 finale, Ruby is revealed to be the writer of the Necronomicon, thus making her indirectly responsible for everything that's happened in the whole franchise.
Birds of Prey: The Joker is only seen in flashbacks and is said to currently be locked away somewhere far from New Gotham, but it is also established that he crippled Barbara Gordon and hired someone to kill Helena's mother, making him indirectly responsible for their respective careers as Oracle and Huntress. In addition, Dr. Harleen Quinzel has the intention to take the Joker's place as the head of crime in the city, partly because she feels the need to fill in the void left when her lover was brought to justice.
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, with his minions like Krazy-8, Tuco, the Cousins, Hector, and Juan Bolsa all being Arc Villain material in their own rights. 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
Chouseishin Gransazer has the Bosquito, an ancient and destructive evil that the Warp Monarch sought to eradicate by wiping all life off of Earth. Belzeus later unseals one as part of his plan to get the Warp Monarch to attack the Earth.
Majin Daruga, Kaiser Hades' older brother, for the first half of Justiriser. While his younger brother's Hades Army are a sect of his Daruga Imperial Army, he and his forces remain distant from the story until receiving word of Hades' death.
King Neo Descal is the man behind the Descal Pirate Fleets in Sazer-X, but he is absent from the plot for the first two thirds of the show, leaving Garade as the Big Bad for most of it.
Cobra Kai: While JohnKreese is dead by the time of the series, his toxic influence on Johnny in his youth ends up causing many of the problems in the show. In particular, Johnny's insistence on imparting the lessons Kreese taught him onto his own students ends up turning them into the same kind of bullies that he used to be. This is underscored by The Reveal that Kreese is not actually dead, and the implications that he will be taking a more active role in the second season.
Deus Salve O Rei: Dom Bartolomeu, a Grand Inquisitor whose witch hunts indirectly led to the events of the series. To wit: the witch Brice had to gave up her only baby daughter for adoption just so she could survive the hunts. Said girl was adopted by King Augusto, who also lost his child after his wife Queen Cecilia gave birth to her and knowing she couldn't bear her death (as she was unable to have anymore children), he passed off his adopted daughter as his biological one. Said daughter would grow up to become Princess Catarina, the series' Big Bad, all thanks to Bartolomeu's deeds.
The Cult of Skaro and the Void Ship in Season 2, as the Void Ship is what allows the Cybermen from Pete's World to cross-over into N-Space.
"Demons of the Punjab" has the British imperialists responsible for the Partition of India, who only appear as voices on a radio. However, as a result, they are ultimately responsible for all of the violence and death caused as a result.
FargoSeason 2: Hamish Broker, a senior head within the Kansas City Syndicate. It's Joe Bulo who draws up the plans to acquire the Gerhardt territory in the Upper Midwest, and Mike Milligan who provides the main muscle, so the two alternate positions as Big Bad. Broker is the one who okays the operation, and supplies them the manpower and resources to do it.
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.
The White Walkers (and their leader, the Night's King) to the War of the Five Kings and the villainous characters responsible for it (Tywin, Joffrey, Littlefinger, Balon, Cersei, etc.). Their threat overshadows any other in the setting, but most factions aren't even aware of them and are busy facing lesser but more immediate enemies. The Night King finally steps into the Big Bad spotlight at the end of the Season 7 finale, when he uses Viserion to destroy the Wall at Eastwatch and march his undead army into the Seven Kingdoms, beginning the Great War.
Daenerys is seen this way by much of Westeros, including Robert and, of all people, Joffrey, being exiled to Essos but preparing to return and claim the throne. She isn't a major concern to them anymore due to the civil war and her lack of power at the start of the series, but is steadily becoming a more dangerous threat. In Season 2, while preparing the Siege of King's Landing, Varys tells a sceptical Tyrion about the fact that she has dragons and how the present Civil War in Westeros is small potatoes compared to what will happen when she gets here. In Season 4, Tywin Lannister is willing to engage in an alliance with the Martells against the Targaryens and improvises a gambit to halt Daenerys' tracks in Meereen: reveal Jorah's former service as a spy on Varys' payroll. Of course, Varys ultimately decides to cast his lot with Daenerys anyway and he and Tyrion serve as her advisors.
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.
House of Anubis: Rufus Zeno in seasons 1 and 2. He was much more dangerous and insane than the other villains, but had little to do with the main plotlines. Instead, he was more of a subplot on both of occasions and caused a lot of problems that weren't directly connected to the main mystery but did influence things.
Justified: Theo Tonin, the head of the Detroit mob, is this in Season 3. His adoptive son, Robert Quarles, is the actual Big Bad of the season, providing all of the drama, and driving the plot without any instructions from Theo. That said, Theo is the one who made Quarles who he is, and is the reason he's in Kentucky in the first place. In Season 4, Theo takes over as the Big Bad, sending Nicky Augustine to Kentucky with specific orders to kill Drew Thompson.
Kamen Rider Double had Foundation X, a nebulous organization that helps fund the Museum in return for data on the Gaia Memories. It's later shown that they funded the Necro-Overs from The Movie until they decided the project wouldn't produce the results they wanted, and as Museum collapsed they shifted their focus to the "King's Medals" before a renegade member of the group becomes the Big Bad of Movie War Megamax. It seems that Foundation X was intended to be a Greater Scope Villain for the entire "Heisei Phase 2" era of Kamen Rider, but the plot thread was dropped post-Megamax since the plots of subsequent series wouldn't really accommodate such a conceptnote Though some fans choose to interpret a Freeze-Frame Bonus in Gaim as proof that the Yggdrasil Corporation has ties to Foundation X, and a special in Ex-Aid brings them back for real.
Kamen Rider OOO has The Original OOO, who had alchemists make the Core Medals, including the ones that'd give birth to the Greeeds, in an attempt to take over the world.
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. An even bigger case in point? Near the finale, all the villains are taken care of save for Helheim, whose avatar personally appears and reveals himself to two big bad wannabes (who both wind up getting pushed out of the conflict soon after). The final battle isn't with him, but rather with Kaito who had obtained the same level of power as the Overlords. The closest thing Kouta did to defeating the actual Greater Scope Villain is moving his operation away to a far off distant planet, and depending on how you view his reaction, the avatar of Helheim is cool with it.
Kamen Rider Build has one, revealed only in the post-series V-Cinema. It's Killbus, the Ax-Crazyolder brother of Big Bad Evolt and ruler of the Blood Tribe, who devoured the Blood Tribe homeworld and instigated the Blood Tribe's universal campaign of planet eating, which ultimately led to Evolt and his cohorts destroying all life on Mars and later coming to Earth.
Kamen Rider Zi-O: Over Quartzer reveals Oma Zi-O's rise was manipulated by a band of time travelers known as the Quartzer, who sought to use him to distract from their own plans. Interestingly, their leader is an alternate version of Sougo Tokiwa/Kamen Rider Zi-O, making this a case where the Greater-Scope Villain was behind himself.
In the first series of The League of Gentlemen the demonic butcher Hilary Briss was a secondary character who appeared only in the background and held some dark obviously secrets about his meat and its origins that he was selling to a select few customers and was conspicuously giving away to important figures to get them hooked, which were not elaborated upon, but were obviously part of something big, of an overarching plot. By series two his meat (and especially the effects it has on consumers) acquires a dubious position in the history of Royston Vasey and he is featured more, getting replaced in this position by the two misshapen and mysterious figures that supply him with it.
Legend of the Seeker: Darken Rahl acts as the Big Bad of the first season. After his defeat, it's revealed that all this time he has been serving the Keeper, who now takes a more active role in the world. Rahl becomes the Keeper's Dragon in Season 2, although he plots to escape the Underworld and manages to do so with Richard's help.
At the end of Mech-X4's third episode, we find out that Principal Grey reports to a higher up boss, who communicates with her via audio only.
Nikita: For the first season, Oversight was this to Division, officially giving Percy his orders even as he was recognized as series Big Bad; in the season finale, they step out of the shadows and take a more active role in the plot. Later, in the tail end of the second season, the series introduces The Group, a cabal with apparently even more control over global affairs, which remains in the background until the last third of season three.
Rumplestiltskin can be seen as this for much of the series, with his manipulation of many characters causing them to develop into main villains in their own right.
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.
Peter Pan, the Big Bad of Season 3A, can be seen as this for much of the series. Aside from being The Man Behind the Man to Greg and Tamara in the second half of Season 2, his actions were also a major contributing factor to making Rumplestiltskin what he is. Which makes him indirectly responsible for every villainous act taken by both Rumple and his various students (Cora, Regina, and Zelena) throughout the run of the show.
The Dark One for dark magic as a whole. No, not just Rumplestiltskin, but anyone who has inherited the name of The Dark One, as their actions eventually lead to the rise of not just the Big Bads, but also for The Heroes. Just take a look at Rumplestiltskin. Eventually it's revealed that the Dark One is more Greater Scope than one can think, as it is literally darkness that binds itself to a soul, known as the Darkness. Season 5 gives us more information on the origin of The Dark One. It turns out that the first Dark One is Nimue, who started using the powers granted to her by the Holy Grail for revenge, corrupting her powers and giving birth to the Dark One. Since every previous Dark One exists in the current one, Nimue is the Greater Scope Villain for every other Dark One and the reason they exist in the first place.
Hades claims to have been collecting and hoarding all the souls killed by every single Big Bad or Greater-Scope Villain in the past, not to mention that he terrifies Rumple and Cora, and uses both of them as pieces in his game. Oh, and should we mention that he, being a god, is the most powerful and oldest villain of them all, bar none? Small wonder why Nimue the other Dark Ones and Peter Pan were so desperate to escape the Underworld, where they would always be second to someone else.
The Black Fairy, Fiona, is the ultimate example of the series. She may be younger chronologically than Hades or Nimue, but she more than makes up for it in scale. She is the mother of Rumplestiltskin and severed his fate as the Savior upon his birth to gain greater power and avoid losing him, causing her banishment and leaving him with Malcolm, turning both Rumple (the Dark One) and Malcolm (Peter Pan) into eventual monsters. She is also the real mastermind behind Gideon becoming the man who would eventually kill Emma (though Emma turned out to be Not Quite Dead). Oh, and she created the Dark Curse. If she hadn't turned to dark magic, Emma would never have faced all the horrible villains she did without the Curse. Also an indirect Nice Job Fixing It, Villain! since destiny dictated that Emma had to survive all other villains to fight in the Final Battle against Fiona and Gideon at the end of the Storybook.
Season 7 indicates Victoria aka Lady Tremaine, cast this new curse on the people of Hyperion Heights. It turns out her daughter, Ivy, truly did and secretly acted like she was cursed as well as she worked against her mother. But it finally comes out that it was Mother Gothel who played both of them and has been working on her ultimate plot to unite a coven of witches and seek ultimate power.
Mighty Morphin' Power Rangers: Lord Zedd was this to Rita Repulsa, banishing her for her utter failure in conquering the Earth. He starts off well, destroying the Dino Zords and the Green Ranger, but he eventually suffers so many defeats at the hands of the Rangers that he devolves into a mere Big Bad himself.
Master Vile was also this to both Rita and Zedd. After his final invasion was thwarted by the Aquitian Rangers he decided to leave the Earth before he started permanently suffering the same bad luck as the other two villains.
Power Rangers Turbo: The finale reveals Dark Specter, the Greater Scope Villain behind Zedd, Rita, Master Vile, the Machine Empire, and Divatox. In Power Rangers in Space he gathers together all the Big Bads of the franchise to that point under him and sics newcomer Astronema on the Rangers. In the end, he's done in by The Starscream after having never faced the Rangers directly.
Power Rangers Lightspeed Rescue: Queen Bansheera was a fearsome demonic entity who began the series in a crippled, statue-like form, unable to strike out on her own. Once her body was restored in the finale of the season, she sought out to kill everyone in sight to meet her own ends - Even her own loyal followers.
Power Rangers Wild Force: The original Master Org. The one the Rangers had been fighting was Dr. Viktor Adler, a former friend to Cole's parents who consumed the remains of the original for revenge and became the new Master Org. After being killed by the Orgs when they discovered his deceit, Dr. Adler grows a real horn and comes back to life. In the final six episodes, he returns and kills off two of the traitors, and talks as though he and the original Master Org are now truly one.
In Wild Force's team-up with Time Force, the Mut-Orgs. They granted Ransik his powers that helped him become the most feared criminal of the year 3000. They were plotting to travel back in time to rewrite time in favor of the Orgs.
Power Rangers RPM: Alphabet Soup was a corrupt government facility that kidnapped child geniuses and forced them to work for them by lying about an allergy to sunlight and drove them either to being near emotionless (Dr. K) or completely child-like (Gem and Gemma). Dr. K created Venjix for them and used it in an attempt to break free, but they stopped her before she could program a firewall. Because of them, Venjix broke free and began his assault on humanity, but they tried to kill Dr. K so that no one will know where Venjix came from. By the events of the series, it's members were either arrested, captured by Venjix or killed.
Power Rangers Megaforce: Emperor Mavro is the father of Vrak and Vekar (the latter serving this role in the first 20 episodes) but doesn't appear in person until the last three episodes.
Power Rangers Dino Charge: Lord Archenon. A galactic conqueror, he had plans to control all the Energems, and as such hired Sledge and turned Heckyl evil. He set the series in motion, and eventually joined the fray around Episode 33.
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 a Greater-Scope Villain 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.
In Sherlock, Moriarty is this for "A Study In Pink", "The Blind Banker", and "A Scandal In Belgravia", assisting the main antagonists of those episodes in one or another from behind the scenes. Series-wide, however, we have Eurus Holmes, the third Holmes sibling, as she was the one responsible for Sherlock becoming emotionally stunted. She was also the one who was responsible for John's implied infidelity, as she disguised herself as an attractive woman in order to gain John's attention, and was the one who sent Sherlock and John after Culverton Smith. Finally, she met with Moriarty at some point before his death, and was behind the "Moriarty's return" hoax as seen in "His Last Vow".
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 Greater Scope Villain 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' Greater Scope Villain 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.
Carmine Lupertazzi. After he and his empire are referred to merely as "New York" in the first two seasons, he finally appears in-person during Season 3. Despite being a longtime ally of the Dimeo crime family, Carmine's organization is almost universally viewed by Tony and his associates with wariness and suspicion (not least because the former regularly uses its vastly greater size and resources to coerce the New Jersey mobsters into "sharing" their profits on local business ventures). After the relationship between the two families deteriorates in Season 4, the Lupertazzi crime family ultimately becomes the story's preeminent antagonist and remains so until the end of the series.
In seasons nine and ten, the Ori are the Greater Scope Villain, 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.
In Season 2, Stranger Things has the Mind Flayer, an Eldritch Abomination which controls everything within the Upside Down. Apparently, the Demogorgon from Season 1 was merely its attack dog, with no real will of its own; the Mind Flayer is the true threat which the Upside Down poses to our reality.
Lilith is the Big Bad of Seasons 3 and 4, but the main plot of S4 is her trying to free the one who turned her evil, Lucifer himself.Lucifer becomes the outright Big Bad in S5.
In the tenth season's finale, it's revealed that even Lucifer had a Greater Scope Villain in the form of The Darkness, which was the original source of evil in the Universe; not only is it the primordial force of nature that controlled everything before God and his angels, but also the one responsible for turning Lucifer evil.
Emperor Ackdos Gill from Kaizoku Sentai Gokaiger is the ultimate leader of the Zangyack empire. However, he only appears during the final arc of the series, with his son Warz Gill being the Big Bad for most of the series.
Zyuden Sentai Kyoryuger was revealed to have one in the final episode. When Deboth, the Big Bad of the show, was defeated, he revealed in his dying words that he was only a creation of a much more powerful being. Said being, Creator Devius, appears as the Big Bad in the Vs ToQger special.
Space Squad: Gavan Vs. Dekaranger has Prophet Fumein, the apparent leader of the revived Metal Heroes villains, with Madgallant serving as the present Big Bad. Fittingly, Madgallant also serves his father Satan Gorth, who resurrects during the course of the movie.
In season 1, Nina's German contact is heavily implied to be this to the Drazen family's Big Bad.
Season 2 has Max and Alexander Trepkos,. They are far more connected to Big BadPeter Kingsley than the season 1 example, and it seems Max is superior to Trepkos. Max ends up stepping down to Big Bad status via The Man Behind the Man in The Game, while Trepkos disappears and may have been implied to have been arrested in a throwaway line in a later season.
A possible example from season 3, again featuring Nina, is Nina's unnamed client, one of the potential purchasers of the Cordilla virus.
Then-Vice President Charles Logan, season 5's Big Bad, may have been this to season 4, as he at the very least took advantage of the opportunity created by the President's incapacitation.
Season 5 has the unnamed individuals (one of whom is revealed in season 6 to be Graem Bauer, Jack's estranged brother) consulted by PresidentCharles Logan towards the end of the season.
Season 6 retroactively establishes Jack's father and brother, Phillip and Graem Bauer as this to Day 5. Cheng Zhi's superiors in the Chinese government may also count.
Season 7 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.
Season 7 also has Alan Wilson and the other members of the prion variant cabal, possibly the Greatest Scope Villains featured on the entire show, who while taking on the ultimate Big Bad title in that season are retroactively this to season 5 and possibly 6, and possibly season 4, through their puppet Charles Logan.
Ultraman Nexus gives us Dark Zagi, alias Mitsuhiko Ishibori, also called Unknown Hand. He's the one who sent all the Space Beasts, including the one in the prequel Ultraman The Next.
iZombie: Vaughn Du Clark is the one responsible for the zombie outbreak, however, he is only encountered in the season one finale, and it is Blaine DeBeers who acts as the Big Bad of the season; Vaughn takes up the role in Season 2.
The Wire: While most of the story and characters are very local to Baltimore, in season 2 The Greek runs a major international criminal organization. It appears that he is responsible for much if not all of the drug shipments to the city.
V (1983) has the unseen, unnamed Leader of the alien Visitors who is ultimately responsible for the invasion of Earth, but not directly involved in it until the very final episode— and even then, only his voice is heard. The actual Big Bad of the series is instead his underling Diana, who personally causes almost all the conflict outside of the initial invasion itself due to her aggressive, genocidal attitude.
In season two, we're led to believe Katherine Pierce is going to be the main villain; however, we soon learn that every single one of her actions, including her very arrival in Mystic Falls, were dictated by her need to escape from a dangerous Original Vampire named Klaus.
In season three, Klaus and his siblings Elijah, Rebekah, and Kol are supposed to be the main villains, but once their mother Esther is revived, she takes over with her plan to exterminate all vampires, causing the main cast and the Originals to collaborate.
Season Five has Silas act as the Big Bad in the first half of the season, but soon the witch Qetsyah, who created the Other Side (Realm in which all souls of supernatural beings go after they die) and can thus return from it at a whim, returns. Qetsyah was the witch who created Silas' immortality spell, and can be considered a Greater Scope Villain for the entire series, as her immortality spell also created the doppëlgangers ("Copies" of the original immortals, Silas and Amara, meant to die in their place as the balance of nature required every living creature to die eventually); Esther's spell that created the Original Vampires was based on her immortality spell, Klaus' goal was to obtain Elena's doppëlganger blood (As it was a necessary ingredient for his spell to create Werewolf-Vampire hybrids), and Katherine herself was a doppëlganger.
The Travelers were originally the coven which Silas and Qetsyah belong to, thus acting as Greater Scope Villains to even those two. Katherina also used to be one of them.
Wynonna Earp reveals in Season 2 that the demon Balshaar (aka Sheriff Clootie) is responsible for most of the events on the show — he was the one who cursed the Earp family to face the revenants of all the people Wyatt killed, in revenge for Wyatt killing his children, something that his wife Constance (the Stone Witch) takes her own vengeance for by making Doc immortal and trapping him in a well, while spending Season 1 trying to resurrect those sons. It's also shown that before being put down, Balshaar was personally responsible for Season 1 Big Bad Bobo del Rey becoming a revenant himself, and it turns out that the Widows, the Big Bad Duumvirate of Season 2, are more of Balshaar's wives, and they're seeking to resurrect him.