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.
See also Big Bad Wannabe, Hypercompetent Sidekick, Supporting Protagonist and especially Non-Action Big Bad, whom Dragons-in-Chief (sometimes) work for. Compare/Contrast Deceptive Disciple.
Examples:
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Anime & Manga
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. Majin Vegeta might also counts, and he does realize that Babidi is inferior.
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 than Supreme Commander Red.
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 Sengoku's orders. Nevertheless, he causes the most damage to Whitebeard and his allies, from deceiving Squad, to provoking and killing Ace.
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.
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...
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.
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?
Comics
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 the recurring villain of the series... a rarity.
Lord Hebi (a giant snake!) fills this role in ''Usagi Yojimbo."
Thulandra Thuu in King Conan, as the advisor 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 ''The Black Island" Müller appears to be working for Puschov.
In King Ottokar's Sceptre Musstler is working for Kurvi Tasch. The same applies to Sponsz in The Calculus Affair and probably Miller in the two moon adventures, although Tintin never comes into contact with Kurvi Tasch himself.
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.
In The Return of Jafar Jafar plays this an incredibly obvious version of this trope as Abys Mal's genie.
Nigel from Rio. While his owner still drives the plot to some degree, Nigel is the more direct threat and far more menicing and evil than the poacher he's working for.
Planet51 General Grawl is this to Professor Kripple.
The titular 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.
Dominic Greene to the leaders of Quantum in Quantum Of Solace, although he really is the man with the plan.
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, 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.
Mr. Freeze to Poison Ivy in Batman & Robin. Mr. Freeze actually existed longer than Poison Ivy in this film. Whilr Poison Ivy was more evil, Mr. Freeze gets the sympathetic backstory that get's the audiances attention, and Freeze actaully outlasts Ivy and somewhat poses a threat to her. The fact she was manipulating Freeze, and the fact Freeze has a Heel Realization is what makes Ivy the Big Bad.
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.
It's likely he included them just because he thought it would be funny. He has no need for their influence and little need for their money. When he finally gets paid, he burns the money.
In the Martin Lawrence film The 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.
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 very long way away. The scene was probably cut from theatrical because this dynamic was already extremely obvious.
Word ofGod 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. Darths & Droids restores Vader to this position by making Palpatine a good man who (through Vader's manipulation of both him and the Jedi Council) evolve into a Well-Intentioned Extremist .
In Iron Man 2 Ivan Vanko is recruited by Justin Hammer's 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
Alexander Minion in the first Spy Kids movie, to both the fake Big Badand the real Big Bad.
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.
In The Texas Chainsaw Massacre, 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 3 D and in that one is to avenge his family.
In The Hills Have Eyes, like Leatherface, Lizard is credited as the main antagonist even though he answers to Big Brain, who spends the movie sitting in a room he never leaves.
Stephen in Django Unchained. 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.
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. Col. 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.
Literature
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.
Renegade Russian Colonel Yegor Viktorvich Zakharov from Dale Brown's Act of War, who acts as the head of operations for the GAMMA eco-terrorist group. While Ruiz recognises his military talent, he doesn't realise that Zakharov is a Deceptive Disciple, and neither do us readers for some time.
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 to 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.
The In Death series: Ceremony in Death introduces Selina Cross as the Big Bad and Alban as The Dragon with a cult of Satanists. However, Alban kills off Selina in an You Have Outlived Your Usefulness manner, reveals that he was actually in charge, and that the cult was supposed to be just a long-term con that evidently turned into Serious Business.
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."
Live-Action TV
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 Prop Joe.
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.
Gatehouse from The Shadow Line. While he's technically subordinate to the leaders of Counterpoint, he's the driving force of much of the plot, and he's undoubtedly the main antagonist. And in the end, he ends up killing his bosses and becoming a Dragon Ascendant.
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.
In season one of the The Vampire Diaries John Gilbert serves as this to both The Founders Council and Kathrine Price respectivly, although technically, the Founder's Council where pawns in Kathrine's own scheme.
Season Three's Big BadEsther molds Alaric into this, combining his evil alter eago and his new found vampirism. Alric wasn't very loyal and kills Esther for threatening Jeremy and Matt, but still tries to carry out her plan..
Video Games
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 probably fits more into the trope, 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 the captain of the Red Wings Golbez that everyone is worried about. However, it later turns out not even Golbez is the real bad guy, but Zemus. Golbez was actually brainwashed.
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.
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, 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.
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.
Justified by Caesar being stated to be a brilliant leader when it comes to charisma, intelligence and generally leading a nation. Legate Lanius just 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."
Yes Man becomes this if you side with him, as he controls the Securitron army and Hoover Dam, your two primary resources, at the end of the game.
Though it is not played completely straight as You are this to Yes Man before the Battle of Hoover Dam, and he honestly respects your abilities even after he gains total power. Also unlike many in the position of having a more powerful Dragon you are still one of the most significantly powerful, knowledgeable, connected, resourceful, and outright dangerous beings alive, as well as having access to and complete control of one of the few places where the resources to stop him could be found, the Big MT.
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.
Speaking of, 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.
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 Assassins 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.
The only reason he kills his father is because Rodrigo got fed up with Cesare and tries to poison him. Cesare figures it out and feeds Rodrigo his own poison.
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.
Thanatos actually is no one's Dragon, he just swoops into the story twice before taking over the evil Empire's plot for his own nefarious purposes and becomes the final Big Bad.
Fire Emblem Jugdral: Prince Yurius. He's being manipulated by Manfroy and was specifically "bred" by him for his plot to resurrect the dark god. The point being for Yurius 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. 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.
Galcian in Skies of Arcadia. He is subordinate to Empress Teodora, but he's the biggest threat to the protagonists. He is not the Final Boss, however; that role is filled by his own Dragon, Ramirez.
At the end of Pokemon 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.
Shin Super Robot Wars: In the Earth Route, Lu Cain gives orders to the Ze Balmary Empire, but gets his orders from Laodecia. In fact, Laodecia never makes an appearance in the Earth Route.
Web Comics
The Order of the Stick: 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.
Also deconstructed in the prequel book Start of Darkness, which shows what happens when a villain is nominally subservient to a Well-Intentioned Extremist. Xykon is initially The Dragon to Redcloak: despite being more brutish and less intelligent than his "boss", over the course of the story he evolves from The Dragon to Dragon-in-Chief to Big Bad, by virtue of his total lack of moral compunction... though the fact that he's a lich with access to a wide array of arcane spells while Redcloak is a mere (albeit high-level) mortal cleric might help, too.
Except, recently, Redcloak revealed that he's been manipulating Xykon for years, so this trope still appears to be in effect.
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. 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.
Western Animation
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.
Some fans believed that Azula was this for her father, until Ozai's full powers were revealed later on.
Which would explain why Azula backstabs many people and wants to be crowned the next Fire Lord, but never actually tries to take him on. Azula would know not to pick a fight she can't win.
