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.
Most Mortal Kombat games have a Dragon, although none are as iconic as Goro, who served as one for Shang Tsung in the very first game. MK2 had Kintaro, a Goro Expy. MK3 had a centaur named Motaro...
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.
Before he became the Big Bad, it was revealed that Shao Kahn was The Dragon and The Starscream himself to the Dragon King Onaga, until Shao Kahn poisoned him and took over.
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 dragon is Legate Lanius. 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.
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).
In Killzone 2, Mael Radec is this to Scolar Visari.
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 Disgaea: Hour of Darkness, the boss of the second chapter is Flonne, a little angel girl that can only heal the other enemies. However, she has a very strong enemy protecting her... and it's actually a dragon.
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).
In League of Legends 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.
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.
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 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).
In Halo 4, the Covenant remnant considers Jul 'Mdama to be this to the Didact. In the post-single player Spartan Ops co-op campaign, Jul seems to have his own Dragon in Gek.
The Arbiter in Halo Wars for the Prophet of Regret.
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.
In Fallout 3, Colonel Augustus Autumn is the Dragon for President John Henry Eden, leader of the Enclave. However, Autumn actually turns against Eden towards the end of the game, and as he was the commander of the Enclave's military, his loyal soldiers defect with him. Awesome.
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.
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.
The Black Knight serves as the Dragon for the Fire Emblem games Path of Radiance and Radiant Dawn. In the first, he 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.
Every game in the series seems to have one of these. Particularly bizarre in the first game where a priest takes this role for a literal Dragon.
An even more bizarre example happens in Fire Emblem: The Binding Blade: An actual dragon named Idoun can be 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, Yahn, who is her Dragon. Try to wrap your brain around that one.
In Fire Emblem Limstella is The Dragon to Big bad Nergal and In The Sacred Stones Riev is the Dragon to Prince Lyon who is in turn is the Dragon to the Demon King.
The Dragon appears to be several people in Tales of the Abyss - While it's obvious that the Big Bad is Van, his 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 his cause. In fact, most of the God-Generals could count as The Dragon at some point; making it more of a case of DragonDuumvirate. 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 Heel-Face Turn of sorts. The only ones who don't qualify for the role at some point are Dist, who has no interest in the Big Bad's goal, and Arietta, who fights not because of Van but because of her Bodyguard Crush.
In the first OG, we had Ingram Prissken who acts like The Dragon for Levi Tolar (unwillingly, actually)
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.
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 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.
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. Their Co-Dragons in all honesty, anyway.
Maleficent, the Dragon to Ansem, although she herself was unaware of it. Coincidentally, when he did reveal himself, he turned her into a Dragon. Before that, her Dragon was Captain Hook, 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.
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.
Most of Sonic's rivals were depicted as dragons in their debut games:
Like stated above, Metal Sonic is an example of this trope.
Knuckles was Eggman's dragon in Sonic 3 & Knuckles.
Shadow could be considered Eggman's dragon in Sonic Adventure 2.
Silver was Mephiles' dragon in Sonic 2006.
Mecha Sonic was Eggman's dragon in Sonic 2
Axel Gear, the Evil Counterpart 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.
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 main antagonists of individual eras have a distinct Dragon of their own. Azala had the hulking brute Nizbel for a bodyguard, never mind that his 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.
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 the first game, 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...
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 the fifth game, 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.
Imperishable Night particularly has this subverted with a touch in gameplay. Kaguya Houraisan is a powerful Lunarian and has a powerful Battle Butler Eirin Yagokoro. Canon-wise, Kaguya is definitely more powerful (she is immortal after all), but gameplay-wise Eirin is more difficult to defeat than her boss. Thus Eirin is somehow Kaguya's Dragon and this leads to a Stupid Statement Dance Mix: "HELP ME, EIRIIIIN!!!!"
Many Stage 5 bosses in Touhou games are The Dragon to the Stage 6 Big Bad, with Sakuya of Embodiment of Scarlet Devil and Youmu of Perfect Cherry Blossom being just two of many. Sanae of Mountain of Faith and Shou of Undefined Fantastic Object also count. A case could be made of Yuyuko and Ran being Yukari's Co-Dragons.
Secondary protagonist Marisa Kirisame was The Dragon in her first appearence.
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 the freeware game 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 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.
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.
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.
In Silent Scope, Monica (a heavily armored fighter) is the terrorist leader's Dragon.
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.
Then in Pokemon 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 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.
Kammy Koopa, Lord Crump and Nastasia in the Paper Mario games. Though in the case of Lord Crump, Grodus doesn't seem to value him, even pulling a Uriah Gambit with him at one point. The closest thing that game has to a dragon is Quirky Miniboss Squad leader Beldam, who may be thought of as a Dragon by Grodus but definitely is by the Shadow Queen.
Wesker also makes many people believe that he's acting as the dragon for Oswell E. Spencer, but he was really a cause for his Villain Decay, and eventually his death.
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.
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.
Sarevok is resurrected in Throne of Bhaal and available as a party member. If the player chooses him as a party member, he'll offer to become The Dragon to the player character upon the latter's ascension to godhood.
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.
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. Botta to Yuan, and Pronyma to Yggdrasil.
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 Heel-Face 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.
Taking Cortex's role as The Dragon in the second GBA game is Dr. Nefarious Tropy, who hatches a plan to hypnotize the Bandicoots by means of his friend N. Trance, who acts as Tropy's Dragon.
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."
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".
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.
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.
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.
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.
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.
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.
In addition, the "Eternal Ones" have their own powerful race of "Heralds", who would've been another Dragon if not for the fact that the Eternal Ones are infinitely strong to begin with.
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.
Majordomo for Ragnaros
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.
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.
In Donkey Kong Country/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 independantly like most other cases on the page.
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.
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.
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.
In the arcade game 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.
Metroid. Ridley. He's usually close to the end in some form in each Metroid game, and is usually That One Boss. He is even a literal Space Dragon.
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.
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.
As of Mass Effect 3, Kai Leng is The Dragon to the Illusive Man.
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
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.
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.
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.
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.
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.
In the fantasy-themed combat-chess game Archon: The Light and the Dark, 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 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.
Also, Theseus is The Dragon to the Sisters Of Fate.
Atlas has served as a Dragon to both Cronos in the Titanomachy and to Persephone in Chains of Olympus.
The Castellan is Dragon to the Warlord in Anvil of Dawn. Since you don't fight the Warlord, the Castellan is more or less the Final Boss, despite being one dungeon early.
In the Gears of War series both Raam and Skorge act as Dragons for Queen Myrrah.
Mankar Camoran serves as Mehrunes Dagon's Dragon in The Elder Scrolls IV: Oblivion. 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.
In Nine Hours, Nine Persons, Nine Doors, Zero's Dragon is Santa, who does almost all of the dirty work, mainly because Zero is in a loop that decides her existence, which is the reason for the game.
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.
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.
Before them, Xenobia (and in the remakes, her sisters Royce and Phacia) to the Magic Emperor in Lunar: The Silver Star.
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.
Crown Prince Valerian Mengsk subverts this trope, as Raynor thought he was Mengsk Jr, but the crown prince shows otherwise.
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).
In Sly Cooper: Thieves In Time, Ms. Decibel serves as this to Le Paradox, even falling in love with him. She later pulls a Heel-Face Turn after he attempts to leave her behind in the past after Sly defeats her in battle.
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.
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.