The Dragon-in-Chief serves as the de factoBig Bad of the story. Though he's nominally subordinate to the "real" Big Bad, he's just so much smarter, stronger or more skillful (and almost always scarier) that it's clear who's really the bigger menace. He tends to have almost no respect for the Big Bad due to their comparative lack of vision, courage or common sense. The Big Bad, for his part, either seriously or fatally overestimates The Dragon's loyalty, or is just too afraid of him to be able to do much. In a nutshell, the Dragon-in-Chief is the main villainous driving force behind the plot, even if he or she did not initiate it, to the point that the Big Bad is pushed aside or even endangered by them, and rendered less important by comparison.
The defining feature of a Dragon-in-Chief is that the Big Bad's Evil Plan completely falls apart without them; essentially, the main story ends with the Dragon's defeat. The Hero turns out to be way too much for the Big Bad to handle, and The Dragon is really the only significant threat in his arsenal. Typically, he and The Hero come from the same place, the same (usually violent) world and not the kind of environment in which the Big Bad normally operates. The Dragon and The Hero may have heard of each other by reputation, brewing a rivalry between the two. Alternatively, The Hero might have been after The Dragon to begin with, such as for revenge for a past misdeed. In either case while the Big Bad might stake all his fortune and dreams in the outcome of the fight, The Dragon and The Hero see the Big Bad as nothing more than an annoyance who should stay out of the way. Often the Big Bad's only hope of survival is that these two destroy each other. Sometimes, the only way for a Big Bad to still be the main villain, is for The Dragon to have a Heel-Face Turn.
Because of their disrespect, there are few straight Dragons amongst Dragons-in-Chief: They are either a Dragon with an Agenda, a more dangerous Starscream, or just a more inevitable Dragon Ascendant (and don't be surprised if they are Dragon Their Feet). The Dragon With an Agenda type will probably be using the Big Bad for his own ends, working as a mercenary to fund his own projects that usually turn out to be much more threatening (or interesting) than the Big Bad's goal.
If one of the other kinds, then they will probably be complaining about how the Big Bad runs things — typically, they think the Big Bad either lacks ambition, or is just an idiot. These ones are often junior partners in the Big Bad's business: After years of hard (but fun) living as a dangerous felon, he has found himself steady employment with the Big Bad and hopes to take over the business some day or retire on the fortune made from his latest Master Plan. This is when he starts to complain about his unambitious or just plain incompetent way of running things, though the Big Bad might retort that his way is from experience and The Dragon's ways will ultimately lead to ruin. Occasionally, their warnings turn out to be right.
The most important thing is that the Big Bad is just not a significant factor if The Dragon is gone. This Big Bad must be much more manageable and less dangerous than their underling, or less likely to make a splash. The Dragon-in-Chief is either the main villain or the star of the show in his own right, and the actual Big Bad ends up relegated to supporting villain status. The Dragon can became the real Big Bad, while the theoretical Big Bad, would be moved to the position of the Evil Genius.
When a character fills this role because the Big Bad is merely absent from the main story (or simply not as important to the main character), then they are The Heavy, possibly to a Bigger Bad (if they're operating entirely on almost entirely on their own).
See also Hypercompetent Sidekick, Non-Action Big Bad, Supporting Protagonist and especially the Big Bad Wannabe, whom Dragons-in-Chief (usually) work for. Compare/Contrast Deceptive Disciple.
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Zabuza from Naruto is this to Gatou. Gatou may be a billionaire shipping magnate and crime lord, but he stands no chance of defeating Team Kakashi without this badass missing-nin.
Chigusa in Mahou Sensei Negima! has been implied to have been a simple pawn; even her actual dragon was defeated by an overpowered Vampire arriving on scene. The arc was effectively over with the defeat of Fate Averruncus.
A lesser example is shown later with Dynamis actually being the real boss of Cosmo Entelechia. However, Dynamis is still plenty powerful and very clever, so he realizes he needs to stall Ala Alba from getting to the more dangerous Fate. And succeeds.
Majin Buu is more or less this to Babidi; though in a subversion, since he starts out as an overgrown baby, Buu takes a while to realize how little power Babidi has, and quickly kills him when he does. Majin Vegeta might also counts, and he does realize that Babidi is inferior, and almost ignores him when he turns on him and instead focuses on stopping Buu.
Dr. Gero is inferior to (and killed by) his android creations, though his Dragon Cell never meets him, as Gero dies before he wakes up. Cell expresses admiration for Gero for being so smart as to create him, but it's reasonable to assume that, if Gero were alive, that would probably not have saved him.
In the Red Ribbon Army, there's Officer Black, who is much more competent and threatening (and has more morals) than Supreme Commander Red. When he finds how petty the wish Red planned with Dragon Balls, making himself taller, he kills him.
For most of his first appearance, Broly is under mind control from his much weaker father Paragus, who led the Z Fighters to the planet to fight his son. When Broly is freed, he quickly disposes of him.
In One Piece, Rob Lucci is the Dragon-in-Chief to Spandam, since despite being leader of the CP 9 Spandam is vastly inferior to Lucci (and the rest of his team), and it is Lucci that Luffy ultimately has to defeat to secure a proper victory.
Eric the Whirlwind serves this role for Commodore Nelson Royal, as well as being a Starscream. Nelson Royal is an extremely fat man who can't even walk anymore - though apparently he's at least reasonably competent at naval warfare, and hires Eric the Whirlwind to do his dirty work, since they share the same goal. By the end, Eric kills Nelson.
One could argue that Admiral Akainu is this. Though he's considered the main antagonist of the Marineford Arc, he was still under Fleet Admiral Sengoku's orders. Nevertheless, he causes the most damage to Whitebeard and his allies, from deceiving Squad, to provoking and killing Ace.
After the timeskip, Sengoku retires and Akainu is promoted to Fleet Admiral, but he's still a Dragon-In-Chief. Now it's to the Five Elder Stars, the ruling council of the World Government, who don't bother getting involved in the wars fought on their behalf and whose ability to put up any sort of fight is completely unknown. Given that Akainu is a madman and basically a walking volcano, it's likely that even if they can fight he's still more dangerous than all five of them combined.
During the beginning of the series, several people in-universe thought that Zoro was Luffy's Lancer-in-Chief, not knowing how powerful Luffy actually was...and seeing the former's serious and ruthless demeanor when compared to the latter's behavior as Idiot Hero whenever he's not angry.
The World Nobles are the Chiefs to the Marine's dragon, while the Marines as a whole are a Hero Antagonist, they're still at the beck and call to the Nobles, who are the epitome of cruel and evil (slaveholding and genocide being among their crimes) and set draconic laws for which the punishment is death, all while hiding behind immunity from justice for their deeds because their ancestors were the ones who civilized their world. Assaulting (or just angering) a world noble immediately makes you one of the greatest enemies of the law even if the reason for it was an unambiguously good deed as Luffy learned when he punched out a celestial dragon at a slave auction.
Younger Toguro from YuYu Hakusho is the man who drives the plot and everything behind the whole Dark Tournament saga, but he is in all reality just the unstoppable muscle of Sayko. Even Sayko admits it, as his ultimate goals are almost completely unrelated to the main character conflicts.
In Rurouni Kenshin, it seemed that Shinomori Aoshi was this; once Kenshin arrived on the scene, he began openly disrespecting Kanryuu, the real Big Bad. He proves to be Kenshin's biggest challenge and nearly kills him. However, Kanryuu manages to get ahold of a Gatling gun... And for once in shonen, guns aren'tworthless.
Amshel of Blood+ is the de facto leader of Diva'sChevaliers, and he's the one who engineered the events which allowed Diva to become a threat in the first place. He's smarter, more ambitious, and more level-headed than Diva is. But being a Chevalier, he doesn't have the kind of unique, raw ability that Diva possesses, so he puts up a facade of subservience while manipulating Diva and his fellow Chevaliers into getting him what he wants. Diva isn't bothered by any of this because she just doesn't care about such larger schemes. Nor does Nathan, the only Chevalier who's explicitly more powerful than Amshel.
By the time Mobile Suit Gundam has gotten started, Gihren Zabi has usurped control of Zeon from his father, Degwin. He's isolated his father from the people, cut him out of the running of the war, and turned him into little more than a figurehead. When Gihren decides he has become a liability, Degwin dies a horrible death by Wave Motion Gun.
Soukou No Strain has Ralph Werec, the protagonist's once-idolizedbrother and the best pilot either side of the war has ever had, and Vivian Medlock, the immediate superior he's got around his finger. Care to guess which one leads the final battle and which one gets screwed over?
Double subverted with Kawarino from Yes! Pretty Cure 5. While the Non-Action Big Bad Desparaia is much powerful than him and he is loyal to her, Kawarino is the greatest threat to the heroines and he's the most evil and the most competent villain in this season. The only reason why Desparaia accomplishes her goal is because of him, her strongest and most loyal employee. While Kawarino is the most difficult villain the girls have to face in this season, the only things Desparaia does during the Grand Finale is summoning Mooks, blocking the attacks with a barrier... and undergoing a High Heel-Face Turn! And that's not only that: Kawarino survives the team's Finishing Move.
Kawarino was also responsible for the invasion and destruction of Palmier Kingdom, the homeplace of the mascots. And he's pretty much responsible of enslaving its inhabitants.
Legato to Million Knives in Trigun, Legato proving to be more Badass and actually manages to drive Vash into killing him. This is especially true in the anime since it ended before it go around to the points where Knives got more active after Legato's death, in which Legato can be considered the anime's actual Big Bad with Knives as a distant Bigger Bad.
The Red Skull was this to Hitler towards the end of the Reich. Especially in certain versions of the Marvel Universe that refer to World War II as a war against Hydra instead of Nazi Germany.
HermannvonKlempt provides an interesting variation on this in Hellboy: Conqueror Worm. While he's still under the control of Rasputin, whom he believes to be the Angel of Death, and is following the latter's gameplan to the letter, he is still the de factoBig Bad of the story. This is due to Rasputin having been reduced to an impotent ghost; when Von Klempt is slain, he can't step in and fix things. The heroes actually believe Von Klempt to be the Big Bad, and never find out about Rasputin's involvement.
Terra was this to Slade in the Teen Titans "The Judas Contract" story. Slade barely had to lift a finger while Terra did most of the work bringing down the Titans. The moment she turned against him, he knew his plan was screwed.
From the same series, when the Fearsome Five were under Doctor Light's leadership, Psimon fitted the bill perfectly.
Sin City dragons tend to be more physically capable than the Big Bads. Manute, for instance, was Ava Lord's dragon. Ava was only dangerous if you were a man who didn't know she was untrustworthy. Manute, on the other hand, is so dangerous that he has been a recurring villain in the series... a rarity.
Thulandra Thuu in King Conan, as the adviser of King Numidides.
Prometheus is this to Lex Luthor in the JLA "World War III" arc. Prometheus is a vastly superior combatant to Luthor, his intellectual peer, and implied to have been the one who came up with the Evil Plan to begin with, but he lets Luthor think he's in charge because the scheme depends on LexCorp's resources and Luthor's connections in the supervillain community.
In New KryptonLex Luthor plays this role to General Sam Lane. Lane is in charge of the Human Defense Corps, but his plans only work because he has Luthor's technical know how and supervillain experience. Remove Luthor from the equation, and the entire plan falls apart.
Played with in The Immortal Game. General Esteem is a much more serious threat than his direct superior Prince Empyrean who, despite being a Physical God, is a Royal BratHarmless Villain. When Empyrean is finally confronted by the Mane Six, he goes down easily, as opposed to Esteem, who is fought multiple times and is ultimately only defeated for good when Twilight Sparkle taps into the full power of the Elements of Harmony and becomes a Physical God herself. On the other hand, Esteem's real master, Empyrean's father Titan, is far and away more dangerous than any other character in the story; even his avatars are magnitudes more powerful than Esteem.
Queen Of All Oni: Flashbacks to Tarakudo's rebellion show that Hiruzen was this to the Oni Elders. Hiruzen was so strong and skilled that Tarakudo only defeated him because Ikazuki defied orders and intervened in their duel to help him; the Elders, on the other hand, were so decrepit that Tarakudo easily killed them.
Queen Of Shadows: The Yojimbo is this to the Queen of the Shadowkhan. While there have been six Yojimbos and 98 Queens (counting the one Jade has replaced), this has always been the case — the Queens are inherently physically weak, being meant to rule and create new Shadowkhan, while the males are fighters (with their abilities varying between them, but always being vastly more skilled than the Queens).
Nigel from Rio. While his owner still drives the plot to some degree, Nigel is the more direct threat and far more menacing and evil than the poacher he's working for.
Planet 51 General Grawl is this to Professor Kripple.
In South Park: Bigger, Longer & Uncut, Saddam Hussein was more or less this to Satan. They are in a homosexual relationship, and Satan calls him his partner in evil, with Saddam emotionally abusing him and comes out as the main antagonist of the film. When the boys hear Saddam Hussein and Satan are coming to Earth, the boys seem more scared of Saddam. When Saddam and Satan finally arrive on Earth, Saddam tells Satan that he's better seen and not heard.
The title character of The Man with the Golden Gun, Francisco Scaramanga. He's the world's premier assassin but in the film he has started to work with Corrupt Corporate Executive Hai Fat in their plot to sell stolen solar tech. He's obsessed with 007 and thrilled when their paths cross (since he hopes to duel him to the death), but gets tired of Hai Fat, who freely admits to being out of his league with the secret agent. Ultimately he kills Fat and steals the tech (and his company), only to be unceremoniously shot by Bond by the end of the film.
Rosa Klebb is working for Blofeld in From Russia with Love. Some consider Red Grant, who is also a henchman, to be the main villain of the film as well. The same could be said for Kronsteen. In the book Klebb and Kronsteen are both main villains, and are both working for General G, who is replaced with Blofeld in the film.
Le Chiffre to Mr. White and the higher authorities in Casino Royale.
Frank from Once Upon a Time in the West may be the Ur Example. He's a cold blooded killer who is now working as muscle for a crooked (he's handicapped) railroad mogul who has a dream of expanding out West (so he can see it) - the violent Frank makes it clear to his face he wants to take over the business and doesn't care about his bosses' dreams. Their plans hit a snag when they have to get rid of a widow with land and a house in the way of the track. She is defended by a mysterious harmonica playing cowboy who, it turns out, is really after Frank. Cue epic western masterpiece. Subverted somewhat though, in that the Big Bad is able to convince all of Frank's men to betray him in exchange for money, and would have succeeded in having him assassinated were it not for the hero's interference.
In Scarface (1983), Tony Montana briefly acts as this to small time drug lord Frank. Tony wants to change supplier and expand the business; Frank thinks small is safe and warns Tony that ambitious guys in their trade tend to meet bad ends. When Tony sets up his own operation Frank sends guys to kill him - it doesn't work out, and Tony lets him know how he feels about things like that.
The Joker in The Dark Knight offers to work as The Dragon for the mob to take out Batman, but he really wants to use their money to bring chaos to the streets and become Batman's archenemy. He doesn't think highly of the mob and believes the city deserves a better class of criminal... so he takes over. In a decidedly hostile way.
In the Martin Lawrence film Black Knight, Percival (played by Vincent Regan) is this. He's the only one who distrusts The Hero early on (King Leo trusts him completely), and he's the final enemy who's defeated at the end of the movie. During the rebellion, he kills King Leo out of annoyance for his cowardice.
Bill "The Butcher" Cutting from Gangs of New York works as The Dragon for Tammany Hall's Boss Tweed, but that doesn't mean their views don't clash. The Butcher doesn't much like that Tweed keeps wanting to bring in these "foreign hordes" of Irish workers, while Tweed thinks Cutting's semi-racist views are outdated. But while Tweed might be the Mayor, it is Cutting who runs the gangs and therefore Cutting who has the monopoly on violence. As Hero Amsterdam is on a mission of vengeance against the Butcher and since Tweed is merely corrupt, and not murderous, Cutting serves as the main villain of the story. The cagey Tweed manages to outlive him and survives the film.
Tweed wasn't even mayor - as the Boss of Tammany Hall, the main Democratic Party institution of New York City, he was himself a bit of a Dragon in Chief to the Mayor and actual elected officials in the city. At the time of the film's setting, he not only wielded the most political influence in the city, but also was one of the largest landowners, and was a director for railroad, banking, printing, and hotel companies. Effectively, he controlled the city completely during the height of his power, despite not holding any elected government position.
Hitman Benedict in Last Action Hero is this to mob boss Tony Vivaldi. He hates his boss for his stupidity and especially for his idiotic quips, which often make no sense. Benedict kills him halfway through after Vivaldi's plan fails (which he blames entirely on Vivaldi) and uses the magic ticket to start an inter-dimensional crime spree.
Though Parker Selfridge is the nominal leader of the human forces in Avatar, the main antagonist of the film is Colonel Quaritch, who runs his mercenary army exactly how he wants to and ultimately becomes the real power in the operation — and it's clear they both know it. About the only things that keep Selfridge in place are the fact that he's paying, and that Quaritch can't be bothered with the administrative details. At the end of the movie, Quaritch is killed in an epic battle, while Selfridge is subsequently shipped off-planet with a minimum of fuss.
A deleted scene made this explicit. In it, Selfridge threatens to terminate Quaritch with a phone call to Earth. Quaritch, who is much larger than Selfridge, grabs his nominal superior and points out that Earth is a very long way away. The scene was probably cut from theatrical because this dynamic was already extremely obvious.
Word ofGeorge Lucas is that Darth Vader was intended to be this early on (possibly sharing the spot with other Imperial officers). Traces of this remain as late in the game as the A New Hope novelization, which describes The Emperor as a weak-willed man controlled by ambitious underlings. The actual movies as released, however, make it plain that while Vader is incredibly powerful and evil, the Emperor is worse on every imaginable scale.
The original movie, in which the Emperor does not appear, displays the trope in a more straightforward manner. Moff Tarkin is Vader's nominal superior, and Vader has at least a little respect for his authority (the Expanded Universe later establishes they really are old friends, like Tarkin indicates), Tarkin is far less of a threat.
In the prequel trilogy, it was strongly implied that Darth Vader was initially well on his way to becoming this when he first joined the dark side: his powers were growing so rapidly that even The Emperor himself theorized that Vader would soon eclipse his own abilities and potentially overthrow him. However, after Vader suffered his near-fatal injuries on Mustafar (including having all of his natural limbs amputated), his powers with the Force were greatly reduced and he was never able to exceed the Emperor's skills again.
In Iron Man 2 Ivan Vanko is recruited by Justin Hammer as the only one who knows how to mimic Tony Stark's Iron Man tech. But he constantly berates Hammer for the quality of his Iron Man knockoffs and at the end of the film he takes control of Hammer's battle drones and becomes the final villain.
Simon Phoenix is this in Demolition Man, until he's finally had enough of Dr. Cocteau. While Cocteau is Genre Savvy enough to program Phoenix to be unable to kill him, he neglects to do this for the other criminals Phoenix has released. Oops.
Davy Jones became this in part 3 of the Pirates of the Caribbean trilogy to Lord Beckett. He had formerly been the Big Bad in part 2, but was forced into servitude due to Beckett's leverage (Jones' Cursed Heart). In the final battle, Jones seizes his opportunity to regain control of his ship, where he promptly kills Mercer, Beckett's regular Dragon.
A bizarre chain-Dragon-in-Chief scenario appears in the awful Dungeons & Dragons and its vastly-superior-but-still-awful sequel, Wrath of the Dragon God. In the first film, Profion is utterly useless by himself, and relies on Damodar to do everything for him. At the beginning of the sequel, Profion is dead and Damodar has ascended to the mantle of Big Bad — whereupon he, too becomes completely impotent, and has to rely on the lich Klaxx the Malign to do everything for him. This is hilariously lampshaded near the end, when Damodar tells Klaxx to kill the onrushing hero. Klaxx Deadpan Snarkers back, "Kill him yourself, O great and powerful Damodar," and flies away. Damodar, being wimpy but Genre Savvy, flees for dear life.
In Commando, Bennett is considered to be a much bigger threat than Arius and his army.
In Oz: The Great and Powerful, Evannora- the future Witch of the East- is the villain responsible for the threat the characters face, but her actions turn her sister Theodora into the more ruthless and insane Wicked Witch of the West.
Leatherface is considered the main antagonist, even though he is clearly the subordinate of his family. This is kind of a subversion as the only movie in the series where Leatherface has his own agenda is Texas Chainsaw 3D and in that one is to avenge his family.
Sheriff Hoyt from the remakes, even more so than Leatherface. While Luda Mae is the head of the Hewitt family, he's the one who got them into cannibalism in the first place, and a Word of God interview says Thomas Hewitt (Leatherface in this contnuity) basically followed Hoyt like a puppy, giving Hoyt complete control of Leatherface.
Stephen in Django Unchained is a rare loyal example. He is far brighter than his nominal master Calvin Candie, and all but runs his slave-staffed plantation for him. He also proves to be a much bigger threat than Candie, discovering the protagonists' plan and dismantling it effectively, while Candie remains in the dark about their intentions until Stephen tells him. He also outlives his master, and while Lara Candie then becomes his new superior, he's still effectively in charge and Django's main target.
While Cobra Commander is the Big Bad, Zartan is the most prominent antagonist in G.I. Joe: Retaliation and does more to set Cobra's evil plan in motion, with Cobra Commander being largely a plot-irrelevant antagonist whose only real purpose of the film is to get broken out of prison at the start and then pull a Villain Exit Stage Left at the end to set up a Sequel Hook.
In the second film in The Karate Kid series, there's Chozan to his uncle Sato. While Sato is a rich industrialist and the one calling the shots, he is rivals with Miyagi, wereas Chozan bullies Daniel throughout the movie. When Miyagi and Daniel save Sato's life, Chozan refuses to help them. Sato, who has a Heel-Face Turn disowns Chozan and as a result, he becomes a Death Seeker and the Final Boss of the film.
The Patriot. Colonel William Tavington takes his orders from General Cornwallis and his direct subordinate, but he's by far the biggest threat in the film to Martin and the militia as the British troops' field commander, a more vile villain, and much better at hunting them down.
Elysium: Kruger, who, albeit subordinate to Delacourt, is the main villain in the story. And by the end he becomes The Starscream as he kills Delcourt and takes over her conspiracy for himself.
Lieutenant Colonel Korn, from Catch-22, to Colonel Cathcart. He easily manipulates Cathcart throughout the novel, and most of the schemes are his idea. He remains Cathcart's subordinate due to lower rank and because he doesn't want to take the fall if something goes wrong.
Arguably Martel from The Elenium. Though the Big Bad, Azash, is far more powerful, he's too much of an Eldritch Abomination to understand humans well enough to effectively plot against them, and his high priest is, to put it bluntly, an idiot. As a result, Martel's scheming drives the vast majority of the plot, while at the same time he is the hero's rival, Worthy Opponent, and Shadow Archetype. He definitely fits this role in relation to PrimateAnnias, as it's made quite clear that Annias's drive for power would go nowhere without Martel's resources, skills and brains to back it up.
In The Malloreon by the same author, Nahaz is Dragon-in-Chief to both Urvon, who is completely insane, and his Bastard Understudy, Harakan, an Evil Sorceror who needs Nahaz's Demons to both do his fighting, and help him maintain his Mengha persona in front of the Demon-worshipping Karandese. Without Nahaz, both their plans would quickly fall apart, and it's worth noting that he both outlives Harakan (who originally summoned him) and dies in the exact same moment as Urvon, who he drags into hell with him. No one who has read this will be surprised to learn that Nahaz has his own agenda, which would more or less have resulted in the end of the world if successful.
Ghend is this in The Redemption of Althalus, as his boss, Daeva, is never encountered, due to rules against the gods interfering personally in human affairs. As a result, it's Ghend who drives the plot, and the story ends with his defeat.
The ogre Grand Lord Golgren from the Dragonlance Minotaur Wars and Ogre Titans trilogies is this to the Ogre Grand Khan, being much smarter and more charismatic than his boss and being capable of overthrowing him at any time, only keeping him around because he likes the perks his current job has. And then he decides he wants his boss's job too. The Grand Khan is dead in hours.
In The Dresden Files, Lara Raith appears to be this to the world at large after breaking her father's will. In fact, she's the one who runs the show.
In Animorphs, even before his promotion to Visser One, Esplin 9466 AKA Visser Three serves as by far the most horrifying and powerful of the Yeerks. For a significant portion of the series however, he is outranked by the original Visser One. The series is roughly half over before he is assigned full control over the invasion of Earth and he does not become Visser One until the final installments. Even then, he is under the orders of the Council of Thirteen, the high command of the Yeerk Empire.
In Dune, Baron Harkonnen is far more dangerous than The Emperor, though the Emperor is quite formidable himself and would be able to pose a major threat to our heroes without Harkonnen cooperation. Still, it's the Baron who fills the antagonist role, while answering to the Emperor, at least for appearances' sake.
It's a little more complicated. Both houses officially answer to the emperor making him the Combat Referee. The Emperor changes into a bad guy upon becoming convinced that the Artreides were becoming too powerful.
In Warrior Cats, Big Bad Tigerstar's son Hawkfrost serves as the main villain for the New Prophecy arc. However, unlike usual, Tigerstar is every bit as powerful and cunning as Hawkfrost, but is severely hampered by the fact that he's dead and communicating through the afterlife.
In Septimus Heap, Simon Heap serves this purpose in Flyte on behalf of Dom Daniel, who is still only a pile of bones.
In Romance of the Three Kingdoms, Dong Zhuo's ascent from western provincial warlord to Imperial Chancellor and almost-Emperor was contingent on swaying the warrior Lu Bu to his side by offering Red Hare and some gold, as he'd been the mightiest warrior and bodyguard for the one court official who stood up to him. Unfortunately for Dong Zhuo, a man who could be swayed by worldly things could be swayed by worldly things again — such as the hand of Diaochan, a dancer and adoptive daughter of the Minister of the Masses — and eventually Dong Zhuo's advisor Li Ru outright tells him: "Sir, you aspire to be ruler of the empire. Why then for a small fault do you blame the General? If he turns against you, it is all over."
This could apply to quite a few people, actually. Most of the big movers and shakers of the story were not kings or emperors. Cao Cao, as another Imperial Chancellor, is probably the most powerful person in the story. Even Zhuge Liang, Chancellor of Shu, was the one really calling the shots for most of the kingdom's existence.
King Joffrey is not really the power on the Iron Throne in A Song of Ice and Fire: his mother and later his grandfather are. When Joffrey does manage to slip his leash and do what he wants to do (when it doesn't conform to what his family wants) the results are usually horrific.
Varys and Littlefinger are not really Dragons to Joffrey, but do wield significantly more power in court than might be otherwise suspected, and both shore up the way King's Landing works in such a way that it begins to crumble when Littlefinger leaves his role as Master of Coin.
Really, the consistent thread in the work seems to be that the Hand of the King's true job is to do all of the work in managing the affairs of the kingdom while the king tackles whatever addles his own mind. Tywin ruled where Aerys was insane, Jon Arryn and Eddard Stark mitigated Robert's drunken stupor, and Tywin and Tyrion tried their best to limit the lackadaisical sociopathy of Joffrey. As Jaime says, "the King shits, and the Hand wipes".
Mace Tyrell is Lord Paramount of the Reach and Head of House Tyrell. However in both of these fields he's clearly behind someone else. In the military side, his bannerman Randyll Tarly is the one that really wins his battles for him and most of the Tyrell dynastic politics is dealt with by his scheming mother Olenna.
Game of Thrones has Lord Tywin Lannister as the Dragon-in-chief to his grandson, the incompetent, teenaged King Joffrey Baratheon, pictured above. Perhaps best exemplified by the scene in which Joffrey insults Tywin. In response to this challenge, Tywin just sends Joffrey a Death Glare, which Joffrey quickly buckles under after a just few seconds of attempting to keep eye contact. Tywin then casually declares that "the king must be tired", and has Joffrey sedated and dragged off to bed despite Joffrey very insistently protesting that he isn't tired.
Tyrion: You just sent the most powerful man in Westeros to bed without his supper. Tywin: You're a fool if you believe he is the most powerful man in Westeros. Tyrion:A treasonous statement. Joffrey is king. Tywin: You really think a crown gives you power?
Olenna's role as Dragon-in-Chief of House Tyrell is played up in the TV adaptation to the extent where most other Tyrells are barely characters once she appears.
The Prisoner gives us a revolving-door version of this. Within the Village, Number Two's authority is absolute and he functions as the episode's Big Bad, but he still answers to a Number One who we never see. The twist is that each Number Two gets replaced each episode (and the twist on THAT twist is that each new Number Two acts almost as if he's had this job all along).
In the Law & Order: Criminal Intent episode "Cuba Libre", Joel Grey plays a Badass Senior who is definitely a Magnificent Bastard and openly defies Det. Goren in his role as the Big Bad... until Goren does some psych profiling and discovers that the evil gang leader Joel's character has been relying on to carry out his hits is really The Chessmaster, and has been using him in an elaborate scheme to get out of jail. Goren cracks the case by getting the two to turn on each other, after telling him how the gang leader imagined the feisty old man as a puppet, sitting on his knee.
From seasons 1-3 of The Wire, Stringer Bell. Stringer is technically second-in-command to Avon Barksdale (in their drug-trafficking operation) but is the brains and muscle of the organization. During Avon's incarceration, Stringer takes full control of all operations, and orders the secret murder of Avon's nephew D'Angelo, and makes a treaty with Avon's hated enemy "Proposition Joe" Stewart. However, towards the end of the third season it's shown that he's not as thoroughly in-control as he might think.
For Power Rangers in Space, Astronema takes on this role in the grand scheme of things. She is the strongest foe in Dark Spector's inventory but secretly plots against him behind his back, and she would have been the one to kill him if Darkonda didn't beat her to it. And ultimately the heroes never face Dark Spector directly, and Astronema remains their primary enemy to defeat by the end. (Another reading of the show is that Astronema is the Big Bad; Dark Spector is the Bigger Bad.)
In Power Rangers Samurai, Serrator becomes this for a good chunk of the second half. The regular Big Bad, Master Xandred, is more of The Brute and is perfectly willing to let others come up with battle strategies - which lets Serrator direct the enemy forces to further his own schemes. Of course, when Serrator makes a misstep, Xandred gets ticked enough to remind people why he's the Big Bad, nearly turning Serrator and the Rangers into smears on the wall.
Chuck: Shaw ends up as this, after coming back from the dead and downloading an intersect into his head. His superiors are all senior bureaucratic types, like General Beckman, and they don't interact with Chuck or his team in any way other than getting captured at the end of the season 3 arc.
In Fringe season 1, Nina Sharp is set up as this to William Bell. Turns out, while both are morally gray, they are both without a doubt good.
Mr. Gold in the first season of Once Upon a Time. Technically, Mayor Mills rules over Storybrooke with an iron fist, but he's the Bad Samaritan with a Chain of Deals that has everyone in his back pocket, mayor included. Plus, he's the Storybrooke identity of Rumplestiltskin, who is the Bigger Bad in the Big Bad Ensemble. He's also the one who created the curse for Regina, but did it for his own reasons.He even invokes this idea in Storybrooke to get Emma elected as Sheriff over Regina's personal pick, by getting her in a position to finger Gold himself in a crime but admit there is no hard evidence to prove it. He tells her later, to win she needed to do more than stand up to Regina, she needed to show she would take even him on to convince enough people and thanks her for being the woman he expected her to be.
Season Three's Big BadEsther was menacing on her own she molds Alaric into this, combining his evil alter ego with mega-powerful vampirism. Alaric, when his good side is in control, kills Esther for threatening Jeremy and Matt, but Evil Alaric still tries to carry out her plan.
Lizzie McGuire has this zig-zagged with Claire Miller to Kate Sanders. While Kate is usually the main antagonist of the series, Claire was even worse. This is best demonstrated when Kate breaks her arm and Claire takes over the cheerleading squad, and starts treating everyone as if they are below her and showing Kate no sympathy for her, that was until Kate's arm healed and she took back her place as head of the cheerleading squad. Whenever Kate has Defrosting the Ice Queen moments, Claire would also pressure into not befriending Lizzie again, it should be noted that Kate's Heel-Face Turn in the movie was likely because of the lack of Claire's influence.
At the end of the second V miniseries, Diana claims that she really was the driving force behind the Visitor invasion of Earth and that Admiral John was a useless figurehead who only held the crown. A disgusted John notes that she can have it, as it will only make her the queen of a poisoned realm after she annihilates all life on Earth with a nuclear bomb. She later ascends to Big Bad level in the weekly series.
Stargate SG-1: Lord Yu's First Prime, Oshu, ended up basically running Yu's domain for him after his master, the most ancient of the current crop of Goa'uld System Lords, began to go senile. Oshu stayed loyal to his master right up to the part where they were both killed by the Replicators.
JAG: In "Scimitar", Colonel Ahmad Al-Barzan who obviosly works for Saddam Hussein, but for plot purposes he is the highest ranking official the heroes have to deal with.
Defiance: Stahma Tarr, wife to the Castithan Don Datak, was implied throughout the first season of the series to be the real brains behind their operation. Datak, while not stupid by any means, was short-tempered and prone to reacting with violence to any perceived disrespect. Stahma, meanwhile, was quiet and calculating, able to subtly manipulate her husband to what was best for the family. By Season Two, with Datak imprisoned, she's dropped all pretense and is running things herself, making it clear to her weak-willed son Alak that she's only allowing him to appear to be in charge because the male-dominated Castithan society won't let her be.
Ocelot from Metal Gear Solid could be the trope example in the page description. Not only does he trick his supposed allies into believing they are in charge not one, not two, but three times, he also does it in only two games! (Liquid, Gurlukovich, Solidus) In the third game he's a Dragon with an Agendabut really just got the Big Bad's trust to steal from him. In the fourth game, he's takes the role of the actual Big Badbut to not much suprise at this point, he isn't. He's not the trope creator of Chronic Backstabbing Disorder for nothing.
In the first game he may have genuinely wanted Liquid to succeed. He certainly did nothing to stop him, and his only "treachery" was not being there at the end (fat lot of good he would have done with only one hand), and selling the Metal Gear design to various countries after the events of the game are over, something that might actually have furthered Liquid's goal anyway. At one point he tells Snake that he greatly admires Liquid and that he is the one man who can make his dreams come true, and while he lies and says the dream is the revival of Mother Russia, he does briefly admit that his real motivations was to reignite conflict because it was the only thing that allowed humanity's emotions to be revealed, something he feels the current age was suppressing, which are actually very similar to Liquid's goals, or more specifically Big Boss's goals.
Liquid himself fits this trope too, if only in spirit, in regards to Big Boss (even though he technically isn't Big Boss's dragon due to Big Boss being dead/in a coma during the events of the game). Although he intends to bring about Big Boss's dream, he hates Big Boss for his role in his creation, and also implies that he's really only bringing about Big Boss's goal in order to further tarnish his already soured reputation ("Now I'll finish the work that father began. I will surpass him... I will destroy him!").
Seemingly invoked with Final Fantasy IV, where despite Baron and the King being the enemy for the first third of the game, it's Golbez, the captain of the Red Wings, that everyone is worried about. However, it later turns out not even Golbez is the real bad guy, but Zemus. Golbez was actually brainwashed.
Golbez subverts the trope with regards to Baron, as it turns out, he had the King killed and replaced with one of his subordinates by the time the player returns to it, Golbez was in charge the whole time, hence he's assumed to be the presumed Big Bad for most of the game.
In Final Fantasy X, though it turns out all of Yevon is evil and corrupt, before and after this it's Seymour who serves as the game's main villain besides Sin. Sin itself is also this in a way, being the beast the game centers around before The Reveal that Sin (or rather, the current incarnation of Sin) is just Jecht as the Final Aeon under the control of Yu Yevon.
Even before he unveils his true agenda, Seymour is Mika's.
Final Fantasy XII, Emperor Gramis is the leader of the Arcadians, but everyone is worried about Vayne, Gramis' son and a ruthless, power-hungry politician that has everyone worried about another war. He eventually kills Gramis and assumes the throne.
Pious Augustus in Eternal Darkness:Sanity's Requiem if he's working for Chattur'gha.
A variation occours in Mass Effect 1, as it is revealed later on that Saren is not actually the Big Bad in control of an invincible ship, but the ship Sovereign is the true villain and Saren only its Dragon. To outsiders it would seems that Sovereign is a Dragon in Chief, but they both knew that Sovereign was the master and Saren just his most valuable minion.
By the time of the sequel, two years of 'verse time later, nobody believes that Sovereign was in charge. Everybody's back to blaming Saren for everything, not seeing the threat that's staring at them.
You as Aldo Trapani in The Godfather: The Game sit on the line between The Dragon-normal and this. While you're undeniably loyal to Michael and he's the one with the plan, he's no active gunfighter like Sonny. Since It's Up to You, his plans would surely fall apart without you to help pull triggers as needed.
For that matter, if you accept it as canon, much of the actual movie couldn't have happened without you being in the right place to help out the characters.
The final villain of the second Ace Attorney game does not dirty his own hands, but rather, hires an assassin to carry out his murder plot. The assassin himself is a very gentlemanly and honorable person, which helps tie up the case for Phoenix.
In Fallout: New VegasCaesar is commonly stated to be a brilliant leader, but he is more than content to let the Legate lead the attack on Hoover Dam because Lanius happens to have a much stronger physical presence and be better at leading an army on the frontlines.
You can also be this, should you side with Mister House. If you end the game with Evil Karma, the ending slide even states that House "afforded [the Courier] with every luxury at his disposal in the Lucky 38, partly out of gratitude, and partly out of fear."
Sindri from Dawn of War. While Lord Bale appears to know about and share his goal, it is clear that Sindri is the one in charge. He is very disrespectful of Bale, at one point even being openly annoyed at him interrupting a ceremony. Even when Bale threatens him, he just respond sarcastically. But despite all this, Bale appears to think he is the one in charge. In the end he is betrayed and left to die, while Sindri reaches his goal alone, which was clearly the plan all along.
This dichotomy is played up again in Dawn Of War II: Retribution. Eliphas the Inheritor is the leader of the Chaos Warband, and sorcerer adviser Neroth (who even has the same voice actor as Sindri). In this case however, Eliphas is shown to actually be mostly competent, just occasionally more interested in self-preservation and personal power than the overall battle plan. Neroth hangs around to ensure he sticks to said plan. And when Eliphas gets too lippy, Abbadon The Despoiler psychically intrudes on their conversations to remind both of them who's really in charge.
Eliphas served as this role in the previous Dawn of War II expansion Chaos Rising as well. His master, Araghast the Pillager, is certainly a badass and competent villain, but Eliphas successfully betrays him and proves to be more dangerous than he ever was.
Assuming you play as the Dark Eldar in Soulstorm Tahirl will play this role to the leader the Dark Heart Kabal, Asdrubael Vect, since Tahirl is the character the player controls and upgrades, and Vect won't even take part in a battle outside of the Dais of Destruction.
In Mega Man Zero 3 Omega serves as this to Dr Weil. While Weil is FAR from helpless without him it is Omega who serves as the final boss and his defeat completely DESTROYS Weil's plot for game 3.
Cesare Borgia from Assassin's Creed: Brotherhood. His father, Rodrigo, is the game's Big Bad, but Cesare is the most visible antagonist and the one that poses the biggest threat to the Assassins. He also believes Rodrigo lacks vision for being content with consolidating his power in Rome following his failures in the previous game, rather than proactively trying to conquer the rest of Italy. Like many of the examples on this page, he eventually kills his father and takes over as the proper Big Bad. Granted, this is about the time where all of his plans go to helland back.
More like the other way around: Charles Lee is the figurehead and most prominent public figure the templars had, and he was the spearhead of his plans, displaying authority both with the general public and within the order itself, however, it was Haytham Kenway who came up with the ploy, appoointed Lee on the position of power, but takes a backseat to the plan itself, merely aiding the templars on his own, much like the assassins player characters usually do.
Dimentio from Super Paper Mario. Though he at first appears to be a servant of Count Bleck, the Big Bad of the game, he eventually proves to be a far worse threat, so much that the heroes are aided by Bleck himself in their efforts to defeat him.
Fire Emblem Jugdral: Prince Julius. He's being manipulated by Manfroy and was specifically "bred" by him for his plot to resurrect the dark god. The point being for Julius to eventually take his rightful place as the dark god for himself... which he does, seizing all effectual control of his kingdom and acting as the game's Final Boss.
Gilgamesh is arguably this in Fate/stay night. He is vastly more powerful than Kotomine, the actual Big Bad of the Fate route, and he is by far the greater threat to the heroes. When he dies in Heaven's Feel, Kotomine lacks the capacity to carry through with his plans on his own. In Unlimited Blade Works, he becomes the Big Bad after Kotomine is killed. Atypically, Kotomine is still probably more effective as the Big Bad, because he is a cunning and ruthless planner, whereas Gilgamesh's massive ego prevents him from using his power effectively most of the time.
Azel from God Hand could possibly count. He's not really considered equal with the other four big bads since he's human, but he has a God Hand and really knows how to use it well. He could easily take out any of the demons whenever he wants to. Although he did underestimate how much of a bastard Belze was, leading to him becoming the sacrifice to bring back Satan. Whoops.
Deathwing in World of Warcraft: Cataclysm. The Old Gods are the real Big Bads, but due to their imprisonment by the Titans, they can't use the bulk of their power and are mostly limited to slowly corrupting and influencing the inhabitants of Azeroth. Deathwing presents a much more immediate threat with his titular Cataclysm, and is the driving force of the expansion's plot, to the point where he's the Big Bad of the expansion while the Old Gods are a distant Bigger Bad. Unlike most examples of this trope, however, Deathwing actually is loyal to his masters. Also, he happens to be a literal dragon.
Surprisingly, the Genma Triumvirate of Onimusha: Dawn of Dreams are both this and not at the same time. They fit as The Dragons of Hideyoshi, but it is clear early on that they're simply using him as a means to an end and revive their god who they're truly The Dragons to.
Wild Dog of the Time Crisis series, at least in the first game.
Namir is this to Zhao in Deus Ex: Human Revolution he is an effective, powerful, and plain-out scary fighter to his fragile boss.
In Halo Wars, the Arbiter Ripa 'Moramee is the main villain, while subordinate to the Prophet of Regret. His orders come the Prophet, but he commands enough authority as a general to be as much of a military threat, and is far more powerful physically as well. Fortunately for Regret, 'Moramee is a straight example of this trope, fanatically and unwaveringly loyal to the Hierarch and the Covenant he stands for. Regret himself isn't fought until the events of Halo 2, as a Disk One Final Boss.
In Halo 2, Tartarus plays this role to the Prophet of Truth for mcuh the same reasons.
At the end of Pokémon Black and White, Ghetsis reveals that N was a false hero, intended to outlaw Pokemon husbandry in Unova so that Ghetsis, who considers himself above that law, could use Pokemon to rule unopposed.
Castlevania: Death occasionally fulfills this role. Though Dracula is still considered the main villain of the series, it's often Death that helps to revive him and pose the major threat to the heroes.
Jack Layzon from Cannon Dancer. While he's technically the Big Bad and the reason Kirin is out for Revenge, he has no fighting skill whatsoever, and even dies in a cutscene, without fighting back. The three assassins he hired, all Kirin's former comrades, are the actual threat.
In Tenchu Z, Shigi is much more of a threat than his boss, Lord Ogawara, and pretty much the actual antagonist in the game. While the latter is no slouch in combat skills, Shigi has just stronger and better ninja tricks up his sleeves.
Lord Yuna from Breath of Fire IV was one of the dragons of Emperor Soniel, but the latter has all but an insignificant role in the story (in fact he's only scene in the game has him getting killed by Fo-Lou), whereas Yuna is pretty much behind most of what happens.
An interesting Villain Protagonist example in Grand Theft Auto V. The two main antagonists, Steve Haines and Devin Weston are virtually helpless without the protagonists on thier side. What makes them the antagonists is that they also make a mistake of turning agaisnt two of the protagonists, Michael and Trevor. The conflict between Michael and Trevor has more effect on the plot then either antagonist. It should be noted, the only way Steve or Devin can win is if Michael or Trevor dies, and even then they need help from the third protagonist, Franklin, who canTake The Third Option.
In Lost Eden, the Tyrann, not Moorkus Rex, are the genuine threat. Moorkus Rex never leaves his lair, lies literally every time he opens his maw, and underneath the fearsome exterior is a tiny little mouse, which the tablets reveal at the end.
The Legend of Zelda: Skyward Sword has this most of the game with Ghirahim, who for all practical purposes can considered the game's Big Bad as his master Demise is spending most of the game trying to escape his imprisonment. That said, when Demise does get free, he quickly shows himself to be the bigger menace.
First Kar'Ukan in Star Trek Online is a de-facto version, with Loriss as a Non-Action Big Bad. Technically, being Dominion, they are all under the Founders, but circumstances have cut them off from that, leaving them to operate on their own. Loriss, as a Vorta, speaks for the Founders, making her Kar'Ukan's superior, but he (being a Jem'Hadar First) is the military leader and much more physically imposing. The military leader aspect becomes important when the Federation arranges for a Founder to show up and order them to stand down. Loriss complies and transports to the Founder, Kar'Ukan refuses and orders a last stand, with his Jem'Hadar following his lead.
In the comic proper they have a complicated relationship. Redcloak is the one Xykon's hobgoblin army recognizes as their leader, despite Xykon being more powerful and the de facto boss. And there are definitely hints that Redcloak will turn into The Starscream once their goals irreconcilably diverge (meaning when ritual to control one of the Gates is carried out; once that's done and Redcloak's god has control of the Gate, it won't actually matter if Xykon kills him on the spot, he'll still have won). On the flip-side, Xykon is far more powerful, dangerous and evil, and might be more intelligent than Redcloak gives him credit. Further, Redcloak is visibly horrifed when he realizes he's becoming more like Xykon, and regards working with him an extremely unpleasant necessary evil. Also, Redcloak himself is The Heavy for The Dark One, his Bigger BadGod of Evil, so he is technically The Dragon to somebody else.
Within the Empire of Blood, General Tarquin holds this position: the Empress (an actual dragon) is more concerned about where her next meal is coming from. Tarquin's band of six adventurers fills this in various places all over the western continent. Each of them prop up governments and switch around as the situation demands. Since kingdoms in the region are routinely overthrown, the group preempts this by doing the "overthrowing" themselves, ie killing off their current figureheads periodically and installing new ones.
Darths & Droids restores Darth Vader to this position (see the Star Wars example above in the movies section) by making Palpatine a good man who (through Vader's manipulation of both him and the Jedi Council) evolves into a Well-Intentioned Extremist
Shego of Kim Possible is almost this to Drakken. The only thing that stops her fulfilling all the criteria is that for most of the series, she lacks the ambition to become the bigger threat — she (mostly) helps Drakken carry out his schemes rather than invent and execute any of her own. But we know she has the power to completely overthrow Drakken if she wants to — see A Sitch In Time.
What stops her is that Drakken is a significant threat in his own right, and still drives the plot of most of their stories. Without her around he's somewhat less competent, but that's just as likely to make him even more dangerous as his plans are more likely to Go Horribly Wrong (case in point, creating advanced killer robots that end up turning on him). He is smarter than Shego — she just has a lot more common sense and can actually fight on a near-equal level with Kim.
Barry Dylan in Archer is this to Odin head, Len Trexler and later Nikoli Jakov, head of the KGB. More so to the latter. He is the Arch-Enemy of Sterling Archer, and when he is in Jakov's services, he eventually becomes a cyborg and plots to ruin Archer's life. To get support for this, he usurps Jakov as head of the KGB, and has his men hunt Jakov down, event though as we see later, Barry is more then capable of hunting him down himself. It turns out his motive for this is to hurt Archer who was bonding with Jakov under the assumption that Jakov was Archer's father. Then after he steals Archer's One True Love, she takes on this role before usurping him officially
Parodied in The Simpsons. It turns out Mr. Burns is actually the de-facto head of the Nuclear Power Plant. He placed a Canary as the head of the power plant, that way if he got the Plant in trouble, the Canary would take the fall. Homer lets the canary go and Mr. Burns eventually become the offical head of the Plant.
Played With in "The Coon Trilogy" of South Park. Cartman, as the Coon recruits Cthulhu to carry out his will, having Cthulhu go on a rampage across the country to forefill his Knight Templar beliefs, but when all was said and done Cthulhu is still the domminate threat to humanity even without Cartman, and seen as the Big BadIn-Universe.