The Big Bad of .hack// could go one of two ways: Cubia (although defeating him doesn't really solve anything other than getting him out of the way), or Morganna, although you never really fight her directly. She simply uses the phases to interact and fight for her. Once Kite "kills" Aura, she is able to come back and defeat the last phase of Morganna, and truly be born.
The Man in Glasses from 1213turns out not to be. He's the only person who was actually on your side throughout the entire game, while everyone else — including your apparent "ally" that he kills — were trying to stop you from performing the mission you were created for, believing you were too irretrievably damaged to be successful.
Baldour, the evil being of the Silver Star in Alisia Dragoon. His followers are trying to revive him through most of the game, and eventually do succeed... Alisia, of course, tears him a new one.
Alien: Isolation: The Alien drives the conflict even after it is defeated halfway through. APOLLO also qualifies, since he is responsible for turning turning the Working Joes against the humans on the station and outlives the Alien.
The original game has Vincent St. Claire, a school principal who runs a criminal empire that is the cause of much of the rampant crime in Santa Lina. His drug dealing was foreshadowed as far back as mission 4, and it's his actions that start Anaksha on her quest.
A Sea of Fire has Frank, a local club owner who has plans to import and sell anti-tank weapons to local gangs, which could escalate gang war.
A New Threat has Trent, a drug dealer who is a minion in an organization that is spreading a new drug, Pixie Dust, throughout the Hell's Cats district.
Dark Angel has Tony Valentino, aka Big-V, the head of his aptly-named V-syndicate that is responsible for spreading and dealing Pixie Dust, as well as the kidnapping of Ivonne and the murder of DeMartini, which Anaksha was framed for.
Angels of Death: Doctor Daniel "Danny" Dickens is the one who recruited the other killers of the Tower and brought Rachel to the tower in the first place, and is hell-bent on making sure Ray and Zack never leave.
Angry Birds series: King Pig is the leader of the pigs and the one who leads the operations to steal the titular birds' eggs.
Aria's Story: Clyde Harow the Librarian is the creator of the dark book world and the monsters inhabiting it, and is the one who trapped Aria inside, because he wants to test her and see if she can behave like the real Aria; on the other end is the Rabbit, the In-Universe Big Bad of Lewin's story that the book world is based on, who leads the monsters in trying to kill Aria in order to preserve themselves against Clyde's orders, as Clyde plans on disposing of them if Aria completes her journey.
Arkanoid series: DoH, or Dominate Over Hour, is the Reality Warper that attacks the titular mothership and goes after the Vaus spacecraft. In Revenge of DoH, it takes over the Xorg spaceship to get revenge, and in DoH It Again, it lures the Arkanoid with a fake planet to destroy Vaus.
The Armed With Wings series has Vandheer Lorde. He's the series' most recognizable antagonist and serves as the Final Boss of most of the games. The main exception is Armed With Wings 2, which has Vandheer Lorde as the Villain Protagonist and the Armed With Wings/Lone Warrior the Hero Antagonist. Network is sort of The Man Behind the Man to Vandheer Lorde in Armed With Wings 3. However, the latter still serves as the Final Boss while Network is the second-to-last boss.
The overarching plot of the Assassin's Creed series has the Templar Order/Abstergo Industries, with Warren Vidic being their most prominently villainous member in the main games. Following Vidic's death, Juhani Otso Berg becomes the most prominently seen Templar. Juno was also revealed as a chessmaster villain at the end of III, and from then on acts as the Greater-Scope Villain to both factions. Each game also has its own Big Bad:
Assassin's Creed I has a Big Bad Ensemble between Rashid ad-Din Sinan AKA Al Mualim and Robert de Sablé, rival Templar leaders who seek the Piece of Eden for their own plans.
Assassin's Creed: Rogue has an interesting example of this trope. Considering you are playing as Shay Patrick Cormac, a Templar, and do battle with the Assassins, the primary antagonist of the game is Achilles Davenport, though he's portrayed as an Unwitting Instigator of Doom who has caused countless innocent deaths through a mix of recklessness and incompetence.
Assassin's Creed Origins has a Big Bad Duumvirate example in the form of Flavius Metellus / The Lion and Lucius Septimius / The Jackal, the leaders of the Order of the Ancients in Rome and Egypt. The Hidden Ones DLC on the other hand has Gaius Julius Rufio as the sole Big Bad.
Assassin's Creed: Valhalla has a Big Bad Ensemble between King Alfred The Great, who is the Grand Maegester of the English Order of the Ancients and is responsible for reforming the Order into the Templars after his exile had ended, thus making him a Greater-Scope Villain, and Basim Ibn Ishaq/Loki, who turns out to be Evil All Along and serves as the Final Boss. Basim also takes on the role of the Big Bad for the modern day segments of the story alongside Aletheia, another Greater-Scope Villain, since the two manipulated Layla Hassan into giving them the Staff of Hermes Trismegistus so that the former could be resurrected. Arguably, Odin himself is also a Greater-Scope Villain since he is the reincarnation of Eivor and is responsible for the death of Loki's son Fenrir, thus setting Basim's vendetta against Sigurd, and eventually Eivor, into motion.
In the regular storyline of Asura's Wrath, Lord Deus and Gohma Vlitra are the primary forces that are plaguing the world that Asura finds himself in. In the Grand Finale DLC, however, it turns out that Chakravartin, the Creator, is the one responsible for the Gohma, and by extension, all the horrible things the earth gods did to try to fight them.
The Atelier series rarely gets a Big Bad. Most of the games have No Antagonist since they're mainly coming-of-age stories about an alchemist striving to prove themselves to the world, with the Final Boss often being a Giant Space Flea from Nowhere that only serves as the final test for the alchemist to overcome. There are a few exceptions, however.
Atelier Iris: Eternal Mana: Mull is an alchemist who abuses mana believing that it will benefit humanity and serves as the Foil to Iris and Klein. Towards the end of the game, he gets usurped and killed by his own creation, The Almagam, who takes his place as the final boss.
Atelier Iris 3: Grand Phantasm: Crowley, once an unassuming raider, came into possession of the Shadow Gem, which granted him powers over darkness. However, it's revealed that he's been possessed by an unnamed evil alchemist inhabiting said gem, and by Chapter 7, he is defeated and killed by the heroes, leaving the Greater-Scope Villain Uroborus to be the last threat they face.
Atelier Rorona: The Alchemist of Arland: Meredith Alcock is the Minister of Arland who issued the order to close down Rorona's workshop so that he can build a factory in its place. Once it becomes apparent that Rorona is passing the king's assigned tests, he becomes frustrated and starts sabotaging her efforts directly and indirectly, though most of his attempts are foiled by Rorona's mentor Astrid.
Balan Wonderworld: Lance serves as the primary antagonist, being the source of the Nega Tones plaguing the dream worlds and transforming people in despair into monsters.
Amelissan the Blackhearted in the Throne of Bhaal expansion to the second game and the last part of the story.
For the series as a whole, Bhaal might count, but in each individual installment he's the Greater-Scope Villain.
The Banjo-Kazooie series has Gruntilda, a classic Wicked Witch. In the first game, she kidnaps Tootie to steal her beauty for herself, and in subsequent games she plots vengeance against the titular bear and bird for thwarting her.
Joker continues to play a critical role in Batman: Arkham City, but it is Professor Hugo Strange who is responsible for the creation of the mega-prison, the unwarranted arrest of Bruce Wayne and all of the "political prisoners" in Arkham City who either knew too much about the prison's creation or spoke out against it (all without trial, no less), and even supplying the various supervillains with weapons in order to fuel their raging gang wars. At the end, it is revealed that Strange is a disciple of Ra's al-Ghul (who promised Strange immortality and his position at the head of the League of Assassins in exchange for his help), and Arkham City's purpose was to gather all of Gotham's criminals in one place so that the two could use the dangerously escalating gang violence as an excuse to cure Gotham City's criminal problemby exterminating all of the prisoners via a huge military airstrike.
Joker's also in Batman: Arkham Origins as the true man responsible for hiring the eight assassins to kill Batman after stealing Black Masks's identity. Though this time, the role of Big Bad is split between him and Bane, who poses a much greater threat to Batman's identity and serves as his final real opponent.
Scarecrow fills this role in Batman: Arkham Knight, with the titular villain serving as his Dragon who ends up pulling a HeelFace Turn in the end. Joker is also present as a part of Batman's mind as the remnant of a virus caused by his exposure to Joker's blood in Arkham City which is strenghtened by Scarecrow's fear toxin and tries to take him over from within.
A Tale of Two Brothers has Talrach, the orcish warlord who force necromancers Mordak and Rotharik to kidnap Baran.
An Orcish Incursion has Rualsha, the leader of the orcish army who are attacking the elves
The South Guard: The Urza brothers at first, who has kidnapped Mebrin and force him to raise undead for them to use. However when we meet the last brother, he reveals that Mebrin has gone insane and supplanted them as the Big Bad.
Heir to the Throne: Queen Asheivere.
Legend of Wesmere: Great Chief Brubar, the leader of the orcish army attacking the elves, for the first four chapter. Landar, turning evil from overdose of the dangerous invisiblity potion used for assainating the Great Chief, for the last one.
Eastern Invasion: Mal Ravanal, the necromancer leading the titular invasion against Wesnoth.
The Hammer of Thursagan: Karrag, lord of Kal Kartha.
Bayonetta 2: Loptr, who is revealed to be responsible for Balder becoming the villain of the first game via possession.
The Beginner's Guide: In-Universe, The Machine gradually becomes the main threat in Coda's games, as it is warping the game worlds in destructive ways. However, it is implied to merely be The Scapegoat for the protagonist. Out of universe, Davey Wreden himself turns out to have been responsible for Coda's disappearance, as his tampering with Coda's games drove him away.
Beyond Good & Evil: General Kehck is the Supreme Commander of the Alpha Section of the planet Hyllis who oppresses the people under the guise of protecting them from the DomZ invasion and is the primary enemy of Jade, who seeks to overthrow him. Except he is secretly working for the DomZ High Priest, who leads the DomZ aliens that have been invading Hylis, has drained countless planets to keep himself alive, and secretly controls the Alpha Sections.
Bravely Default II: Adam is the Lord Commander of Holograd who destroyed Gloria's kingdom to gather the crystals and Take Over the World to bring an end to all wars. In truth, he is being manipulated by his right-hand woman Edna, who seeks to awaken the Night's Nexus and destroy everything due to her hatred of humans, having given people the Asterisks not only to drain the power of the crystals, but to ensure that the Nexus could never be defeated.
Call of Duty: Black Ops 4: Savannah Mason-Meyers, a businesswoman trying to resurrect dead soldiers as part of Project Blackout.
Call of Duty: WWII: Heinrich, an SS officer stationed in German-occupied France, seemed like this for the main campaign but he's actually a Disc-One Final Boss. Metz, an SS officer handling POWs, would be the closest to this as he's the Final Boss before the campaign officially ends.
Dr. Peter Straub serves as this for the Nazi Zombies campaign.
The "Chaos" Story has the High Priest of Chaos, leader of the Order, and the Oracle of Delphi/Medusa.
Call of Duty: Ghosts: Gabriel Rorke, the brainwashed former leader of the Ghosts, now the top agent of the Federation. The current leader of the Federation appears to be a Greater-Scope Villain of sorts. He's never seen or referred to by name, but Rorke seems to hold him in great respect.
Cannon Dancer features Jack Layzon as the primary antagonist who used and betrayed the main character, Kirin, for his own needs. The mysterious goddess Slaver, however, uses Kirin's revenge as a way to enslave him to her will, and ends up becoming the Final Boss for her troubles.
Capella's Promise: The previous king of Ilnacia, who built the Mother superweapon to convert his citizens into monstrous soldiers. However, he's eventually killed by his son, Prince Zanara Capella, who takes over as king and fuses with the Mother.
Captain Commando has Scumocide (Genocide in Japanese), the leader of a genetically-enhanced breed of "Super Criminals" terrorizing Earth.
Chrono Trigger: Magus the Fiendlord, from the medieval era, is the creator of the planet-consuming parasite Lavos, whose influence is felt in every time period and who is ultimately responsible for not one, but twoextinction-level events (extinction of the Reptites and start of a long ice age in 65,000,000 B.C., and the destruction of the magical Kingdom of Zeal in 12,000 B.C.). The heroes are trying to prevent a third which will occur in 1999 A.D., and must kill Magus to prevent him from creating Lavos. Except he merely summoned and was trying to kill Lavos, who is actually an alien from another world and is the real threat causing the extinction-level events.
Chrono Cross: Lynx is the demi-human soldier who aims to gain control of the Frozen Flame and El-Nido, putting him in conflict with Serge and his party, whom he wants to kill. However, he is being mind-controlled by the supercomputer FATE, who was built as a bulwark against the Dragon Gods and their race of the Dragonians, evolved Reptites, and their alternate universe, which seeks to invade this one. But all of them were manipulated by Belthasar, FATEs creator, to stop the true threat: the Time Devourer, an evolved form of Lavos who wants to destroy time and everything else.
CIMA: The Enemy: Pike Nighttrap is one of the Crimson Nine (the most powerful CIMA) and the effective leader of their Alien Invasion. He and his fellow CIMA feed off the hope of humans and seek to destroy the Gate Guardian heroes.
City of Heroes has a number of especially powerful and influential bad guys that compete to take over the world.
The Center, the mysterious leader of the fascist paramilitary group known as The Council.
Cloé's Requiem: Cloé's curse is the thing keeping her trapped in the mansion, and Michel must destroy the curse to free her. It is later revealed that Alain Ardennes, Cloé's abusive father, became the curse after she killed him in self defense.
Command & Conquer 3: Tiberium Wars has the Scrin, who invade Earth after the fighting between the Global Defense Initiative and the Brotherhood of Nod draws their attention to the amount of Tiberium on Earth, replacing the (seemingly dead) Kain as the Big Bad for once. However, it later turns out that Kane (having faked his death, as always) intentionally led the Scrin to invade Earth so he could get his hands on their technology.
Command & Conquer 4: Tiberian Twilight has a Big Bad Ensemble between Gideon, leader of the Nod Separatists, and Colonel Louise James. Kane has a major role in the game, but it's as, bizarrely enough, the Big Good working with the GDI to contain the spread of Tiberium before it warps the whole planet. Instead, the conflict is drummed up by the former two each leading Renegade Splinter Factions on either side trying to disrupt the alliance between Nod and the GDI and sabotage their attempts at stopping Tiberium.
Command & Conquer: Red Alert 2 has Premier Alexander Romanov, who reignites the war between the Allies and the Soviets in the Allied campaign. Though it later turns out he was being used by the psychic Yuri, who fills the Big Bad role more directly for the Soviet campaign and the expansion Yuri's Revenge.
In the original PC-98 game, Sachiko is also the antagonist, although her backstory differs somewhat.
Yoshikazu or rather, Sachiko takes a back seat in 2U, leaving Yuuya Kizami to take the position. He antagonizes the other students throughout in many ways, including attempting to sabotage the cooking competition and stealing the Book of Eibon to hijack Heavenly Host.
Corruption of Laetitia: Cardinal Alfredus Marian starts the game by betraying the heroine and stealing her powers as part of his plans to bring order to the two countries he has influence over. He's also responsible for starting an industrial revolution for the sake of bolstering his military power, but ignores the environmental damage he causes to both his own people and various monster races, making his downfall the main goal of the game.
Cosmic Star Heroine's chief villain is Dominic, director of API who aims to use the Mind-Control Device the protagonists found in the lab on Rhomu to eradicate free will of everyone. Later he is superseded by Eternity, an Eldritch Starship that is less subtle in its methods, its first action being to head straight to Rhomu to rain destruction on the Scimerex hive.
Uka Uka from Crash Bandicoot. While Dr. Neo Cortex seemingly was behind all the events in the firsttwo Crash games, it was eventually revealed in the third game that he did everything under Uka Uka's orders. However, in Crash: Mind Over Mutant, Cortex double-crosses Uka Uka and becomes the villain himself. There are also a few standalone villains:
Cuphead: The Devil, who forces Cuphead and Mugman to collect the souls of his debtors. In return, they get to keep their souls (that Cuphead foolishly bet). In the end, the two decide to fight the Devil and free all of the bosses they fought from his contracts.
Cyberbots has the Earth Force Federation and its creation, G.O.D., a giant brain-like lifeform that has decided to wipe out humanity after considering it is its own greatest enemy.
Demon's Souls: The Old One is the source of the Colorless Fog, the spread of the demons, the fall of Boletaria, and the slow death of the world. It's also the source of the setting's magic (called soul arts), and is heavily implied to be "God".
Artorias of the Abyss DLC: Manus, Father of the Abyss who is implied to be the Furtive Pygmy, is the one who defeated and corrupted Artorias, kidnapped Princess Dusk of Oolacile, and is spreading the darkness of the Abyss over the land of Oolacile.
Dark Souls II: King Vendrick, the founder of Drangleic, is the one who brought his kingdom to ruin in the pursuit of power, and is the Final Boss. Except he is a Disc-One Final Boss. The true villain and final boss is his wife Queen Nashandra, who is a Soul Fragment of the aforementioned Manus, and seduced Vendrick into warring against the giants, while also being the one who spread the undead plague so she can get the First Flame for herself. Aldia the Scholar Of The First Sin, the brother of Vendrick and co-founder, is the True Final Boss after the game got updated.
The Abyss Watchers, members of the premier unit of Farron's Undead legion are the collective first Lord, and seek to protect humanity by eradicating the spawn of the Abyss, but are overzealous in achieving this goal.
Aldritch, Saint of the Deep/Devourer of Gods, and Pontiff Sulyvahn are the two leaders of the Cathedral of the Deep and the antagonists of the first half of the game, much of which is spent dismantling forces they either directly command or created. Sulyvahn has alliances with numerous other evil sects including Rosaria's Fingers and the surviving nobility of the Profaned Capital, multiple lore-vital characters and settlements were victimized by him, and he was implied to be The Corrupter who caused Lothric to lose his faith in the Fire to begin with. While Sulyvahn is outranked by Aldrich, he's the one who fed Gwyndolin to Aldrich (thus allowing Aldrich to ascend to godhood), the one actually ruling Irithyll and the Cathedral while Aldrich feeds in a basement, and the one taking action. The only thing keeping them from being the wholesale villains is that they are killed 2/3 of the way through the game, though their legacy is felt until the end.
Yhorm, the Giant, is the descendant of an ancient conqueror, and by far the nicest of the Lords. He is either the second or third Lord fought, depending on the decisions of the player.
Princes Lorian and Lothric are the final Lord faced. They were supposed to rekindle the flame but chose not to, which causes the coming end of the world, and they interfere with the Ashen One's quest, serving as the penultimate boss. However, they do not do anything actively villainous, instead just holding up in their tower. They just want to be left alone.
The final boss isn't a real Big Bad, but it is still important in the overarching plot: The Soul of Cinder/Incarnation of Kings, embodiment of the First Flame and a composite of all who chose to link it, including Gwyn, manifested to defend the First Flame.
Ashes of Ariandel DLC: Sister Friede, altough seperate from the rest of the game's lore and plot, is the de-facto leader of the Sable Church and the cause of the painted world of Ariandel being overrun by the rot. She convinced Father Ariandel not to let the flame burn the Painted World away so a new one may be born, deployed her Corvian Knights to stop both the Ashen One and the forlorn Corvians from ruining her plot, and kidnapped the Painter to make sure she won't attempt to create another world.
The Ringed City DLC: It doesn't have a real Big Bad, but the final boss is important in terms of the overall story: Slave Knight Gael, the embodiment of the Dark Soul, created when Gael ate the Pygmy Lords to make the Dark Soul in himself so the Painter can use his blood, infused with the Dark Soul, to paint a new world.
Forrest Kaysen in Deadly Premonition, who caused most, if not all of, the problems in the story (the murders that take place in Greenvale, and driving the townspeople insane with purple gas). It's even to the point he's responsible for horribly mentally scarring the original personality of the one called York, the original personality being Zach.
Wadanohara: Princess Tosatsu is leading Tosatsu Kingdom in a war against the Sea Kindgom to take the throne from Princess Uomi, as she tried long before. Except she's not the mastermind; Sal/Syake-san, the traitor, is the one who manipulated her into attacking as part of his plan to unseal his master. In the third act, Princess Mikotsu, Uomi's real sister and Sal's boss, takes this position upon becoming unsealed.
Depict1: The benefactor/shadow actively works against the protagonist, lying to them about how to escape, to keep them trapped. The true end reveals them to be the protagonist's Living Shadow who wants to 'protect' them by ensuring they never leave.
Human Revolution doesn't really have a main antagonist, but Hugh Darrow comes the closest. Bob Page from the original game serves as the Greater-Scope Villain though he is never encountered directly, and Pieter Burke is is the antagonist of The Missing Link DLC.
Mankind Divided has Lucius DeBeers, the leader of the Illuminati. However, his actual involvement is minimal, with Viktor Marchenko serving as The Heavy.
Devil May Cry has Mundus, the Demon King, who lures Dante to Mallet Island with the help of his creation Trish so he finish off the last remaining blood of Sparda after he spilled the blood of the wife and kidnapped and enslaved the older twin, Vergil.
Devil May Cry 2 has Arius, the CEO of Uroboros, who wishes to use the power of the Arcanas to resurrect the Demon King Argosax so that he will be blessed with absolute immortality to rule over the entire world.
Devil May Cry 3 has Arkham, who manipulates both Dante and Vergil along with his own daughter so that he can unlock the gate to the Demon World and obtain the ultimate power of Sparda.
Devil May Cry 4 has Sanctus, the leader of the Order of the Sword, who wishes to use Sparda's power as the Savior in order to cleans the world of its evils and rule over it.
Devil May Cry 5 has Urizen, the Demon King, who planted the seed of the Qlipoth tree in Red Grave City, draining the lives of the citizens there in order to bear a fruit that will grant him absolute power. However, he is later defeated and assimilated into his true identity: Vergil, who previously inadvertently created Urizen as part of his desire to gain power to defeat his brother.
Diablo, the Lord of Terror, is the Big Bad of the series that bears his name, though in Diablo II, he shares this status with his two brothers, Mephisto and Baal, as the "Prime Evils." In Diablo III, it's Diablo again using Leah as his vessel, and in the Reaper of Souls expansion, it's the fallen angel Malthael.
Digimon World has Analogman, with his Machinedramon acting as the final boss.
Digimon World 3 initially had a Big Bad Ensemble between the Leader of the A.o.A terrorists, the MAGAMI president, and Lord Megadeath until Snatchmon, a combination of various Vemmon, performed a Dragon Ascendant and merged with the Gunslinger Satellite to digivolve into Galacticmon with intentions of merging with Earth itself to become Gaiamon.
Do It For Me: The Wuffles/Wooffles are black monsters that are terrorizing the protagonist's girlfriend and who he must kill to prove his love for her. However, they're actually innocent classmates- the real villain is the girlfriend, who tries to manipulate the protagonist into killing the students for her own amusement.
Donkey Kong Country Returns has Tiki Tong, the leader of the Tiki Tak Tribe. Tiki Tong has his minions hypnotize the residents of DK Island into stealing his Banana Horde, so that he may use them to expand his forces.
Doom: The Spiderdemon is behind the invasions of Phobos and Deimos, and fighting through Hell to defeat him is the final goal of the game.
Doom II: Hell on Earth: The Icon of Sin is the one who spawned all the enemies in the first place. Considering that it only appears once in the game, and its destruction damages untold miles of Hell's surface, we can assume that it is the big bad of the game.
Doom 3: Dr. Malcolm Betruger, who is singlehandedly responsible for the demon invasion of Mars, is both a Mad Scientist and an Evil Sorcerer in league with Hell itself, and wants to bring about Hell on Earth. He becomes a demonic dragon thing by the name of the Maledict at the end of the game proper, and you finally put paid to the evil bastard in Resurrection of Evil.
Dragon Ball Fighter Z has Android 21, an android programmed to have a strong need to feed on strong warriors. Her goal is to capture all the Z-Warriors, turn them into a giant feast of power for herself, then explore the universe to eat in an attempt to satisfy her endless hunger.
Dragon Quest VI had Murdaw, also known as Mudo until his defeat, upon which you find out evil still plagues the world. After D(h)uran is defeated, he tells them that he, Murdaw/Mudo, and the other demon lords were just pawns of the true Big Bad, Mortamor (also known as Dethtamoor).
Dragon Quest VII had Orgodemir, the Demon Lord who sealed most of the continents of the world to prevent God from defeating him. In the second disk, he tries to seal the continents again, while posing as God Himself.
In NieR: Automata, the sequel to NieR, the Big Bad seems to be Adam and Eve, particularly the latter, but 9S becomes villainous as the story goes on, though the true villains are N2 (Terminal α and Terminal β).
Drawn to Life and it's sequel has Wilfre, a corrupted Raposa who destroyed the book of life and brought the shadows to the world in the first game, and started draining the world's color in the second game.
Drawn to Life: The Next Chapter for the Wii has Circi, a Raposa in love with Wilfre who seeks his resurrection.
Daggerfall plays with it, having several plot relevant faction leaders without having a true Big Bad. Lord Woodborne turns out to have been the one to murder the King of Daggerfall, kicking off the game's main quest, but doesn't fit the role once the plot gets going. The Underking is the being most directly tied to the main quest and certainly looks the part of an evil villain, but as it turns out, is not all that far from being a good guy. Out of all of the faction leaders who can get what they want in the game's Multiple Endings, Mannimarco is the most malevolent and villainous in terms of his intentions, but still isn't a true Big Bad.
Redguard, a Action-Adventure spin-off game which tells a smaller-scale, more personal story, has the corrupt Imperial governor Admiral Richton as the main antagonist.
Embric of Wulfhammer's Castle : Azreala D'Fleur/Tierra del Fuego is revealed in the Final Ending as the one behind all the villains the Duchess has faced, as the events are the Duchess dreaming of the future, but Azraela is influencing the dreams to feed on her despair.
Emerald Dragon: The Demon King Galshia fits this for most of the game, but he's later revealed to working for the true Big Bad, Tiridates.
End Roll: The Indecent One is the source of the monsters in Russells dream, and his biggest tormentor. She represents Russells abusive mother.
Eternal Radiance: Eldareth is the leader of the Shadowborn, an organization that steal Akleim artifacts and assassinates anyone who tries to investigate or obstruct them. He's not the first leader of the organization, but he is the one ordering the recent thefts and plans to use the artifacts to destroy the Shadowborn while most of them are gathered at their base. This has the risk of destroying all of Darencia, which is why the protagonists have to stop him.
Eternal Sonata has Count Waltz, the ruler of The Empire who causes the problems for the heroes with his new drug, the Mineral Drug, which can cure illness, but are addictive and drive humans insane.
Eternal Twilight has Black Magi Supreme Azael, who manipulated Empress Verona into starting a war against Magi, all as part of his scheme to eliminate his successor, claim the COSMOS relic, and Take Over the World.
Era 5: Bolbox. In addition, it turns out the ones accidentally responsible for all of these except King Kuralesache are Martians.
The big bad of Fable is the demon Jack of Blades. Fable II has Lord Lucien. Fable III has The Crawler. It is hinted throughout the series that Theresa may be serving as a Greater-Scope Villain, but this was outright disproven in Fable: The Journey. Theresa actually manipulated everything in order to save the world from The Corruptor (the Big Bad of the game, and the Greater-Scope Villain of the series as a whole up to that point), so she's the Big Good for all intents and purposes.
Fallout: New Vegas: Caesarnote a little trickier since there's an ending path where you join him, but he's still obviously the central figure in the main conflict, and siding with him merely makes your character a Villain Protagonist, with Legate Lanius as The Dragon, who becomes the Dragon Ascendant should you kill Caesar and is the Final Boss of three out of four endings. Aside from Caesar, the DLCs all have their own Big Bads:
Dead Money: Father Elijah, the former Elder of the Mojave chapter of the Brotherhood of Steel who puts explosive collars on you on three others to rob the pre-War Sierra Madre Casino.
Honest Hearts: Salt-Upon-Wounds, war chief of the vicious White Legs tribe who wiped out New Canaan and are now attacking the Dead Horses and Sorrows.
Old World Blues: The insane Mad Scientist Dr. Mobius, later on revealed to be Dr. Klein, head of the Think Tank.
Lonesome Road: The former courier and Legion Frumentarius Ulysses, who is also the Greater-Scope Villain of the DLCs. He wants to nuke the New California Republic to take revenge for the Courier unknowingly doing the same to Ulysses's home, the Divide.
Fallout 4: "Father", the mysterious leader of the Institute that kills people and replaces them with human-like robots called Synths. Though Elder Maxson can also be an antagonist if you don't ally with the Brotherhood of Steel.
The second game The Jackal, an arms dealer selling weapons to both waring factions, APR and UFLL, who you were sent to kill. Subverted as he turns out to be one of the good guys (if you can call it that), and by the end of the game you work with him to combat the factions, led by Nick Greaves and Hector Voorhees respectively, which team up by the games climax and intend to commit genocide on the civilians.
The fourth game has Pagan Min, but it's not like Golden Path leaders Amita and Sabal are any better, in fact the ending shows us they may be worse.
Far Cry: Primal has Ull, leader of the cannibalistic Udam tribe, and Batari, leader of the slave-taking, sun-worshipping Izila tribe.
Far Cry 5 has Joseph Seed, "The Father", head of the Project at Eden's Gate.
Far Cry: New Dawn has Mickey and Lou, leaders of the Highwaymen, and Ethan Seed, the leader of New Eden, the successor to the Project at Eden's Gate. Joseph is still around, but hes not nearly as much of a threat as these three are.
For the FEAR series, it's a toss-up between humongously powerful psychic Stringy-Haired Ghost Girl Alma, telepathic psychopath and son of Alma Paxton Fettel, and Corrupt Corporate Executive Genevieve Aristide. While Alma has undeniably been wronged, her revenge is... rather extreme. Fettel, as revealed by the end of the third game, plans to consume Alma's power in order to take over the world. As for Aristide, she just wants to keep her job, and to hell with anyone who has to die in order for her to do so. Events would never have gotten as hellish as they did if any one of them wasn't in the picture. For the first game and its expansions at least, Paxton Fettel is undeniably the main antagonist: he's the one controlling all the Replica soldiers and directing them in an effort to free Alma.
The Final Fantasy series is famous for its Big Bads. Some of the most well-known, one in every game:
Final Fantasy had The Four Fiends as the initial villains terrorizing the world that the four heroes must defeat, until it's revealed that Chaos aka Garland, the very first boss you fought, is behind the whole thing, just before you fight his true form.
Final Fantasy II has EmperorMateus Palamecia, leader of the Palamecian Empire. He's also the notable exception in the franchise's Rogues Gallery in that he's the major antagonistic force through the entire game.Soul of Rebirth, the sequel quest released with the Game Boy Advance and PSP remakes, puts an interesting spin on this. It's revealed that after the Emperor was killed the first time, his soul split in two, one half going to Heaven and one half to Hell. The Hell Emperor was the Final Boss of the original game. In this one, the party meets the Heaven Emperor... who is also a Big Bad who has upset the natural order of the afterlife and generally made a mess of things (apparently he planned this.) Yes, the Emperor is so evil that even his good half is evil.
Final Fantasy IV has Golbez, leader of the Air Forces of Baron and Cecils brother, though hes nominally working for the King of Baron who is actually his minion. Until later it was revealed he was under the control of the Lunarian Zemus, who wants to eradicate humanity so the Lunarians can reign supreme. Zemus is promptly killed by Golbez, and transforms into the Final Boss Zeromus.
Final Fantasy IV: The After Years has the Creator, a nigh-incomprehensible alien being out to resurrect its long-dead race, no matter whose planet it has to step on to do so.
Final Fantasy V has Exdeath, who at first appears like a conventional Tin Tyrant type character as he aims to destroy the world via the Void, but is actually made up of evil spirits that were trapped into a giant tree, and then said tree manifested itself as a humanoid. The GBA version also reveals Enou, a necromancer who was mentioned in the original game as Exdeath's predecessor, another villain who also tried to control the void, as an optional superboss battle.
Final Fantasy VII Remake only covers the Midgar section of Final Fantasy VII, so President Shinra is the near-unquestioned main villain. After he bites it, the Arbiters of Fate become the main antagonists, as Avalanche decides to destroy them so they can seize control of their own destiny. Sephiroth, for his part, serves as a Greater-Scope Villain and doesn't really become the heroes' primary concern until the epilogue.
Final Fantasy VIII initially has President Vinzer Deling, but he is killed and usurped by Sorceress Edea, the schoolmaster of Galbadia Garden, and then it's revealed that she was merely a puppet for Ultimecia, a sorceress from the future. It is revealed that the final boss battle leaves Ultimecia in a weakened state, in which she goes back in time, and possesses Edea, meaning the game is a time-loop paradox. Also, Edea was the wife of Balamb Garden's schoolmaster, Cid Kramer, who created a special forces military group whose sole mission is to exterminate sorceresses, including his wife.
Final Fantasy IX initially has the tyrannical Queen Brahne, until she is killed and usurped by Kuja, with he and his creatorGarland competing for the position, the winner being Kuja, although Garland, like Professor Hojo from VII, is responsible for nearly everything in the background.
Final Fantasy X has the massive dragon...thing Sin, who terrorizes the land of Spira, but the main human antagonist is Seymour Guado, a man who believes the only way to end the cycle of Sin is to destroy Spira forever. It is revealed Sin contains Yu Yevon, a god-like being with a cycle to reincarnate itself as the creature Sin as long as summoners keep defeating it with a Final Aeon, and formed the Church of Yevon to support itself.
Final Fantasy X-2 has a similar monstrous entity, Vegnagun, who is actually not a creature but an ancient weapon, piloted by the angry ghost of Shuyin, a character with a similar appearance to Tidus. It is implied Shuyin was the actual person the Fayths were inspired by when creating Tidus.
Final Fantasy XI has the Shadow Lord, revealed to originally be a Galka soldier who sold his soul to the underworld after being wronged in a love affair, in the original game and acts as the overall Big Bad. Expansion packs also added new villains:
Rise of the Zilart: Eald'narche
Chains of Promathia: Promathia
Treasures of Aht Urhgan: Alexander
Wings of the Goddess: Probably Lilith or Atomos (flashback sequences also feature the Shadow Lord's origins)
A Crystalline Prophecy: The Seed Crystal, creator of the other crystals which have been causing trouble.
Final Fantasy XIII has Primarch Galenth Dysley, who is actually Barthandelus, the fal'Cie creator and leader of Cocoon. He and Orphan, his fellow fal'Cie who powers Cocoon, collaborate together to ensure its destruction.
Final Fantasy XIV has the Garlean Empire and its numerous Legati, as well as the mysterious Ascians who ultimately turn out to be behind the Empire too.
The first Imperial Legatus to pose a major obstacle to players is Nael van Darnus aka Eula Darnus, who seeks to destroy Eorzea by bringing the lesser moon Dalamud crashing down on the land like a Meteor.
Final Fantasy XIV A Realm Reborn has Nael's occupation force replaced by Gaius van Baelsar, whose forces awaken Ultima Weapon in a bid to conquer Eorzea.
Stormblood has the Imperial Crown Prince, Zenos Yae Galvus at the helm of its conflict, standing in the way of freeing the nations of Gyr Abania and Doma, which he holds dominion over.
Shadowbringers sees players finally face off against the founder of the Empire himself, Solus Zos Galvus who reveals himself as one of the leaders of the Ascians, Emet-Selch, having founded the Empire to further his people's goals. Ultimately, following his death, he is supplanted by his great-grandson Zenos, who returns to cement his place as XIV's true Big Bad, having acquired the powers of an Ascian, and even surpassed their last remaining leader in power.
The only significant antagonists outside the Garleans and Ascians, are the Dragons, with Nael's Meteor project having been influenced by Bahamut, while his brother Nidhogg serves as the Big Bad for Heavensward.
Final Fantasy XV has the Emperor of Niflheim, Iedolas Aldercapt, but the actual Big Bad is Ardyn Izunia/Ardyn Lucis Caelum, the Chancellor of Niflheim and an ancient Humanoid Abomination who was an ostracised Lucian king and healer. He plots to bring about the Starscourge and end the Lucian royal line. He succeeds in the latter when the last of the line, Noctis, sacrifices himself to destroy Ardyn.
Dissidia Final Fantasy establishes that in the Final Fantasy multiverse, the evil god Chaos is the biggest Big Bad. He bosses around most of the people listed above, and the only ones who try to double-cross him are Emperor Mateus, who plans to outlive Chaos to rule the universe and Golbez who, as he was not the Big Bad of his game, decides to help his brother, Cecil, in getting the crystal.
Though Chaos himself actually doesn't boss or even order anyone around at "all". Most of the orders come from either the Emperor, or oddly enough... Kefka and Kuja.
Final Fantasy Tactics had Lord Folmarv, who is actually Hashmal, the second-in-command and acting leader of the Lucavi. Ultima, his superior, would be considered a Greater-Scope Villain of sorts as she is completely incapacitated until the final battle.
The Fire Emblem series is home to quite a few per game.
Fire Emblem: The Blazing Blade (formerly titled just Fire Emblem in the English release) first focuses on Lundgren, as he's trying to kill Lyn so he can rightfully ascend to the throne of Caelin, but he's just the villain in the prologue. After that, there's Lord Darin, but the actual wirepuller is the Dark Druid Nergal.
Fire Emblem: The Sacred Stones features the Demon King, Formortiis, as the main enemy. He had been defeated by the five heroes many years ago, but he has been revived due to Lyon's creation of the Dark Stone from Grado's sacred stone. While indirectly responsible for Grado's military ambitions, and all that followed it, he is directly responsible for the appearance of monsters across Magvel.
Fire Emblem: Path of Radiance stars Ashnard, king of Daein, as the primary antagonist. He desires a world in which the strong dominate the weak, and he seeks to use Lehran's Medallion to awaken a Dark God and gain power. He is the final boss, and most of the earlier bosses are working for him. This includes the Four Riders, most notably the Black Knight.
Fire Emblem: Radiant Dawn mainly has Duke Lekian, who masterminds many of the events, but the game is divided into four parts, each part having its own big bad. In Part I, the primary antagonist is Jarod, a Begnion general who seeks to suppress the Dawn Brigade's uprising in Daein. In Part II, it is Lord Ludveck, who wants to displace Queen Elincia as ruler of Crimea. Part III is unique, in that you alternately play as opposing armies; it could be considered Micaiah, or Ike, but it would better be considered Lekain himself, who orchestrated Pelleas' signing of the blood pact and forced him into a war he had no dog in. In part IV, the true antagonists of the entire Tellius saga are revealed to be Sephiran/Lehran, the seemingly kind priest who was manipulating both Ashnard and Lekian, and Goddess Ashera, the evil and order-obsessed counterpart to Yune (the supposed Dark God Ashnard wanted) who seeks to destroy the world, which she has deemed irredeemable, at the urging of Lehran.
Fire Emblem Awakening has Grima, the fell dragon. In the future, Grima's killing Chrom ushered in an age of darkness and brought mankind to the brink of extinction. To prevent this, the children of Chrom and his allies, led by Chrom's daughter Lucina, used Naga's power to travel back in time to prevent Grima's awakening. It is later revealed that the Avatar was created to be a vessel for Grima - and that Grima, still possessing the Avatar from the bad future, also came back to the past, following Lucina's army to ensure his own existence.
On the Birthright route, Tin Tyrant Garon is the singular main villain you must defeat, although his last words hint at a greater evil lurking in the shadows.
On the Conquest route, Garon is part of a Big Bad Ensemble with Hero Antagonist Ryoma, as you must conquer Hoshido and defeat Ryoma in order to bring the war to a close and then kill Garon to bring peace to the land. After they're dead, Takumi is resurrected by an unseen greater evil and becomes the Final Boss, having become hell-bent on killing Corrin and razing Nohr to the ground.
On the Revelation route and for the game overall, Anankos is responsible for every bad thing that happens in all three routes and is the main enemy who must be destroyed.
Fire Emblem: Three Houses initially sets up a Big Bad Duumvirate of the Flame Emperor (who is actually Edelgard von Hresvelg) and Thales, leader of "those who slither in the dark" (who spends much of the game impersonating Lord Volkhard von Arundel). Between the two of them, they're the cause of almost all the bad things the happen in the game, but the truth of the situation is more complicated. Thales is the one who made the Flame Emperor what they are and caused their Start of Darkness while they serve as his Dragon-in-Chief who does most of the work and is the more visible antagonist while he remains hidden in the background (due to being the Emperor of Adrestia while the very existence of "those who slither" is a secret to most people). However, the Flame Emperor actually hates Thales and plans to betray him and his faction as soon as they accomplish their mutual goals. Which one takes more prominence depends on the route you pick:
In Azure Moon, Edelgard is the single clear-cut Big Bad for the whole route. You actually do face and kill Thales in this route, but he dies before her and you never learn his true identity or importance. This is ironic since some of his past deeds that Edelgard had no involvement in are very important to the story of this route, but you don't learn the full truth about them.
In Verdant Wind and Silver Snow, Edelgard is The Heavy for most of the route, leaving Thales as the sole villain after their death. However, he's not actually the final boss of either route, as there's one more battle after you fight him. On Verdant Wind, "those who slither in the dark" succeed in resurrecting the Predecessor Villain Nemesis, who fights you in one last battle alongside The Remnant of "those who slither". On Silver Snow, Rhea goes insane from overusing her powers and forces you to Mercy Kill her (unless you got an A-support with her, in which case she survives).
In Crimson Flower, on the other hand, you side with Edelgard, so the Big Bad is instead Archbishop Rhea, while "those who slither in the dark" are reduced to being defeated offscreen in the epilogue.
In theory, Thales is the closest thing to the game has to a single Big Bad overall and is the only one to be an antagonist on all four routes, but you can make the case that the real "Big Bad" of the game is the ancient conflict between the Agarthans (the ancestors of "those who slither in the dark") and Nabateans (of whom Rhea and her followers are the last), and the Cycle of Revenge between them that has perpetuated to the present day. Almost every problem in the setting is a result of their conflicts, and every route's ending results in those who remain on both sides either dead or having lost their power.
Book 1 focuses on Veronica, princess of the Emblian Empire.
Book 2 starts off with a Big Bad Duumvirate between Veronica and Surtr, king of Múspell, but Surtr betrays her and becomes the sole main villain from that point forward. Veronica, for her part, has a HeelFace Turn at the end of the book.
Book 3 focuses on Hel, ruler of the land of the dead.
Book 4 focuses on Freyja, ruler of Dökkálfheimr, the realm of nightmares.
Book 5 focuses on Fáfnir, the once-kind ruler of Niðavellir who has gone insane and now hungers for conquest.
Fire Emblem Warriors has Velezark, the evil Chaos Dragon of legend that feeds on dimensions and seeks his resurrection, no matter the cost.
Five Nights at Freddy's 4 has the Brother, who bullied the minigame protagonist and accidentally killed him by stuffing him into Fredbear's mouth, giving us The Bite of '83. He is also connected to the nights, and maybe even the one who has them.
Forest of Drizzling Rain: The Kotori Obake is a malicious Youkai who kidnaps children who step foot in her forest, and Shiori must rescue Sakuma from her and escape her to avoid becoming her next victim.
Forever Home: The rogue Tren general and main antagonist of the game, Barclyss, is determined to wipe out all life on the planet because he believes life is meaningless. To that end, he slaughters countless people to turn them into undead soldiers and later uses an orbital fortress, Affliction, to blast the planet's surface into oblivion. While he's not the leader of his country, he's the biggest threat in the story and even the actual leader of his country teams up with the heroes to stop him.
Forgotten Worlds has the Celestial Emperor Bios, a powerful being bent on taking over all life on the universe, one planet at a time.
The DSiWare game entitled Foto Face: The Face Stealer Strikes has the professor as the antagonist, though the description of the game mentions the professor as the Face Stealer. The professor copies your face and then causes you pure hell by wrecking havoc, causing some to blame you, while some are working for the professor, and the remaining others don't know what the heck they are doing, attacking you for no reason. However, six of the characters are not evil. Anyway, you have to chase down the professor and fight him.
Friendship: Kayako, friend of Risa and Mio, is the one responsible for Mio's disappearance, as she killed both her and her mom and is hiding Mio's body for herself; meanwhile, Mio's abusive mom haunts their house as a spirit, and is the most direct danger to Risa.
Fighting Force Has Zeng, who plunged the world into chaos just to fulfill a prediction of the world ending.
In the Gears of War series, Queen Myrrah is the leader of the Locust Horde and the overall main antagonist of the original trilogy as a whole, with RAAM being The Dragon and The Heavy in the first game, and Skorge being The Dragon and The Heavy in the second. Myrrah herself takes center stage as the main antagonist in the third game.
The second trilogy starts off with "The Speaker", a leading member of the Swarm, The Remnant and the evolved form of the Locusts, as the nominal main antagonist of the fourth game, and the Swarm Queen Reyna Diaz, daughter of Myrrah emerges as the leader of the Swarm in the fifth game.
Genshin Impact has a Big Bad Ensemble between the Tsaritsa (the Cryo Archon and the mastermind behind the Fatui) and the Traveler's Sibling (the leader of the Abyss Order). Overshadowing both of them, however, is the Unknown God in the intro who serves as the catalyst for the Traveler's journey to begin with and may in fact also be responsible for corrupting the Sibling.
Ghost Trick has a Big Bad Duumvirate between Commander Sith, leader of a foreign espionage organization and Yomiel, the Manipulator seeking vengeance by using his ghost powers to manipulate and kill those he blames for ruining his life, as well as being the real man in red instead of Sissel. They've made a deal of mutual benefit to wipe out all the people who knew of Temsik, but each of them has a separate agenda, and it ends with Sith double-crossing Yomiel.
Ghoulboy has The Goblin King, who allows monsters to roam the land of Gunzabar freely, and kidnapped Thulgar's dad in hopes of stopping a prophecy that would end in the king's downfall.
The first game, The Broken Seal, has the trio of Saturos, Menardi, and Alex. The former two are Mars Adepts that lead the original effort to break the seal on Alchemy and bring it back to the world of Weyard, though Saturos is the dominant of the two. The latter is a former Mercury Clan member who betrayed the group and joined up with the other two because he shares their goals.
The second game, The Lost Age, has Alex again, this time joined by the pair of Mars Adepts Agatio and Karst, who seek to continue the work of Saturos and Menardi by lighting the four Elemental Lighthouses and restoring Alchemy to the world, and avenge their deaths at the hands of Issac, though Agatio is the dominant one of the pair, and It's Personal for Karst, Menardis younger sister.
Grand Theft Auto V: Devin Weston and Steve Haines, with Devin having more direct influence.
Gravity Rush has has The Darkness for the series as a whole.
The Great Gaias: Grindelwald Maultor, who is really the dark god Malviticus, establishes the empire of Validus to wage war against the elves and claim the Hourgem of Valnyr, which he plans to use in order to rewrite history in his favor. After he's sealed in the Tower of Illyrium, his servants manipulate many nations to unseal him, resuming his plans to take over all of Tenat and the Celestial Realm.
The Guided Fate Paradox has Satanael Kyogoku, who has felled entire parts of Celestia before the start of the story. The focus of the game is for Renya Kagurazaka to become strong enough to fight him.
All Guild Wars campaigns have Big Bads of some sort, except perhaps Prophecies (which has several evil groups). The Nightfall campaign also makes Abaddon the big bad of the first three campaigns.
Lou the Devil in the Guitar Hero series tries to get aspiring rock-stars to sign his contract so he would get possession of their souls, and also kidnaps the God of Rock in order to get an artifact to drain audiences of their souls.
Guilty Gear has That Man, who created the Gears, who in turn have wreaked havoc on the world. He's a pretty ambiguous guy (no one even knows his name) and not much is known about him or what he's planning. It's subverted however, when he is revealed in Xrd -Sign- to have been Good All Along, trying to stop the Kill All Humans plan of the real villain, Ariels.
In Half-Life, and its expansion packs Decay, Blue Shift, and Opposing Force, the Big Bad would have to be the Nihilanth, the creature that was maintaining the rift all along, while acting as the telepathic commander of the entire Xenian invasion force.
In Half-Life 2 and its Episodes, it's Wallace Breen, former administrator of Black Mesa and the human ruler of Earth under the Combine who commands Les Collaborateurs. However, with Breen's death at the end of the game, the two episodic expansions have his superiors, the Combine Advisors, take full control with a vengeance. You focus on breaking the remnants of the Combine forces on Earth and keeping them from opening a portal back to one of their home dimensions.
The closest thing Halo: Reach has to a Big Bad is the unnamed Elite Field Marshal who seems to be leading most of the Covenant ground troops that the player personally fights (specifically, those of the Fleet of Valiant Prudence).
Halo Wars has Arbiter Ripa 'Moramee. While subordinate to the Prophet of Regret, Ripa is a much more authoritative and physical threat.
Hand In Hand: ???, the shadowy figure chasing the two heroines around in Momoyama Academy, is one of the spirits of the three kokeshi dolls, who kill anyone who removes the dolls from the shrine the heroines happened to be there when the dolls were stolen. Or so it seems, but it turns out to actually be a bank robber who got himself trapped in the school, though there are hints that the spirits may have been involved after all.
A Hat in Time is divided into chapters each with their own set of Arc Villains to deal with like the Mafia Boss in Mafia Town and The Snatcher in Subcon Forest, but the real Big Bad of the game is Mustache Girl, a Well-Intentioned Extremist who is so overzealous about ridding the world of bad guys that she's willing to steal all of Hat Kid's Time Pieces and alter the entire world under her rule. However, she is not very prominent until the final chapter of the game and is mostly out-of-focus for the remaining chapters, with only vague hints that she influenced some of the plot from behind the scenes.
Atticus Thorn in The Haunted Mansion.
Heavenly Sword: The Raven Lord, the spirit of a warlord who corrupted Bohan into villainy to get ahold of the Sword.
Fleeing the Complex: Dimitri Johannes Petrov is the warden of the Wall, a maximum-security prison that Henry is trying to escape from.
Completing the Mission: The Toppat Clan returns as the main villain of the game as it centered around them building a rocket in a secret jungle base in order to launch the remaining Toppat members to the space station which renders them untouchable by the government and depending on the paths Henry took in the previous game, will either find a way to sabotage them or ensure they launch successfully. However, who the leader of the clan is dependant on the route taken in Airship. If Rapidly Promoted Executive or Pure Blooded Thief ending are chosen, then Reginald remains as the leader. In Ruthless Bounty Hunter where Reginald has been arrested, then the Right Hand Man becomes the leader while in Government Supported Private Investigator where both are arrested, Sven Svensson becomes the new leader of the surviving Toppat members.
Hitman 3 concludes the fight against Providence, with the Shadow Client/Lucas Grey who is 47's childhood friend Subject 6 as an ally to 47, while the Constant, Arthur Edwards has betrayed his superiors, the Partners, who lead Providence. The Partners are relegated to Disc-One Final Boss status, and the Constant takes over as the leader of Providence and therefore is the unambiguous main villain.
Each game in the Homeworld franchise has a pretty clear-cut example:
The Taiidan emperor from Homeworld. Spends most of the game in the shadows, but according to the backstory for Homeworld: Cataclysm, he was a twisted, ruthless mess of a ruler who managed to stay on his throne by cloning himself, and who ordered the destruction of a planet — namely YOURS — mostly as a publicity stunt.
The Beast infection is the primary antagonist in Homeworld: Cataclysm, and towards the end of the game it is controlled by The Nagarrok, an ancient alien vessel that picked up the Beast infection in Hyperspace. It even has its own Dragon in the infected lower half of the Somtaaw Command Ship.
The nomadic Vaygr from Homeworld 2 are led by Makaan in their attempts to conquer the galaxy. Unusually for a Big Bad, he's killed before the end of the game, and you spend the last mission fighting off what's left of his fleet as they try to bomb your planet.
The K'Had Sajuuk, leader of the Kiith Gaalsien, in Homeworld: Deserts of Kharak, who seeks to stop the Kharaki space program and destroy the Coalition to bring peace to and protect Kharak.