Interestingly, in ADOM, the normal Final Boss is arguably the Dragon. To close the Chaos Gate, you first have to defeat a random immensely powerful demon called Fistanarius, the Greater Balor. If you actually went through the gate, which has quite difficult prerequisites and isn't required for the normal ending, you would face Andor Drakon, the ElDeR cHaOs GoD.
A literal case in Alundra, where the Big Bad Melzas sends a dragon to attack you before deciding to get his own hands dirty.
In the fantasy-themed combat-chess game Archon, the Dark forces have a literal Dragon, who is more powerful in every way than any of the other Dark pieces, including their leader, the Sorceress. The equivalent for the Light forces is the Djinni. The Shapeshifter for Dark and the Phoenix for Light could also qualify as their respective side's Dragons, but the Phoenix's lack of attack range and the fact that the Shapeshifter is only ever as strong as its opponent made them just a little too quirky to be real mobile slaughterhouses.
In Army of Two: The Devil's Cartel, the Big Bad Esteban Bautista has El Diablo, who is revealed to be Salem, one of the protagonists from the first 2 games.
Mr. Big posed as the Big Bad in the first Art of Fighting, but took his rightful place in the second game when Geese Howard came back to Southtown. In Art of Fighting 3, Sinclair was Wyler's dragon.
Bodhi to Irenicus in Baldur's Gate II: Shadows of Amn. Once you've got past her and get to follow Irenicus to the almost-final area, he also pulls out a literal dragon in his service you have to deal with before getting to him.
In the sequel Baldur's Gate II: Throne of Bhaal, Draconis is Abazigal's dragon. Odd in that, as Draconis is also Abazigal's son, Abazigal is himself a dragon. (And it may be argued that all five of the mini bosses of the expansion are dragons to the expansion's Big Bad, Amelisan.
In Battletoads, Robo-Manus is considered this to the Dark Queen, being generally depicted as her most dangerous minion, both in terms of story and gameplay. He's even served as a Final Boss in her stead for two of the series' games.
In Brave Fencer Musashi, Colonel Cappriciola is The Dragon to Fuhrer Flatski, ruler of the Thirstquencher Empire. However, near the very end of the game, you find out that Cappriciola is actually your buddy Jon, who's been helping you during the game, and HE is secretly the son of the Emperor & Empress of the Thirstquencher Empire, whose deaths Flatski arranged in some unspecified manner that was meant to look like an accident (Jon, who was a child at the time, was meant to die with them). Unfortunately, he is shot in the back by Flatski's son Rootrick before he can take his revenge on Flatski, and then later stepped on by Dark Lumina.
In Musashi Samurai Legend, Rothschild is The Dragon to Gandrake. However, Gandrake was originally Ganryu, but was mind-controlled by Amestris, who was sealed within the Archnembulus, into becoming her Dragon as Gandrake. The epilogue shows Ganryu presumably back to normal after being defeated by Musashi for the last time, at that point, Rothschild becomes the new Big Bad, with Shiraz as his Dragon.
In Cave Story, Misery serves as the Dragon to the Big Bad, the Doctor, and she and Balrog form a Quirky Miniboss Squad of sorts, most of the quirkiness coming from Balrog. Misery, however, doesn't have any real loyalty towards the Doctor, and she and Balrog are simply bound to serve the wearer of the Demon Crown. In the hidden best ending of the game, she sends Balrog to save Quote and Curly from certain death after they destroy the source of the Crown's power.
In Chrono Trigger, Queen Zeal takes this role next to Lavos. What's interesting is that the game seems to suggest that Lavos doesn't seem to really care one way or another about her.
On a smaller scale, many of the local antagonists of individual eras have a distinct Dragon of their own. Azala had the hulking brute Nizbel for a bodyguard, never mind that her pet Black Tyrano was practically a literal dragon. Dalton plays this role for Queen Zeal and takes a crack at becoming the new king after she leaves for bigger and better things. Ozzie is an odd variation in that while he is indisputably Magus' right-hand man and field general, he is also a coward who flees and hides behind his goons whenever there is real danger.
Lord Recluse, Big Bad of the City of Heroes games, has four Dragons: Scirocco, Ghost Widow, Black Scorpion, and Captain Mako. (It may be more accurate to call them a Quirky Miniboss Squad, but they have far more independence and characterization then a true QMS.) Each of these lower ranking Arachnos members has a Dragon of his own, namely Ice Mistral, Wretch, Silver Mantis, and Barracuda, respectively.
Played with in Crackdown: You, the player, are the Dragon to the game's realBig Bad, the Director of the Agency. You face down other Dragons of rival bosses.
Cuphead: King Dice serves as the right-hand man to the Devil, which he boasts about in his Villain Song. His role is to block the brothers from meeting his boss and ends up serving as the penultimate boss in the game before the Devil himself.
Also, in both games he's the last boss you fight before Dr. Cortex himself.
In the first game, it's N. Brio who's The Dragon, who's got more health, and is also smarter than Cortex too. He just doesn't have enough of a spine to become the big bad, and then has a HeelFace Turn in the sequel.
Technically, Dr. Cortex has always been the The Dragon to Uka Uka, although this isn't revealed until the third game.
Walton Simons serves as Dragon to Bob Page in Deus Ex. Sorta, Simons appears to be equal in rank to Bob Page, but due to being more inclined to get his hands dirty and being faced earlier in the game he serves the narrative role of a Dragon even if he technically isn't one.
In Deus Ex: Human Revolution, the Tyrants, specifically their leader Jaron Namir, serve as this for the rest of the Illuminati, and supply three of the game's four boss battles, with Namir's being the last before the endgame.
Also, depending on how you play him and your view of Sarif Industries, Adam himself to David Sarif.
The Chaos Lord in Digimon World 2 has three dragons known as the Chaos Generals.
In Donkey Kong Country 3: Dixie Kong's Double Trouble! (and Donkey Kong Land 3), the evil KAOS (a laser beam firing/circular saw using) robot plays this to King K. Rool, who's secretly controlling him as Baron K. Roolenstein. Although in the Land game, he fights independently like most other cases on the page.
Loghain's Co-Dragons are Arl Howe and Ser Cauthrien. The former is a ruthless murderer and racist, while the latter can actually be reasoned with.
In Dragon Age II, Knight-Commander Meredith's is Knight-Captain Cullen. However Cullen does eventually decide that Meredith's completely insane and turns against her in the final battle.
In Dragon Age: Inquisition, depending on whether or not you sided with the Mages or Templars in the first act, the Elder One's Dragon will either be Samson (if you sided with the Mages) or Calpernia (if you sided with the Templars). He also has an actual dragon at his command, which you have to kill during before your final showdown with him.
In Dragon's Dogma, the dragon (not this trope, we're talking about the huge, red, horned flying bastard who stole your heart and destroyed your village) actually seems to be the Big Bad. In the end, he actually isThe Dragon. (Yes, now we mean this trope.) Grigori serves under the Seneschal in order to seek for a new Arisen who can finish the cycle of Eternal Return, should you failed while having an audience with the said Seneschal, you become one.
Bishop Ladja in Dragon Quest V is a particularly good example. In this case the Dragon is even more evil, as he's personally responsible for the death of Pankraz, the hero's father, murdering him right in front of the hero. He then went on to enslave the hero for ten years, forcing him to construct a monument of blasphemy. The hero was 6 years old at the time. He would go on to dish out even morePlayer Punches over the course of the game. In fact, he could make a good Big Bad in his own right if he wasn't completely loyal to Grandmaster Nimzo.
In Dungeons & Dragons: Tower of Doom, near the end you have the option of taking one of two paths in order to get to the tower of the final boss. The first path leads to a fight with a beholder. The second leads to a fight with a massive red dragon. Funnily enough this dragon is arguably harder than the final boss and his "dragon" who is a drow elf.
In the Dynasty Warriors series; Lu Bu is Dong Zhuo's dragon...until Lu Bu turns on him and puts a pike through his head.
Zhuge Liang could be seen as Liu Bei's dragon, as he orchestrates a lot of Liu Bei's victories...plus his nickname is "The Sleeping Dragon."
Yue Ying could be seen as Zhuge Liang's dragon.
This trope does get played with a lot. In Wu, Sun Jian appears to have Huang Gai as his dragon, in lose terms, first, with Sun Ce relying on Zhou Yu second, and after that Sun Quan gets Zhou Tai as his bodyguard, and you will generally end up facing him before Quan. In Wei, Cao Cao has the Xiaou family protecting him, each holding some form of power over when you face Cao Cao, with Dian Wei and Xu Zhu acting as tough as steel bodygaurds, and Simi Yi holding only slight dragon status unless he if the focus. In Shu, While Zhuge Liang is the main strategist, Guan Yu seems to act as the battle dragon, and his weapon is called the "blue dragon".
Takios serves this role for the Eternal, Temuorin in Eien no Aselia. He also has some sort of connection to Yuuto's sword which is never elaborated on. They're even voiced by the same person but it's unclear if this means anything.
Actually Tel'Arin The Shadow Elf seems to fit the role better in Shadow Over Mystara, although he definitely plays this role to Archlich Deimos in the prequel, Tower of Doom.
In Dungeon Siege 2, you actually get to fight a massive dragon, but it isn't The Dragon. Valdis' actual The Dragon is his Dark Wizard Archmage. But in a twist at the very end, it is revealed that Valdis is himself nothing more than an unwitting Dragon to an even more powerful Dark Wizard, whom you only get to fight in the expansion.
The same is true in Dungeon Siege 1. The literal dragon is the second most powerful boss, but Gom's actual Dragon is Gresh.
In the third game, Rajani served as this to Jeyne Kassynder though you fight her early on in the game. After defeating her you're given the choice of either killing her, imprisoning her or setting her free. The latter choice will result in her performing a Heel Turn Face and trying to help you.
In Oblivion, Mankar Camoran serves as the Dragon to Mehrunes Dagon. Dagon is the real threat to Tamriel, but Camoran serves as his enforcer/mouthpiece in the mortal plane, and must be defeated before there is any hope at all of stopping Dagon. Camoran is also The Heavy, serving as the impetus for the game's plot when his Mythic Dawn Cult assassinates the Emperor and his legitimate heirs.
In Skyrim, both sides of the Civil War questline have a leader who is served by a very capable second-in-command (General Tullius by Legate Rikke and Ulfric Stormcloak by Galmar Stone-Fist). Which one is the Dragon and which is The Lancer depends on which you side with.
Emerald Dragon has Ostracon as this to the Demon King Galshia. He's a human who joined the demons and became their army's head general. He's the one directly doing most of the demon army's evil acts, and serves as the main obstacle for the heroes for most of the game.
Also Colossus fits this role in Etrian Odyssey 2, since he's Overlord's guardian.
And in 3, Kujura serves as this to Armoroad's Princess Gutrune, while Olympia fills this role for the Deep City's King Seyfried.
In Elemental Master, Clauss, the Big Bad's general, can transform himself into a black dragon, though the Boss Battle where he does so turns out to be only the third to last unique one.
You get your very own in Evil Genius. Maximilian starts with the disgraced samurai Jubei, Alexis has the afro-sporting ghetto gangster Eli Barracuda, and Shan Yu has Lord Kane, the man behind every major evil deed of the 20th Century (although he maintains the Titanic thing was an accident).
Fallout has the Super Mutant Lieutenant being the Dragon to the Master. Also Morpheus is, more or less, the dragon to the Master, even though he is trying to imply they are partners.
Fallout 2 has Frank Horrigan, a secret service agent doped to the gills with FEV as the dragon for the president.
Fallout 3 has Colonel Autumn, the leader of the Enclave forces acting as this for President Eden. He's also the Final Boss of the game, though by himself he's fairly unimpressive and it's possible to talk him into walking away.
In Fallout: New Vegas, there are lots of them. Most notably, Caesar's Co-Dragons are Legate Lanius, commander of the Legion's main combat forces, and Vulpes Inculta who serves as the leader of the Frumentarii (the Legion's spies, saboteurs, and intelligence agency). In the past, Joshua Graham "The Malpais Legate", served as the war cheif of the tribes the Legion had amassed until the First Battle of the Hoover Dam where his poor and inflexible tactics lead to defeat and Graham being burned alive with pitch and throw into the canyon below to die. The president of NCR Aaron Kimball has General Lee Oliver. The player could also become a dragon to either Mr. House, Caesar, or NCR command. Or they can make like The Starscream and co-opt Mr. House's piece of the pie and make Yes Man their dragon.
In the original Fatal Fury, the game would have you believe that Billy Kane, Geese Howard's right hand man, is the final fight, but not long after the game starts, it becomes fairly obvious that Billy is only The Dragon, and that Geese Howard, the Big Bad, is the true final boss. Subverted later on in Fatal Fury 3, where Billy is defeated in story but not in-game, Geese is apparently The Dragon, with Yamazaki seeming to be the Big Bad, until Yamazaki's defeat reveals the Jin Twins, the true Big Bads of the game.
Also in the Fatal Fury series: Lawrence Blood is Wolfgang Krauser's Dragon, and Grant is Kain R. Heinlein's.
Subverted in Final Fantasy VI, where Kefka, who had appeared as The Dragon up to that point, pulls a Starscream halfway through the game and becomes the Big Bad himself.
Jenova of Final Fantasy VII becomes one of these to Sephiroth, despite probably being more important to the plot (and a great deal creepier). Her fully reconstructed form Jenova Absolute is the last boss you battle before confronting Sephiroth himself.
Final Fantasy VIII has a chain of dragons: Raijin and Fujin act as Dragons for Seifer, Seifer is Dragon to Sorceress Edea. And they were all Dragons for Ultimecia in the end.
Subverted in Final Fantasy Adventure. The opening makes it look very much like Julius is the dragon to Dark Lord, but you kill Dark Lord halfway through the story.
Final Fight: Dumb Muscle wrestler Abigail is touted as the Dragon to the Big Bad Belger, since he's the last boss you fight before facing Belger. It's also possible that Rolento (the boss before Abigail in the Industrial Stage, which was cut from the SNES port of the game) is in fact the Dragon, since he's the one in charge of Mad Gear's military power and connections.
A bizarre example happens in Fire Emblem: The Binding Blade: An actual dragon named Idunn is the Dragon to Big Bad Zephiel, but if you get all the Infinity +1 Sword-esc weapons, you actually get to have an extended story where the dragon is actually the Dragon to Zephiel... who really is the Dragon to the exact same dragon. To make it even more confusing, said dragon can have another dragon, Jahn, who is her Dragon. Try to wrap your brain around that one.
In Fire Emblem: Path of Radiance and Fire Emblem: Radiant Dawn, the Black Knight serves the Big Bad Ashnard as a member of the Four Riders. He does this in conquering Crimea and searching for Lehran's Medallion, and killing the main protagonist Ike's father. This eventually leads to a Duel Boss fight between him and Ike. (Although Ike's sister Mist can help with healing Ike.) In Radiant Dawn, he turns to serve as the Dragon for his true master Sephiran under his true identity of Zelgius, the noble leader of the Begnion Central Army. There he has a true Duel Boss fight with Ike by creating a magical barrier that separates the two of them from their respective forces. Sephiran can be considered a Dragon as well, as he must be fought and defeated so the party can reach the goddess Ashera, whom he serves.
The Death Knight is initially introduced as the Flame Emperor's most prominent enforcer. However, once you learn their true identity, it becomes apparent that Hubert von Vestra was their real second-in-command all along. If you defect to her side afterwards, Byleth becomes The Lancer, Hubert becomes The Smart Guy, and the Death Knight becomes your Token Evil Teammate.
On the Crimson Flower route, after Rhea's Freak Out, Seteth goes from her Lancer to her Dragon. Once he either bites it or books it in Chapter 15, Catherine assumes the role of her Dragon and retains it until the very end of the game.
In the Gears of War series both Raam and Skorge act as Dragons for Queen Myrrah.
Azel, the evil equivalent of protagonist Gene in God Hand, is seen as a Dragon to Belze, leader of the Four Devas, but he leaves the group before Belze is killed.
Atlas has served as a Dragon to both Cronos in the Titanomachy and to Persephone in Chains of Olympus.
God of War III: Poseidon acts as The Dragon to Zeus, even though he is defeated in the very beginning of the game. One could argue that Helios took over this role after that.
Travis is Heath Oslo's dragon in Grisaia no Rakuen, but he soon shows that he's not actually that impressive when Sachi blindsides him and takes Yuuji away from him. Near the end of the story, he confidently strolls to the battlefield only to find his entire side has been wiped out by Yuuji and has both hands cut off before being killed. Overconfidence does that to you.
Abaddon of Guild Wars Nightfall has two Dragons, The Lich and Shiro, the two Big Bads of the previous campaigns. Also, Varesh.
Meanwhile, Mallyx, the boss of the elite area accessible after downing Abaddon, has four dragons, known collectively as the Lords of Anguish. As the Lords are bosses in their own right, some of them even have their own dragons.
In Guild Wars Prophecies, good ol' Prince Rurik is forced to play the role of dragon for the Lich.
The Henry Stickmin Series has one in Infiltrating the Airship. The Right Hand Man is the right hand man of the leader of the Toppat Clan. He's almost a Dragon-in-Chief, as in two of the four endings the Leader spends most of the time running away from Henry, while the Right Hand Man actually fights him. They both don't do much in the other two endings.
In Hitman: Blood Money, the initial Big Bad appears to be Mark Parchezzi III. After 47 puts a Silverballer round right between his eyes, however, the real Big Bad reveals himself in the form of Jack Alexander, the head of the FBI and the owner of The Franchise, which is The Agency's chief rival assassination contract company. The climax of the game is a shoot-out between Alexander's FBI goons, 47, the wheelchair-bound Jack Alexander himself, and an innocent priest and reporter who wind up getting caught in the crossfire.
The Ravager serves as Kai Lan's dragon, being the reanimated corpse of Black Whirlwind's brother Raging Ox who is forced to do Kai Lan's bidding.
The United Cities and Trader's Guild in Kenshi have Eyegore. Should you piss them off sufficiently, they'll send armies of men after you. If you defeat them, Eyegore and his men come after you instead, and you'd better be prepared. According to some conversations you can overhear in-game, the leaders of the UC and Guild are terrified of him themselves.
In Killzone 2, Mael Radec is this to Scolar Visari.
In The King of Fighters '95, Big Bad Rugal Bernstein brainwashed Saisyu Kusanagi to fight the KOF victors, becoming The Dragon in the process.
In The King of Fighters '97, ordinary band members Chris, Shermie, and Yashiro Nanakase are revealed to have been The Co-Dragons to Orochi all along. Goenitz, the Big Bad of The King of Fighters '96 is also a Co-Dragon and the Dragon-in-Chief to Orochi.
Krizalid, the Big Bad of The King of Fighters '99 was revealed to have been the Dragon for Zero, the Big Bad of The King of Fighters 2000, until he chose to betray NESTS for his own cause.
The Original Zero serves as the Dragon to Big Bad Igniz in The King of Fighters 2001, again until he chose to betray NESTS to become a new god.
Mukai, the Big Bad from The King of Fighters 2003 reveals himself to have been the Dragon for Saiki, the Big Bad from The King of Fighters XIII.
Shion is also the Dragon to Magaki in The King of Fighters XI, until he betrays his boss.
In Kingdom Hearts II, who The Dragon is in Organization XIII (or if there even is one) has had some mild debate, even on this wiki. The general consensus seems to be between Xigbar, who actually is Number II, has a bit of a backstory, and arguably has the most battle prowess (Still debatable - Some may find other members to be harder), and Saix, who acts in a position of authority, gets more screentime, and is actually the boss fight before the final boss. If one were to nitpick, Saix as number VII is in the middle of XIII, and half of XIV. 358/2 Days points even further towards Saix, as he's the one who actually assigns missions to the other members. (As well as the only one besides Xemnas who never accompanies Roxas to missions)
Xigbar, or rather Braig, is more like the Dragon to Xehanort himself, and by extension Xemnas' past. However, as the Leader of the Organization, Saix is the Dragon to Xemnas as the Superior. They're Co-Dragons in all honesty, anyway.
Maleficents Dragon was Jafar, then it was Captain Hook, and then it was Riku. In KH2, she has to settle for Pete as her permanent Dragon.
There's also Vanitas, The Dragon to Master Xehanort and the only boss in the game fought roughly seven times across all three stories. And to most people, he's That One Boss almost every single time.
Kingdom Hearts III, has Ansem, Xemnas and Young Xehanort as Master Xehanorts Co-Dragons in the Thirteen Seekers of Darkness.
In Kingdom of Loathing, there appear to be a number of dragons to the final boss the Naughty Sorceress. The most obvious would be the fight with your shadow. Although, the Sorceress' tower could be seen as a dragon in and of itself. Then there are a number of required minibosses, such as the Goblin King, the Boss Bat, and either the Man, the Big Wisniewski, or both.
All Three Mage Sisters are technically Hyness' dragons in Kirby Star Allies with Zan fitting the description best.
In Knights of the Old Republic, Saul Karath is sort of the Dragon for Malak (and Malak used to be the Dragon for Revan). In the sequel, Traya has gone through three Dragons (Nihilus, Sion, and Atris), with Nihilus having his own Dragon (Visas).
Talon is General Du Couteau's dragon, and though labeled a mercenary by the community, takes orders only from him.
General Darius (aka the Hand of Noxus) is also the Dragon of Grand General Swain, often left to 'evaluate' the strength of others with his axe.
Jarvan IV, the prince and exemplar of Demacia, has a dragon in the form of Xin Zhao. Xin swore loyalty to him after the previous king risked himself to free him from his hardcore gladiatorial arena.
Legacy of the Wizard: Keela's four chief subordinates are Tarantunes, Erebone, Archwinger and Rockgaea. They are the four bosses who guard the crowns which the heroes need to destroy Keela.
In The Legend of Heroes: Trails of Cold Steel, Crow Armbrust essentially does the bidding of Vita in Cold Steel I (despite Crow being the leader of the terrorist organization that Class VII opposes throughout the entire game) and Duke Cayenne in Cold Steel II.
The Legend of Zelda: A Link to the Past: Agahnim, the first time in the series that Ganon has someone doing his dirty work for him. The English translation suggests that Agahnim is actually Ganon in a form which can travel to the Light World, though only with limited powers. On the other hand, the way Ganon reveals himself (his spirit rising out of Agahnim's body, with the latter not even disappearing when Ganon turns into a bat) would suggest that Agahnim was a victim of (or willing accomplice through) Demonic Possession. The Japanese translation and all adaptations in either language make it clear that Agahnim is a separate entity from Ganon.
In Painful, Buzzo serves as this to the game's Greater-Scope Villain. He is a distributor of the Fantastic Drug Joy, which was created by said Greater Scope Villain, Dr. Yado, and spends Painful as the "face" of the Joy drug trade. All while his secret boss appears to just be a random gag NPC until a possible Stinger.
In Joyful, the Joy Mutant Sweetheart takes over as the Dragon to the same main villain, as it is one of the most powerful Mutants in the game and his preferred Right-Hand Attack Dog.
In Lufia: The Ruins of Lore, the King of Gratze's conquest is assisted by a mysterious man named Ragule. Ragule ends up being The Starscream and kills the King before the party can confront him.
The main villain in Mass Effect 2 is the Collector General, which also goes by the name Harbinger. In the final moments of the game, Harbinger RELEASES CONTROL of the Collector General. It's just a slave, The Dragon to Harbinger's Big Bad. Just what is Harbinger? Another Reaper.
Harbinger has a second dragon too, Amanda Kenson from the Arrival DLC.
Miranda may be the Illusive Man's Dragon, though given his credentials and her eventual character she could be nothing more than a useful pawn. And given the Paragon ending to Mass Effect 2, she's probably now a thorn in his side.
In Lair of the Shadow Broker, Tela Vasir is The Dragon to the Shadow Broker.
Turns out the Reaper are co-Dragons to The Catalyst
In Mega Man ZX Advent, Albert plays the role of the big bad, and when you fight him as the final boss takes on the form a three headed mechanical dragon.
The true Dragons as defined by the Trope are probably Prometheus and Pandora, though they turn on Albert as well as plot to kill him.
On the subject of Mega Man, Bass becomes the Dragon for his creator Dr. Wily after he was eventually built in Mega Man 7. Adaptations of the story covering earlier times usually show Protoman as Wily's first dragon, but in the games he was just a deluded pawn who turned good by the end of his debut appearance.
The Mega Man X series seems to make a point of featuring a Dragon, usually as cover for Sigma.
VAVA/Vile serves as the dragon for Sigma in the first X installment, although the Updated Re-release seems to show him as more of an independent troublemaker.
X5 establishes Dynamo as Sigma's Dragon, although he runs away after a few fights.
Then, in X6, the minor character Isoc becomes the Dragon to Gate, although it's hinted that he's really another old villain in disguise.
While Shadow Man's multiple appearances in Rockman 4 Minus Infinity could be chalked up to Author Appeal, there is a reason for it. In the official materials, Shadow Man is described as Wily's bodyguard/right-hand man. It would make sense if Shadow Man himself does the field job. One encounter even has him maintaining Pharaoh Man's level.
Typically, in Metal Gear, the titular Metal Gears serve as this; the players apparent ultimate challenge before they can have a climactic showdown with a final boss.
Most games don't have a human and plot-based dragon, but Gray Fox is a very clear-cut one in Metal Gear 2, piloting the Metal Gear before fighting Snake on foot. After his death, Snake gets the final encounter with Big Boss.
Ocelot serves this role in the first three Metal Gear Solid games. Sort of.
Metroid. Ridley is very high up the Space Pirate chain of command, though he is very rarely the highest ranking officer present in the game. He is usually fought very late in the game, and often provides one of the tougher fights, but is almost never the greatest threat around nor the final boss. Bonus points for literally being a dragon.
Metal Slug has Allen O'Neal. He is General Morden's right-hand man, and is occasionally fought as a Mid-Boss. In 4, a cyborg version of Allen appears as the Mid-Boss of the final mission. After being absent in two games, he finally returns as the boss of Mission 6 in 7/XX.
In addition, after being demoted from Big Bad after the first game, Shang Tsung is often the last opponent you'll fight before facing the Dragons, being in essence a combo of The Dragon and The Starscream to Shao Kahn.
D'Vorah nominally serves as the The Lancer to Kotal Kahn in Mortal Kombat X, who became Outworld's new ruler after overthrowing Mileena. But it turns out that she was The Mole and Evil Genius for Quan Chi and Shinnok from day 1, and decides to betray Kotal Kahn after she steals Shinnok's prized amulet from him.
Aribeth is the Dragon for Maugrim, who is himself the Dragon for Morag in the original Neverwinter Nights campaign; and in Hordes of the Underdark Mephistopheles serves as the Dragon for the Valsharess (or maybe it is the other way around).
Neverwinter Nights 2 has a couple. Lorne and Torio together serve as The Dragon to Garius, who is something of The Starscream, but then the King of Shadows uses Garius' plot to steal his power to turn the wizard into his own Dragon with the four Luskan mages serving with him being Garius' Dragons.
In Mask of the Betrayer, Kelemvor has his Voice, Myrkul sort of has you, and Akachi had/has three: the blue dragon, the demilich with delusions of grandeur, and the fallen angel.
In Nine Hours, Nine Persons, Nine Doors, Zero's Dragon is her brother Santa/Aoi Kurashiki, who does almost all of the dirty work, mainly because [[spoiler:Zero (AKA June/Akane Kurashiki) is in a loop that decides her Nintendo Wars: Grit to Olaf in the first Advance Wars'', being the only other Blue Moon CO shown in the game.
Sturm also has a Dragon in the first game in a clone of the Orange Star's Andy, who is an essential part of his plan to trick the other nations into fighting each other. In the second game, he has Hawke as his second-in-command, who commands all the other Black Hole COs.
Advance Wars: Dual Strike has Kindle acting as the right hand of Von Bolt.
No Straight Roads has Eve, who was NSR's first megastar and is shown assisting Tatiana early in the game. She's also the semi-final boss before Bunk Bed Junction can get to Tatiana.
Ōkami has so many dragons it's not funny. You're led to believe that Orochi is Lord of Evil (Orochi is actually a dragon) but that's wrong. Ninetails claims to be Lord of Darkness, but he was exaggerating. Then it's said that Lechku and Nechku may be the source of all evil. It's not until the defeat of those villains that it's revealed that all of them come from the same source of evil.
One Must Fall 2097: Raven is the Dragon to the game's Big Bad, Hans Kreissack. However, he's also a Dragon with an Agenda, as his biography in the game's manual states that he wants the position of successor to the WAR company for his own purposes (instead of as a representative of Kreissack, as the other man intends) and is always looking for an opportunity to allow one of Kreissack's would-be killers to "slip through" the company's security system.
In Persona 5Goro Akechi does double duty as the dragon to both Masayoshi Shido and the fake Igor, Yaldabouth.
While the non-linear nature of Sid Mier's 2004 Pirates makes any boss optional, the two "big" ones are the evil Marquis who imprisoned your family and Baron Reymundo, who knows where the family members are hiding.
Then in Pokémon Black and White, you have Ghetsis serving as N's Dragon. Until it's revealed that Ghetsis is really the Big Bad and is using N as his Dragon. Ghetsis and N also both use a literal Dragon type Pokémon as the strongest member of their respective teams during their final battles against the player, with N's dragon (Reshiram in White and Zekrom in Black) filling an important story role and essentially serving as his main weapon/companion/form of tranport.
Most of the villains in the series have Dragons. In 3rd Gen, Maxie has Tabitha and Archie has Shelly and Matt, and in 4th Gen, Cyrus has Saturn. 5th Gen has already been mentioned. Arguably even 2nd Gen has the Rocket Executive Archer as Big Bad and the female Rocket Executive Ariana as his Dragon—and one or both of them could be considered the Dragon for 1st Gen's Giovanni. In Gen 7 Plumeria served as Guzma's Dragon who in turn served as Lusamine's Dragon.
Punky Skunk: Commander Chew is this to Badler. At the end of every island he will challenge Punky in some way to stop him.
Several Quest for Glory villains have one Dragon or another on their side, using both the "intelligent sidekick" variety and dumb, physically powerful monsters.
In Quest for Glory I: So You Want to Be a Hero, the Brigand Leader is guarded by the Brigand Warlock. As it later turns out, though, there's a funny twist to the setup...
Quest for Glory II: Trial By Fire gives us Khaveen, captain of the guard in the decaying city of Raseir and right hand to the maniacal Ad Avis. Come the endgame, while the Fighter faces him in a straight-up duel and the Magic User doesn't interact with him much at all, the Thief engages in a more creative "showdown" with the corrupt captain by breaking into his house.
Ironically enough, the villain of Quest for Glory V: Dragon Fire, is actually trying to summon a dragon. In the meantime, he has to settle for The Assassin. His identity is a mystery for much of the game, and ultimately turns out to be a throwback to the series' first installment.
Napoleon himself, when he's revealed to be a man named Leonard Bonar, is revealed to be the Co-Dragon to the real Napoleon Bonaparte, along with Raphael/Phantom R's father, Issac.
Axel Gear, the Evil Counterpart of Sparkster from the Rocket Knight Adventures series, serves as the Dragon in all three games. Despite the fact that each of them involves a different invading empire, of a different species to boot, Axle Gear is the Dragon to each successive Evil Overlord. It seems that repeatedly losing to the hero has not damaged his resume.
Subverted in Rumble Roses, as you meet the actual evil mastermind before fighting her cyborg (unless you're playing as her). Though in some stories, you fight the girl she brainwashed before her, so kinda counts.
In Saints Row and its sequel each rival gang has a Dragon.
Jyunichi is The Dragon to Shogo Akuji and later to Shogo's father Kazuo once he comes to Stilwater
The closest thing Maero has to a Dragon is Matt, his best friend and right hand. But since Maero is a 7-foot tall musclebound thug he never actually uses Matt to do anything except tattoo him.
For that matter, Johnny Gat is your dragon.
In Saints Row: The Third, the DeWynter systers are co-dragons to Syndicate kingpin Phillipe Loren. They later become Killbane's dragons after Phillipe's demise. When one of the sisters later defects to the Saints, Matt Miller takes over as the dragon.
There are also several more minor examples in the subquests, such as the Genie in the circus tent, who is forcibly serving as Dragon to Kalah. When the player defeats Kalah, they are able to claim the one remaining wish the Genie can grant before returning to its lamp, and among other options can choose to free it or have Kalah resurrected to give him another chance at not messing his life up. Other examples include Lassal, and Mae'Var and Renal Bloodscalp, as Dragons to Bodhi and Aran Linvail respectively.
A Series of Unfortunate Events (2004) has the Hook-Handed Man serve as Olaf's dragon. He does everything he can to stop the children in their quest to escape Olaf. In the final area, he does everything he can to stop Klaus from ascending the tower to free Sunny.
In Nocturne you the player character can become The Dragon for either Hikawa, Isamu, Chiaki, or Lucifer himself depending on which faction you side with. If you join Hikawa or Lucifer their current Dragons Samael and Beelzebub will be demoted to serving under you instead.
Paarthurnax was Alduin's original Dragon, before betraying the latter.
You can become the Dragon to any of the Daedric Princes, most notably Hermaeus Mora's champion was Miraak until you take his place, and his soul. Miraak leaves you with a warning about the position before he croaks
Depending on what side of the Civil War you're on, Galmar Stone-Fist is this to Ulfric Stormcloak while Legate Rikke is this to General Tullius. The ending to the Civil War carries the implication that you are now the Co-Dragon to whichever side you picked. Since the war is all but over, and you're the "good" guy, this doesn't mean much in practice.
In Sly Cooper: Thieves in Time, Ms. Decibel serves as this to Le Paradox, even falling in love with him. She later pulls a HeelFace Turn after he attempts to leave her behind in the past after Sly defeats her in battle.
Sonic the Hedgehog's Metal Sonic, in all his myriad versions, names and incarnations, has often wound up playing this role to Robotnik.
Except in Sonic Heroes where he Took a Level in Badass, locked up Eggman, and masqueraded as him in order to actually see to the end of Sonic by his own hands as that game's Big Bad. He failed and Eggman had to wipe his mind clean as a result.
In Splinter Cell, Vyacheslav Grinko is Nikoladze's own Dragon. He commands the soldiers and mercenaries, deals with all the messy or bloody parts of the "business", including Nikoladze's security, and is such a high-priority threat that he's the only target of an assassination objective in the game, besides Nikoladze himself.
In The Legend of Spyro Trilogy, there are several levels of Dragons. Cynder and Gaul are Malefor's Dragons (Cynder being a real dragon), despite being Big Bad in their first games, they're directly stated to be Malefor's minions. Gaul has the Assassin as his Dragon and it was possible by some of the pictures show that Cynder was actually Gaul's Dragon.
Star Control 3 has the K'Tang, a race of tiny creatures walking around in Humongous Mecha suits and terrorizing everyone else. They like to claim that they are the leaders of the Crux Hegemony, but in fact they are simply The Dragon to the cunning but weak Ploxis. The Ploxis go to great lengths to hide their own status as the Big Bad.
Crown Prince Valerian Mengsk subverts this trope, as Raynor thought he was Mengsk Jr, but the crown prince shows otherwise.
Each of the three paths in Star Fox has the penultimate boss serving this role to Andross. They are fought twice, once in Venom's atmosphere, and a second time in Venom itself. In the first path, it's Phantron. In the second, it's the Galactic Riders. And in the third, it's Great Commander.
In the "Dark Side" DLC available for some versions of the game, Starkiller actually becomes a Dragon with an Agenda appealing to Luke Skywalker.
In Star Wars: The Old Republic, the Imperial characters will likely end up being the second-in-command of a Sith Lord. In the case of the Sith Warrior and Inquisitor, they serve as the enforcers of Darth Baras and Lord Zash respectively though they eventually end up killing their mentors and the Warrior ends up as the Sith Emperor's own Dragon. The Imperial Agent at the end of Act I has the option of serving as Darth Jadus' personal hand. The Bounty Hunter is forced to work primarily for Darth Tormen in Act III and may eventually get a chance to betray him.
During the Street Fighter II series, Sagat was portrayed as M. Bison's right-hand man within Shadaloo. However, the later Street Fighter Alpha prequels established that Sagat wasn't really that close to Bison and only joined since Bison promised him he would fight Ryu again in a rematch. In Street Fighter Alpha 3, Balrog serves as M. Bison's main henchman, with Juni and Juli also fulfilling this role.
In the Streets of Rage series, Shiva usually takes the role of The Dragon, most notably in the final showdown as Mr. X's bodyguard in the second game, and again in Streets of Rage IIIin one of the Bad Endings of the game. In the fan-made remake, his biography states that he also serves as Mr. X's chief assassin.
Shiva also fits the brawn role, but only because Mr. X is one of the few people smart enough to use a gun.
In even earlier games there were the Koopalings. Ludwig is definitely the Dragon in Super Mario Bros. 3. Larry is faced last in Super Mario World, but none of the kids seems to have clear superiority in that game.
Kammy Koopa is Bowser's Dragon in the first two Paper Mario games.
In the first OG, Ingram Prissken plays the part of the (unwilling) Dragon for Levi Tolar.
Shu Shirakawa also served as this role, to an extent, to Bian Zoldark in both Original Generation and the original Super Robot Wars 2.
In the second OG, we have lots of them:
Axel Almer acts like The Dragon for Vindel Mauser.
Alfimi is like The Dragon for (Stern) Neue Regisseur.
Strange that both The Dragonsend up joining you in OG Gaiden.
Mekibos is actually The Dragon for Wendolo, as he seemed to lead the rest of the Quirky Miniboss Squad the Inspectors. And he joins you too, temporarily before he's offed. Like Alfimi and Axel, he comes back and joins your group in 2nd OGs.
In OG Gaiden, Duminuss is The Dragon for Dark Brain. It's also arguable that Wilhelm von Juergen is unknowingly playing The Dragon part for Duminuss.
Subverted slightly in Tales of Symphonia: the battle — which looks like a boss battle — just before going to attack and kill the Final Boss actually is a real dragon. It also turns out to be one of the easiest fights in the game — not even on the level of some normal, random fights. Played more straight though, in several instances in the game, such as Botta to Yuan, and Pronyma to Big Bad Lord Yggdrasil.
The Dragon appears to be several people in Tales of the Abyss - While it's obvious that the Big Bad is Van Grants, or rather Grand Maestro Mohs ( or both of them), their dragon appears to be either Sync (who has the most battle prowess, rightfully so considering he's a replica of the Fon master after all) or Legretta, who always seems to be the most loyal to their cause. In fact, most of the God-Generals could count as The Dragon at some point; making it more of a case of Co-Dragons. Legretta is the most loyal, but not the strongest of them; Sync is stronger, but only follows the Big Bad because of a villainous Enemy Mine situation; Largo has both strength and loyalty, and the most combat experience; Aschdid count once-upon-a-time, and it's clear that Van wants him back, but Asch pulled a HeelFace Turn of sorts. The only ones who don't qualify for the role at some point are Dist, who has no interest in the leaders goal, and Arietta, who fights not because of Van but because of her Bodyguard Crush.
The Tiamat Sacrament: Gyle is Ry'jin's top soldier, capable of inhaling up to three Runes despite not being a dragon. He's in charge of commanding the Nether Garrison to defend his master's territory from the Saphirite rebels, but occasionally patrols Draslin to purge dissenters.
Touhou: Nearly all the antagonists in Touhou games have a Battle Butler who serves as the penultimate boss, but Eirin Yakogoro from Imperishable Night stands out as both the brains and the brawn behind Kaguya's scheme. Not only is she often considered a more difficult fight in-game, canonically she was holding back so as not to overshadow Kaguya.
The Mafioso role in Town of Salem fulfills this role, killing anyone who the Godfather points at, unless the Godfather is roleblocked somehow or dies first. Alternatively, non-killing mafia will be promoted to Mafioso status if there are no killing mafia left alive.
The Tower of Druaga has a literal dragon named Quox, who has to be defeated on Floor 59 before you get to fight Druaga himself.
In the Ultima series, the Guardian has Batlin and Mors Gotha. Each is the final boss of the game they're in (VII and Underworld 2, respectively).
In Vampire: The Masquerade Bloodlines, Prince LaCroix of Los Angeles has a gigantic, mute Nagloper vampire as his right-hand henchman and Sheriff (the one responsible for enforcing Camarilla law in the prince's territory). The Sheriff is, in all but one ending, the game's final boss — LaCroix himself does not put up much of a fight.
If you end up against The British Empire in the VIP:R mod VictoriaIndia will do a good deal of their dirty work, including a lot of the more out and out conquering of uncivs. And will tear you apart.
In the Warcraft universe, Archimonde and Kil'Jaeden split the role of The Dragon to Sargeras (at least they did until Archimonde's death), while each can be said to have their own Dragon in the form of Mannoroth and Tichondrius, respectively. Also, the original Lich King's Dragon was Arthas, and after the two merged into the New Lich King, either Kel'Thuzad or Anub'arak (or both) could be said to take over the role.
A more literal example in World of Warcraft would be Sindragosa for Arthas. You have to defeat the honking big dragon before you can proceed to kill the Lich King.
The Wing Commander series has an interesting variation of this trope - The Dragon is an ace pilot you must dogfight with before destroying the real bad guy (whose death is in a Cutscene, not directly killed by the player). Prince Thrakhath plays The Dragon to the Wing Commander IIIBig Bad, the Kilrathi emperor; Seether plays The Dragon to Big BadTolwyn in Wing Commander IV. For extra value, Seether flies a fighter commonly called the Dragon, in the final flight mission.
In The Witcher, The Professor is the Dragon to Azar Javed.
And, in turn, Azar Javed is a Dragon to the big bad Jaques de Aldersberg, head of the Order of the Burning Rose.
The Wonderful 101: Gimme is this to Jergingha, as the first-class officer of GEATHJERK, he's the penultimate boss in the entire game and shows up in the story's Darkest Hour. He is also one of the two officers who remains in the story after the operation he's introduced, along with Vijounne.
Kazuma Kiryu, the protagonist of the Yakuza games is an interesting take on the trope. He is a former Dragon for the Dojima Family- albeit one who sought to carry out his duties compassionately as possible- and his honorary title The Dragon of Dojima reflects that. Unlike the expected fate of most Dragons he was removed from that position not by dying, but by going to prison due to extremely personal and complicated situations that mark the beginning of the first game.