In Ace Attorney, Phoenix Wright has Miles Edgeworth for most of the first game, although their relationship becomes exponentially more friendly after Wright defends Edgeworth. In the second game, Phoenix has Franziska von Karma, although Franziska eventually admits that she wanted to defeat Phoenix so she could prove herself to be a better prosecutor than Edgeworth. In the third game, Phoenix has Godot, who has a grudge against Phoenix for failing to protect Mia Fey.
Phoenix eventually gets a new arch-enemy in the fourth game of the series, that person being Kristoph Gavin, who was the responsible for making Phoenix lose his badge. Phoenix, in turn, spent seven years working to change the legal system just so he could have a chance to bring Kristoph to justice through Apollo.
Assassin's Creed Origins has a twofold example. Flavius Metellus / The Lion is the Arch Enemy for Bayek of Siwa since he was responsible for causing him to accidentally murdere his son Khemy while his second-in-command Lucius Septimius / The Jackal is also a personal Arch Enemy for Aya.
Jack has Frank Fontaine, his adoptive father who plays Jack like a fiddle throughout most of the game, forcing him via brainwashing and deception to assassinate his real father, before sadistically leaving him to die.
Subject Delta has Dr. Sofia Lamb, who kidnapped his Little Sister at the start of the second game and tried to force him to kill himself.
Charles Milton Porter from the second game's "Minerva's Den" expansion pack has Reed Wahl, his former partner who betrayed him and tried to seize total control of The Thinker.
Comstock is this to both Booker and Elizabeth in Infinite. Elizabeth because he is sort of her father, but also not (it's complicated), and he had her locked away in a tower for years, and later had her kidnapped and tortured so as to harness her power. She eventually makes it her mission to kill all versions of him across all realities. Booker because Comstock technically is Booker, or at least an alternate universe version of him that became a totalitarian and psychotic dictator. He also serves as this to Daisy Fitzroy, who starts an uprising to rebel against the society of bigotry and slavery that he has created and fostered.
Elizabeth could also be said to have The Songbird, who often comes across very much like an abusive ex-boyfriend.
Resident Sadist and Troll, Yuuki Terumi manages to be this to damn near the entire cast. That's right, he's almost everyone's arch enemy, which says a lot on how much of a scumbag he is for getting on so many people's shitlist. Notable ones include his former teammates whom he helped saved the world with (against his will mind you), Rachel who continuously puts in motions to stop him, and finally Ragna, who's life he has ruined to the point where Ragna's motivation for most of the series is to see him dead. Terumi for his part just sees them all as his favorite targets to screw with and rarely takes them seriously befitting his trolling nature. He even manages to weaponize this as the enmity he invokes in people is what keeps him alive and empowers him, mostly from Ragna. It's ultimately Ragna who does him in however, and Terumi even shows him some begrudging respect in their final confrontation.
There's also the siblings Ragna and Jin And by extension, Hakumen to a lesser extent. Jin's made it his purpose in life to kill Ragna because of the threat he poses as a potential reincarnation of the Black Beast that will bring the world to ruin. Ragna acknowledges this and swears to settle things with Jin when everything is said and done resulting in numerous examples of Rivals Team Up throughout the series. They do ultimately bury the hatchet and make up in the end, albeit not after one last fight between them to settle things.
Carl's greatest foe as of Continuum Shift is his father Relius, who added his own daughter (Carl's sister) Ada's body and soul to the Nox Nyctores Nirvana and used the information he gleaned from that experiment to create a superior puppet — using Carl's mother Ignis.
Bang used to consider Jin to be his Arch Enemy, but thanks to Character Development has moved passed this. He now considers the system behind the NOL itself that ordered the attack on Ikaruga to be his Arch Enemy.
Even Taokaka has one. She and Arakune frequently come to blows since he terrorizes the Kaka clan village and she is its protector.
Tsubaki becomes her former best friend Noel's Arch Enemy thanks to Terumi's influence, the trauma of losing her sight to Izayoi, and her deep-rooted jealousy of Noel over her being chosen to be by Jin's side. Unlike most examples, they make up eventually.
Relius Clover has a secondary enemy in Valkenhayn, as the two have a long-standing rivalry prior to the Dark War; this was suspended when Relius fell into the Cauldron the day the Black Beast emerged, but has reawakened with Relius' re-emergence.
Dracula has the Belmont clan (as well as the Belnades and Morris families) as his running archenemies in the Castlevania games.note The Belmonts have to destroy Dracula. They are fated to do so. Dracula makes it easy by actively pissing off the current Belmont. The Morris family, however, has no such problem with Dracula, instead being chosen by the Belmont clan to defeat the vampire out of necessity when they can't. It's a confused mish-mash, but the end result is that Dracula has the Belmont clan as his arch-enemies, but it's one-way and he should really stop exacerbating the situation.
According to the prequel Lament of Innocence, Dracula's real Arch Enemy is Sara Trantoul, whose soul empowers the Vampire Killer.
In the Lords of Shadow reboot series, Dracula and Satan himself are mortal enemies. In fact, so long as the vampire lord exists and walks the Earth, Satan doesn't dare leaving Hell to conquer the human world. When Dracula is revived in modern times, Satan sends out his acolytes and minions to dispose of his hated enemy before he can return to Earth.
The end of the world be damned, nothing will stop GDI and Nod from attempting to destroy the other, an alien invasion bent on killing everyone is only grounds for a short ceasefire, which doesn't even last halfway through the invasion.
Crash Bandicoot — Crash has Doctor Neo Cortex. In the same series there is also the rivalry between sentient voodooo masks Aku Aku and Uka Uka.
Coco has this with N-Gin and Nina, Cortex's dragon and niece respectively.
Bob Page and Walton Simmons to JC Denton in Deus Ex.
Lord Regent Hiram Burrows, Daud and Admiral Havelock to Corvo Attano in Dishonored.
Delilah serves as a series-wide nemesis for the Kaldwin family due to being an illegitimate sister of Jessamine who was tossed to the streets and forced to scrounge through life from the gutters. She served as the central villain of Daud in his DLCs, but refocuses her hatred towards Emily and Corvo in the second game.
The Grey Wardens and the Darkspawn of Dragon Age: Origins. The Grey Wardens were founded specifically to prevent the Darkspawn from destroying Thedas and will do anything to accomplish this task. The feeling is mutual during Blights — Archdemons will go out of their way to kill the Grey Wardens once they can sense their location since they know that only Wardens can permanently destroy them.
Each respective origin (except the Mage and Dalish) end with the Warden gaining one of these. Arl Rendon Howe for the Human Noble, Prince Bhelen for the Dwarf Noble, Jarvia for the Dwarf Commoner and Vaughn for the City Elf.
Teyrn Loghain serves as this for Alistair. Loghain earned Alistair's hatred for his desertion at the Battle of Ostagar, leaving the King and the Grey Wardens to die. Loghain meanwhile fears the threat that Alistair poses to his Regency, since as bastard son of King Maric, Alistair is the closest legitimate heir to the throne.
Shale considers Birds to be her personal nemesis, having endured thirty years of being covered by their droppings whilst frozen as a statue in Honnleath. Indeed, one of the first thing she does after being reawakened by the Warden is to stomp on a chicken and according to Dragon Age II, the pigeon population of Ferelden has mysteriously dwindled since the end of the Blight.
In the sequel, Dragon Age II, some of Hawke's companions have archenemies. Danarius for Fenris, Bartrand for Varric, and Castillon for Isabela. Meredith and Orsino are also mutual archenemies. Anders becomes one for Sebastian after the former destroys the Chantry.
Dragon Quest V: The Hero has a personal grudge against Bishop Ladja. It becomes mutual later in the game, to the point where Ladja is focused on destroying him in the most emotionally torturous way possible.
Dragon Quest IX:The Supreme Sage sealed the Tyrannosaurus Wrecks in a book to prevent him from tearing the world to pieces.
Mordegon to the Luminary, Rab, Jade, and Hendrik. For Rab and the Luminary, he orchestrated the fall of Dundrasil and was responsible for the death of King Irwin and Queen Elenaor, the Luminary's parents and Rab's daughter and son-in-law. For Jade, the fall of Dundrasil caused her to be separated from the Luminary and Mordegon possessed her father, King Carnelian. For Hendrik, Mordegon caused the fall of the Zwaardsrust, Hendrik's birthplace, and he corrupted his friend Jasper and turned him against all of humanity.
Calasmos to Yggdragon. The injuries she received from her battle with Calasmos would cause her to become the World Tree Yggdrasil and she would later choose Erdwin as her champion to defeat Calasmos.
Mannimarco and Molag Bal to the Soulless One in Online.
Additionally from Skyrim, General Tullius (leader of the Imperial forces) to Ulfric Stormcloak (leader of the rebel Nord forces) in the Civil War questline.
In the series' lore, the Ka Po' Tun "tiger folk" and Tsaesci "snake vampires". Both are races native to the continent of Akavir. When the Tsaesci attempted to "devour"note There are conflicting sources as to whether this meant literal eating or was a metaphor for enslavement. Akavir's native dragons, which the Ka Po' Tun revere, the two races went to war. The Ka Po' Tun were victorious, but it left both nations weakened and the remaining dragons dead.
In the series' backstory, the ancient Yokudans (ancestors of the Redguards) and the Sinistral Mer (Left-handed Elves). The two sides fought a devastating war which would render the Sinistral Mer extinct. To this day thousands of years later, the Redguards refuse to speak of them for doing so tends to "darken their days." The modern Redguards have a long rivalry with their neighboring races in High Rock, including both the Bretons and Orcs. Though they have formed an Enemy Mine with each in the past when circumstances required it, they've spent far more time battling against them.
The Altmer (High Elves) and Maormer (Sea Elves) have an ancient, heated rivalry. Throughout the 1st and 2nd Eras, Maormer forces, personally led by their "Undying Wizard King" Orgnum, were said to "ravage" the coastlines of the Summerset Isles. In the 3rd Era, the Maormer allied with the "Wolf Queen" Potema who was attempting to usurp the throne of the Septim Empire. However, when the Maormer fleet attacked, it was swallowed whole in a magical storm conjured by the PsijicOrder. The Maormer were so devastated that it is said they will never seriously threaten Tamriel again.
The Altmer also have another ancient and heated rivalry with the Sload, "slugmen" native to the archipelago of Thras to the west of Tamriel. When the ancient Aldmer, ancestors to the modern races of Mer, came to Tamriel, the Sload claimed the Summerset Isles. The Aldmer fought them and chased them off, but the Sload have remained their enemies ever since.
The Aldmeri Dominion (led by the aforementioned Altmer) has long been the most powerful rival to the various Cyrodiilic Empires throughout Tamriellic history. It took Tiber Septim using the Numdium against the Dominion for mankind to finally conquer the Altmer homeland, with the Altmeri army decimated and their capital city captured in less than an hour of fighting. When the Septim Dynasty ended following the Oblivion Crisis, the Altmer wasted no time in reforming the Dominion and striking back at the remnants of the Septim Empire, reigniting the rivalry.
The Thalmor, a extremist religious sect that took power within the Aldmeri Dominion, are one toward the Psijic Order, an ancient and powerful magical monastic order based on the isle of Artaeum within the Altmeri homeland of the Summerset Isles. The Order is essentially a living Berserk Button for the Thalmor, as they're an Altmer organization with immense magical knowledge but absolutely will not tow the Thalmor line. The second disappearance of Artaeum in the 4th Era is believed to be directly related to the rise of Thalmor influence in the highest levels of the Aldmeri Dominion government.
In the early 1st Era, the Falmer (Snow Elves) became this to the Atmorans (ancient proto-Nords) when the Falmer slaughtered and burned the Atmoran city of Saarthal. Ysgramor, one of the Atmoran leaders, returned to Atmora and raised an army of 500 of Atmora's greatest warriors and led a Roaring Rampage of Revenge that nearly drove the Falmer to extinction.
The Khajiit and Bosmer (Wood Elves) have a long and violent history. Their homelands share a border and disputes are common. One such dispute quickly escalated into the Five Years War, during which the Khajiit took control of some Bosmeri territory and continued raiding deep into Valenwood. It took the Bosmer invoking the Wild Hunt, in which some of them irreversibly transform into nightmarish beasts, to finally end the war.
In Tamriel's earliest history, there existed a race of Bird Men native to the islands that would become the Imperial City Isle in central Cyrodiil. They were lost to history, along with whatever they may have called themselves, at the hands of "cat demons," which modern scholars believe were the ancient Khajiit.
Hagravens and Spriggans are seen to have a strong hatred of one another. Hagravens are a flightless harpy species known for being powerful witches who seem to have life itself as an enemy. This obviously puts them at odds with the Plant People Spriggans, who are "Nature's Guardians" and come into frequent conflict with Hagravens wherever they are found. Hagravens are fond of dotting their lairs with decorative Spriggan heads and parts, including their Taproots.
Arkay, the Aedric Divine God of Life and Death, and Mannimarco, the "God of Worms" and patron of necromancers. Quite logical, as Mannimarco actively works to upset the balance that is Arkay's divine duty to maintain.
Mannimarco also has a fellow "mortal" arch-enemy in Galerion, the founder of the Mages Guild. Both were former students of the Psijic Order who left after disagreeing with the Order's policies. (Galerion believed that magic should be freely taught and shared, not kept in the hands of a select, elite few while Mannimarco openely practiced The Dark Arts, including Necromancy.) The organizations they would found (the Mages Guild and the Order of the Black Worm) would be rivals for centuries.
Arkay. The two have a strong rivalry and Molag Bal created the first vampire specifically to upset Arkay's balance of life and death.
Molag Bal has another in Boethiah, a fellow Daedric Prince whose sphere includes Plots, Deceit, Conspiracy, Murder, Assassination, Treason, Unlawful Overthrow of Authority, Betrayal. The two constantly snipe at one another, attempting to steal or murder each other's followers. Though no reason has ever given for their rivalry, it is a prominent example of the (generally considered) "evil" Daedric Princes averting Evil Is One Big, Happy Family. Molag Bal also doesn't get along well with MehrunesDagon.
He and Meridia hate each other as well, since she finds him utterly disgusting and he considers her a nuisance.
He is also implied to antagonize followers of Stendarr specifically. Since Stendarr is the God of Mercy and he is the God of Domination, it seems Bal enjoys seeing just how capable Stendarr is of protecting his faithful.
Ebonarm, a god of war worshiped in the Iliac Bay region and held in especially high regard by the Redguards, is a noted adversary to all Daedric Princes (except for Sheogorath, for reasons not explained).
Hermaeus Mora, the Daedric Prince of Knowledge, has two. The aforementioned ancient Nord hero Ysgramor was one and, according to old Nordic legends, outwitted Mora regularly. The Skaal of Solstheim are the other, and have managed to keep their secrets safely hidden from him. The plot of Skyrim's Dragonborn DLC is revealed to be an elaborate scheme by Mora to get them.
Sheogorath, the Daedric Prince of Madness, has one in Jyggalag, the Daedric Prince of Order. As revealed during the events of the Shivering Isles, it turns out to be an Arch-Enemy Within scenario. Sheogorath is the Person Shaped Can Jyggalag was sealed inside of. The events of the expansion's main quest see the two split.
From the backstory, Pelinal Whitestrike, the legendary hero of mankind/racistberserker, had one in the Ayleid leader, Umaril the Unfeathered. Part of it stems from Pelinal realizing that he was a sort of indirect creator of Umaril, since if it were not for Pelinal's deeds then Umaril would not be famous. (In Oblivion's Knights of the Nine expansion, you, as "Pelinal Reborn", get to finally defeat a resurrected Umaril once and for all.)
Wulfharth Ash-King, the ancient King of the Nords who has died and come back to life at least three times, despised the Dunmeri Tribunal of Morrowind and wanted to see them destroyed. After initially aiding Tiber Septim in his conquests (as the mysterious Underking), Wulfharth feels betrayed when Septim agrees to the Armistice with Morrowind, seeing it as a validation of the Tribunal religion, and leaves Septim for a time.
Empire Earth's 2nd campaign focuses on Great Britain and France's feud through the ages.
Terry had a personal vendetta with Geese for the murder of his adoptive father, Jeff Bogard. The original game concluded with Terry exacting his revenge by besting Geese and sent him plummeting from atop the Howard Building, to his death. Though in the King of Fighters continuity, Geese survived the fall and returned to antagonize Terry once again.
Real Bout: Fatal Fury is a retelling of the original game's events, which concludes with Terry attempting to save Geese at the end of their duel. But Geese refused to accept out of spite and chose to fall to his death. This time, it was for keeps.
Fate/stay night: Shirou gets two, and which he comes into conflict with depends on what route you're in:
In "Unlimited Blade Works" Shirou's possible future self Archer is the antithesis of his ideals, yet embodies them: He sold his soul into servitude as a guardian for eternity after death because he all he wanted was to save people, but instead he was forced to watch humans suffering forever while being unable to save anybody or even end his own existence. Hating the ideals that betrayed him, he wants to crush Shirou's belief in being a hero of justice and kill his past self so that he can be released from being a guardian. Shirou in turn refuses to stop believing in his ideal, and fights to prove that he is right.
In "Fate" and "Heaven's Feel" Shirou's Arch-Enemy is Kotomine Kirei, who is exactly like Shirou in that he has no real sense of self. At the same time they are irreconcilable opposites because Kotomine finds joy in the suffering of others while Shirou finds his in saving them. In "Fate", Shirou's conflict with Kirei gets personal at the end when he finds out that Kirei was responsible for the disaster ten years ago that changed his life, and caused his father Kiritsugu's death. However in "Heaven's Feel" where this does not come up Shirou figures out that the reason for his instinctive dislike of Kotomine was that deep down he liked Kotomine, but could not admit it to himself. Nevertheless they have no choice but to fight each other over their opposing goals.
He was also arguably Rin's Arch-Enemy, since he stabbed her father in the back and orchestrated the eventually fatal strangling of her mother, which she discovers in "Unlimited Blade Works". In both "Fate" and "Unlimited Blade Works" she gets her revenge on him, although indirectly.
Saber's Arch-Enemy in the "Fate" route is Gilgamesh, who opposes her quest for the Holy Grail because he wants her for himself. He is also the negative image of her as a ruler, since he sacrificed his kingdom for his own benefit while she sacrificed herself for her kingdom.
Initially subverted, since Sephiroth had little regard for Cloud, except as a pawn by which to obtain the Black Materia he needed to summon Meteor. It wasn't until the very end when Cloud defeated him, that Sephiroth took him seriously as an enemy.
The prequel Crisis Core, starring Clouds old friend Zack Fair, introduces Genesis Rhapsodus as a prototype Sephiroth with a clone army. He consistently antagonizes Zack throughout the game and takes the Arch-Enemy role as Zacks answer to Clouds Sephiroth.
The prequel Dissidia 012 reveals the Emperor is actually more an Arch Enemy to the Final Fantasy X cast as an Expy of Seymour — he manipulates Tidus and Jecht into fighting for the sake of his schemes and isn't pleased when Yuna tries to get the two to work out their differences peacefully. In a less direct example Exdeath is the enemy of the Final Fantasy IV cast, being Kain's designated rival and his death in that cycle being caused by Golbez disrupting his control over the Manikins so Kain can get past them and challenge Exdeath. Also puts a new spin on the scene of Exdeath accusing Golbez of treachery and Cecil protecting him.
The Final Fight series has the Mad Gear gang as collective arch-enemies for nearly all of the playable characters. Their first incarnation kidnapped Jessica, Haggar's daughter and Cody's love interest, while their second incarnation took revenge by kidnapping Rena and Genryusai, who are not only the fiancee and mentor of Guy, but also the sister and father of Maki. In the third game, the Skull Cross gang are arch-enemies for Dean as they killed his family. In Streetwise, Father Bella is the arch-enemy of Kyle as he is actually the brother of the first leader, Belger, who was killed by Kyle's brother, Cody. In the Street Fighter Alpha trilogy, Sodom and Edi. E are treated as the personal arch-enemies of Guy and Cody, respectively.
In Five Nights at Freddy's, the Purple Guy, William Afton, found himself at odds with several characters throughout the series most prominently being the Puppet who in the sixth game is revealed to be the daughter of the Cassette Man who is explicitly stated to be Henry from the novel series. In the fifth game, he manages to also earn the ire of his son Michael after tricking him into going to the underground factory leading to him getting gutted by Ennard who then used his skin to escape.
In God of War, Kratos had three different arch-enemies over his life:
The Barbarian King Alrik was his earliest rival, responsible for dealing Kratos his first near-defeat. The prequel comic reveals that they constantly fought each other before the series. It was this near-defeat that drove Kratos down his Start of Darkness, as he pledged Ares to save him and became his enforcer.
Ares, the God of War, for tricking Kratos into killing his own wife and daughter to so they wouldn't burden him. Kratos spent the following decade trying to atone for this horrible deed as well as seeking to pay back Ares, which he gets the chance in the first game.
Zeus himself after he betrayed and killed Kratos in God of War II. One could say that no other enemy, not even Alrik or Ares, commands as much of Kratos' time and energy as the King of the Gods, given that Zeus wants to kill Kratos to restore order to the world, and Kratos is willing to destroy Zeus and Olympus in order to get his revenge.
Dimitri Rascalov, Ray Bulgarin, and Darko Brevic to Niko Bellic in Grand Theft Auto IV. Dimitri is Niko's most recurring and personal enemy throughout the entire game, being responsible for selling out Niko to Bulgarin, burning down the home of Niko's cousin Roman, and later kidnapping the aforementioned Roman. Bulgarin is a russian mob boss and human trafficker who blames Niko for the destruction of one of his freighters and the theft of his diamonds, and is The Man Behind the Man to Dimitri. And Brevic caused the deaths of 12 of Niko's friends, and hunting down Brevic is one of Bellic's main reasons for coming to Liberty City in the first place.
From Grand Theft Auto V: Michael has Steve Haines and Devin Weston, Franklin has Stretch, and Trevor has Wei Cheng and the Lost MC. The Golden Ending of the game has the three helping each other eliminate the others' antagonists in order to clean loose ends without leaving a trail.
The UNSC and the Covenant, which is specially represented by the Spartans and the Elites respectively (though the latter take the rivalry much more personally). They've been fighting for decades, with humanity trying to stave off extinction at the hands of the Covenant. But later, it's revealed that humanity as a whole has a far more deadlier archrivalry with the Flood, a highly virulent and intelligent parasite dating back to the time of the Forerunners.
The Forerunner Saga and Halo 4 reveal that the Forerunners themselves were this to a highly-advanced prehistoric humanity, with the modern form of the rivalry represented in the conflict between the Master Chief vs. the Ur-Didact.
The Prophet of Truth and the Gravemind, the leaders of the Covenant and Flood respectively, both consider Master Chief to be their greatest threat. Truth even referred to Master Chief as "the Demon".
Master Chief also has a grudge against 343 Guilty Spark for betraying him in the first game.
The Arbiter has the Prophet of Truth and Tartarus, who betrayed him and attempted to have his race massacred.
Hammerin' Harry: The President of Kuromoku-gumi, Hyosuke Kuromoku, for Genzo. Only one game in the series has not featured the Kuromoku-Gumi and Hyosuke as major villains.
Iji: Asha the Assassin considers himself Iji's Arch Enemy after losing their first fight. Originally, he was only after the bounty on her head (and the fame), but took his loss so personally he dedicates himself to destroying you. Your actions determine whether this feeling is reciprocated, or you can completely ignore him, which actually leads to Asha killing himself in despair.
There is the Toppat clan and the Government, who are arch enemies to each other.
Dmitri, the Big Bad of Complex is this to Henry and Ellie in the Pardon Pals and Toppat Recruits path of Mission.
Henry himself becomes one to Ellie in the Toppat civil warfare path of Mission, due to him leaving Ellie behind at the wall in Complex and her taking over as leader and having most of the Toppat members turn against Henry.
Ultimately, Sora and Xehanort in the Kingdom Hearts series. Sora is the All-Loving Hero, while all the conflict in the games was caused by Xehanort in one way or another.
More specifically, Xemnas would probably be the individual incarnation of Xehanort that claims the title of archenemy to Sora. He seems to get Sora riled up the most easily and has fought him the most out of any of them. He also made the life of his Nobody, Roxas, terrible.
However, Maleficent also serves as this to Sora, as she constantly antagonizes him during his journey.
Riku's arch-enemy is Xehanort's Heartless/Ansem, the Seeker of Darkness. He represents every bad decision Riku made in the first game, stole Riku's body at the end of those bad decisions, and spent a lot of time as Riku's Enemy Within. Not even being purged from Riku's heart is quite enough, as they end up fighting each other all over again in 3D.
The King of Fighters: KOF '95-'97 essentially boiled down to the ongoing blood feud between the series' protagonist, Kyo Kusanagi, and his arch rival/antagonist, Iori Yagami. It lasted until after the events of KOF XI, due to finding a mutual Arch Enemy in Ash Crimson (who, like Bison before him, has that special talent for pissing off near anybody he comes into contact with).
King's Quest: The Black Cloak Society to the Daventry royal family. The extent of which of the series' foes were part of the Society is debatable, but at least four (Hagatha, Mannanan, Mordak, Alhazred) have some kind of tie. The Fan Remake of King's Quest II cranks it up a bit with a designated Arch Enemy, Morgelien (aka "The Father").
Kirby's title character has King Dedede, downplayed in that while Kirby and King Dedede fight from time to time, he is much more likely to team up with Kirby against a common threat or be the victim of Demonic Possession. He has about the same dynamic with Meta Knight, who takes Kirby much more seriously as a Worthy Opponent. Nowadays, the Dark Matter race seems to fit the deal as arch-nemesis better than Dedede and Meta Knight, with many members of the species having fought Kirby across the series; culminating in Kirby Star Allies, where Kirby seems to face off against Void Termina, which is likely the Monster Progenitor of the Dark Matter.
In the original game, Malak and Revan, and arguably a parallel with Saul Karath and Carth Onasi. There is also one with Zaalbar and his brother, Chuundar.
In the second game, The Exile has three: each of the Sith Lords which reflect an aspect of herself. The most prominent is Darth Traya whose fate is bound up with the Exile whether they like it or not.
Legacy of Kain gives us Malek and Vorador in Blood Omen: Legacy of Kain, The Sarafan Lord and JanosAudron in Blood Omen 2: Legacy of Kain, and Kain and Raziel throughout the series. All of these are slightly one sided, though. While Malek had a deep personal hatred for Vorador, Vorador didn't think much of him and for the most part hated his order and humanity in general. Janos hated the Sarafan Lord for holding him prisoner for four hundred years, starving him of blood but the Sarafan Lord's issue was with vampires in general and he considered Janos little more than a tool. Raziel, likewise, hated Kain on a very personal level, but Kain's actions against him were necessary evils. Kain himself had much more personal grudges against Malek and the Sarafan Lord than he did against Raziel, and possibly his true arch enemy was Moebius. And in the end it turns out Kain was the arch enemy of the Elder God, who manipulated people across centuries to try and kill Kain, due to Kain's destiny to become the Scion of Balance, the only being that can destroy the Elder God.
Regardless, each Link is usually educated about the Triforce and how they are fated to face Ganon some way or another. But particularly Link from The Legend of Zelda: The Wind Waker had a grudge against Ganon for kidnapping his sister and Zelda and Link from The Legend of Zelda: Ocarina of Time was the first Link to face Ganondorf for endangering Zelda, killing the Deku Tree, and directly ruining every other society he had to rescue.
Played for Drama in The Legend of Zelda: Skyward Sword. Ganondorf is the reincarnation of Demon King Demise's endless hatred for Link and Zelda, and that continues to haunt them even as they keep reincarnating. The three are bound to fight for eternity. It also turns out that Zelda is the mortal incarnation of Hylia, the goddess who initially sealed Demise, which means she was his original Arch Enemy, not Link.
Midna from The Legend of Zelda: Twilight Princess has Zant, who is revealed to have usurped her throne, turned her into an imp, transformed the Twilight Realm's inhabitants into Shadow Beasts and disrupted the peace in the Twilight Realm.
Commander Shepard in Mass Effect has a lot of powerful enemies: Saren Arterius in the first game, The Illusive Man and Kai Leng in the third game. However, Shepard's archenemies are the Reapers, and (s)he is theirs. They consider Shepard to be the greatest threat they have ever faced, and Shepard is the only thing in existence that has ever made the Reapers feel fear. Notably, they will turn their dreadnought-killing guns away from entire fleets to target Shepard alone.
Harbinger in particular has animosity for Sheperd. Not only is Harbinger the leader of the Reaper Armada, he killed Shepard at the beginning of the second game, and has gone on to personally confront(and lose to) Shepard countless times thanks to his ability to hijack the bodies of his Collectors. Harbinger becomes furious when Shepard ruins his plans to create a Human Reaper, and most of what the Reapers know about Shepard comes from Harbinger. At the end of the Trilogy, Harbinger personally invades Earth, Shepard's homeworld, and nearly kills Shepard with a laser beam.
Garrus Vakarian has Lantar Sidonis, who betrayed his team to the Blue Suns.
Miranda Lawson also has an archenemy in her father, Henry Lawson.
Jack has an archenemy in Cerberus because of what they did to her. She also has a particular hatred for Miranda though after Miranda quit Cerberus, it tones down significantly and in the Citadel dlc, Shepard can convince the two to settle their differences
Samara's nemesis is her daughter, Morinth.
Liara considers the Shadow Broker to be her nemesis.
Zaeed's nemesis is Vido Santiago.
Max Payne has Nicole Horne in the first game, Vladimir Lem in the second game, and Victor Branco in the third game.
This, like every other trope, gets lampooned in Kingdom of Loathing: the player receives a quest from their guild to retrieve an item stolen by their Nemesis. The player wasn't aware that they even had a Nemesis before that.
In the Metal Gear Solid series the main protagonist, Solid Snake is constantly facing of against Revolver Ocelot and/or Liquid Snake, though none of them'd ever use titles as arch-nemesis. Snake used to have Big Boss, but ended up in a coma for the majority of Solid Snake's story arc.
Ridley in the Metroid games, to Samus Aran. This one is personal, since Ridley trashed Samus' home of K-2L and personally killed both of her parents. Ironically, the Metroid manga (which was made by Nintendo) has a brief scene where a 4-year-old Samus, not yet knowing what Ridley has done, tries to make friends with the giant space dragon.
When Samus approaches him, Ridley is watching the chaos and fire his pirates have caused, and actually gets a sad look for a moment when he sees her. Then Samus' mother runs to save her from Ridley, and he promptly goes back to normal and kills Samus' mother in front of her. He later mocks her about how he killed her parents.
Samus also has Mother Brain. While not quite as personal as Ridley, Mother Brain is still one of the most recurring villains of the series, and earns Samus's ire in various ways, most notably killing the baby Metroid. It's somewhat more prominent in the manga, where she played a part in raising Samus, before becoming one of her adversaries, unlike in Zero Mission where Samus says she grew up on Zebes long before Mother Brain was there.
The Monkey Island series protagonist Guybrush Threepwood has constantly thwarted the plans of the Ghost Zombie Demon Statue Pirate LeChuck. Played with in the second game where Guybrush won't shut up about having beaten LeChuck, most people either don't believe it (Or are just sick of hearing about it) and so he gets no respect for it, but LeChuck does very much remember and actively seeks his vengeance.
Mortal Kombat has these all over the board. Liu Kang's Arch Enemy is Shang Tsung, Sonya Blade has an Arch Enemy in Kano, Scorpion has Sub-Zero and Quan Chi as successive archenemies, Kitana has her evil clone Mileena, Jade has Tanya, Raiden has Quan Chi and Shinnok as archenemies, Kung Lao has a nemesis in Baraka, Jax has his in Hsu Hao, Cyrax has his Evil Counterpart Sektor and all of Earthrealm's heroes had Shao Kahn as a nemesis.
In the Portal games, Chell the silent protagonist has the evil A.I GLaDOS. In the second game GLaDOS in the antagonist for only the first half of the game and is replaced by Wheatley as this for the rest of the game.
The feeling might be mutual for Rachet and Clank, as they've faced a wide variety of enemies, but no enemy has been as powerful, dangerous or persistent as Nefarious has.
Resident Evil: Chris Redfield began the series as one of Wesker's subordinates, but once he learned Wesker was a traitor who was secretly an agent of Umbrella, that changed everything. In each of their subsequent appearances, Wesker was cast as the main antagonist with Chris as his chief advisory. Whereas Jill Valentine all but disappeared from the series after RE3 and wasn't seen again until RE5, where she only had a bit part as Wesker's minion. Then promptly dropped out of sight again, after Chris saved her. After Wesker's death, Chris briefly had Carla Radames, the murderer of Chris' entire squad, until she too was killed at the end of RE6. Then he had Lucas Baker from Resident Evil 7 who like Carla killed all of his men before Chris kills Lucas in the Not a Hero DLC.
In Resident Evil 3: Nemesis, Jill Valentine had the titular Nemesis, who made regular attempts on Jill's life throughout the entire game. Nemesis is responsible for the murder of Jill's comrade, Brad Vickers, making Nemesis a very personal enemy for Jill.
Resident Evil: Survivor is an interesting case of the protagonist having multiple possible arch-enemies. In two early parts of the game, you have the option to advance with three possible routes to your destination. The second time this happens, the game assigns you an antagonist based on the route you took, from the possibilities of Vincent Goldman, Andy Holland, or the Commander of the Umbrella Trashsweepers. All three exist in the story (you even talk on the phone with Andy after the first fork), but only your personal antagonist factors into the cutscenes going forward.
The God Wars Dungeon in Runescape would imply that the four Gods involved consider each other Arch Enemies, since even after thousands of years, the 4-way free-for-all is still going on. Saradomin and Zamorak, even though they aren't technically the "Good" and "Evil" Gods.
The Shantae series has self-proclaimed Queen of the Seven Seas Risky Boots for the titular heroine. It started with Shantae foiling Risky Boots' plans in the first game, which led to Risky getting payback in Risky's Revenge, which then led to an Enemy Mine situation in Shantae and the Pirate's Curse. They've since settled down on a Worthy Opponent situation where Risky tries to take over Sequin Land while Shantae tries to stop her.
The U.N Peacekeepers tend to oppose the Spartan Federation, as the Peacekeeper's peaceful and humanitarian ideals clash with the Spartan's brutal Social Darwinist philosophy. The Peacekeepers also tend to find an enemy in the Human Hive, as the existence of a democratic government is entirely at odds with Chairman Yang's collectivist and communist ideology.
The Gaia's Stepdaughters tend to oppose Morgan Industries. To the former, the latter are a bunch of greedy, amoral bastards who'd happily rape the planet for a quick buck. To the latter, the former are a silly Animal Wrongs Group getting in the way of good free market economics. Morgan Industries also often finds an enemy in the Free Drones, as they're seen by the Drones as The Man trying to keep the little guy down to make money.
The Data Angels often oppose the Hive and the Believers, as they see both as societies that are inherently based on restricting access to information by promoting their respective ideas as "The One True Way". And that's really bad.
Omega, one of Eggman's creations, considers him a sworn enemy because he had abandoned him in a base. Needless to say, Eggman doesn't acknowledge him as a threat.
The Soul Series is riddled with several deadly rivalries.
The Soul Edge and the Soul Calibur swords are destined to fight each other until the end of times. Soul Calibur was created specifically to destroy it, but the Soul Edge keep reassembling itself everytime and this has been going on for ages.
Setsuka regards Mitsurugi as her arch-enemy for having killed her master, and notably, her story has nothing to do with the evil swords as she is purely concerned with killing Mitsurugi. She eventually lets go of her revenge.
Taki and her own father-figure and sensei Toki after he became corrupted by an Evil Weapon. An unconventional example, since Toki isn't a playable character unlike other examples, but Taki pursues him as part of her backstory. Mitsurugi could be considered her rival, too.
Space Quest: Though only really appearing in two games (And revealed to be responsible for a third,) Sludge Vohaul considers Roger Wilco his arch nemesis. He certainly proves it by willing to travel back in time from a future where he already won just to ensure his victory. Some later strategy guides and writer's bibles try to tie the series together by claiming every antagonist across the series is related to or associated with Vohaul in some way.
The Protoss are archenemies of the Zerg, primarily because the Zerg had driven them from their homeworld of Aiur.
The Protoss themselves are divided. The templars are frequently at odds with the Dark Templar, though the Conclave could very much qualify for not respecting the Dark Templar's desire for individuality. However, because of the Zerg, the two factions are being forced to cooperate and may actually begin to respect one another.
During his campaign Raynor makes himself bitter enemies with the Tal'Darim faction of Protoss, by repeatedly stealing their sacred artefacts. When we learn their history in Legacy of The Void, they're the archenemies of pretty much the entire Daelaam Protoss — both the Dark Templar and the Khalai Protoss.
In Star Fox, Fox became Andross' nemesis after he prevented him from conquering the Lylat System. Star Fox 64 was a retelling of the original game's events and made things personal between Fox and Adross, by implying Andross had been responsible for the death of Fox's father, James McCloud.
Cammy was 1 of the 12 girls who were kidnapped and mentally enslaved, via Bison's Psycho Drive, as part of the "Doll Program"note which turned them into his personal squad of sleeper agents/assassins. Ever since freeing herself of his control, she's made it her mission to try to save the others, whom she now regards as her "sisters," and exact revenge against Bison — for all of them.
Rose was first seen in Alpha 2, where she was a fortune teller attempting to seal away Bison in an attempt to prevent her own death, at his hands, which she had foreseen in a vision. Years later, it was changed so Rose was now Bison's other half, who sought to seal away his evil.
Ryu considers Akuma to be his enemy for having murdered his sensei, Gouken. Though Capcomretconned it years later, so that Gouken was merely in a coma, for all that time.
Prior to that, the original iteration of Street Fighter II had Sagat out for revenge against Ryu for scarring his chest. Which served as a permanent reminder of his defeat... until that got retconned to.
In the Streets of Rage series, The Syndicate leader Mr. X is the arch-enemy of the protagonists, specifically in the second game where he kidnaps Skate's brother Adam for contributing to his defeat in the first game, and in the third game where he was instrumental in Zan's transformation into a cyborg.
In the fan-made remake of the game, Shiva is arguably this to Axel, as well as being The Rival. The whole Syndicate is this for Rudra, since they kidnapped her sister to force her servitude.
In Sunrider Mask of Arcadius, Kayto Shields comes to view the PACT dreadnought Legion as his personal Moby Dick. At the very start of the game it conquers his home planet Cera by singlehandedly obliterating most of the Cera Space Force and nuking his home city from orbit, killing his sister in the process. The Legion remains a constant thorn in his side from then on, threatening to turn many of the Sunriders hard-fought victories into crushing defeats thanks to its overwhelming firepower. When the latest run-in with the Legion leaves thirty-two of his crew injured and six dead, Kayto becomes determined to sink it at any cost.
Donkey Kong is another secondary nemesis to Mario. He was Marios first main archenemy during the arcade era, before they each got their own series on consoles, and Bowser took on the role for good in Donkey Kongs absence. Based on their friendly interactions in Spin-Off games it was originally implied that they buried the hatchet for good, but then the Mario vs. Donkey Kong series revived it and it has been going since, albeit to a much lesser degree than the rivalry with Bowser.
With the Luigi's Mansion games, Luigi seems to have gained his own arch-nemesis in the form of King Boo.
Jacqueline Natla to Lara Croft in Tomb Raider. Lara Croft has battled Natla in two separate continuities.
Touhou Project: Mokou vs. Kaguya. Good thing for them: killing each others over and over and over again is how they kill their (potentially infinite) time. Figuring out how to kill each others in new and interesting way is their joy in life, and sometimes they let other people in on their exquisite "pleasure".
Varian Wrynn is technically the Arch Enemy of Thrall, though this is mostly one-sided since it's only really Varian who wants to kill Thrall, while Thrall himself would gladly declare peace. Meanwhile, Garrosh Hellscream represents the anti-Alliance hate on the Horde side. He and Varian almost try to kill each other on a diplomatic meeting.
Almost is being generous, they were trying to kill each other, someone else just got in the way.
Kl'jaeden and their subservient eredar are definite arch-enemies of the whole draenei race and their leader Velen — they once were one race, before Sargeras arrived with The Corruption. From then on, draenei where on the run from eredar for millennia, until they settled on Azeroth for their final stand.
The Arch Enemy concept is also presented with Outland factions. Major bad guys there are represented by two races — blood elves under the rule of Kael'thas Sunstrider and various demons, partly led by Illidan. Major player friendly fractions, Aldor and Scryers, don't get along very well and have different opinions — Aldor chose demons as their Arch Enemy, while Scryers prioritize stopping Kael'thas' elves.
In a lesser example there is Loken, Arch Enemy of Thorim, who orchestrated first his Heroic BSoD, then the recovery from it, which only led into another trap.
Deathwing, leader of the Black Dragonflight, is the Arch Enemy of Alexstrasza and the other surviving Dragon Aspects.
Twilight's Hammer has been the arch enemy of the Earthen Ring, a shamanistic organization dedicated to preserving & protecting the elemental balance of Azeroth and Outland, since before Cataclysm.
Needless to say, group-wise, the Alliance and the Horde are both arch-enemies to each others, though none of them really is evil and people on both sides have attempted multiple times to arrange peace. They can sometimes begrudgingly team up against a common enemy, but overall they tend to be at each other's troath. Some species on each sides also tend to have a particularly personal hate:
Orcs and Humans usually are the two factions who have the most personal dislike for each other, having fought since the First War.
Though not necessarily hatred, Gnomes and Goblins seem to have some rivalry on which of the two is the smartest, both being the eccentricinventors of their respective factions.
Draenei had a particular animosity toward Blood Elves during Burning Crusade, due to the latter abusing them back on Draenor and having enslaved one of the beings their worshiped so they could have their own Paladin. A rarity for this trope, they actually ended up reconciling, with the Draenei helping the Blood Elves solve their biggest crisis and the Blood Elves starting to become paladins the regular way without enslaving anything.