In Alpha Protocol, Conrad Marburg is something of an evil counterpart to Mike; a rogue agent from a previous incarnation of Alpha Protocol called Deus Vult, who like Mike was cut loose and falsely declared rogue because it was politically convenient. Unlike Mike, who's still trying to get to the bottom of the conspiracy, Marburg lost faith in the government and now works for Leland.
Il Lupo (aka The Prowler) in Assassin's Creed: Project Legacy was a fighter trained by the Templars after observing Ezio in action as a countermeasure to the Assassins (specifically Ezio) by equipping him with similar weaponry right down to a hidden blade and teaching him the same skills Ezio knows. Even his attire is similar to an Assassin's. Unfortunately, he was killed before he could ever have a chance to actually face Ezio.
Shay Cormac from Assassin's Creed: Rogue is one to Connor from Assassin's Creed III due to both having very strong morals, and becoming legends for being responsible for The Purge of each other's Orders in the American Colonies/United States, as well as possibly their roles in two of the world's biggest revolutions; the French and American, respectively.
In Assassin's Creed IV: Black Flag, Anti-Hero Edward's counterpart is Bartholomew Roberts: they're both legendary pirates, wear outfits they stole from dead men, have supernatural powers which made them a target by the Assassins and Templars, respectively, and they're both Welsh.
The Baldur's Gate series firmly positions Sarevok as this to the PC. In the first game he's the only other Bhaalspawn you (knowingly) encounter, but even in Throne of Bhaal where CHARNAME's evil siblings are ten a penny, he's still firmly positioned as the example of what CHARNAME could have been.
Aside from that, the initial playable characters and their evil counterparts had all shared special themes in relation to one another. For example, the series' main protagonist Eiji and his evil counterpart Leon had shared a theme of temperament; where Eiji was a hot blooded jerk seeking to get stronger, overtime, he softened up and became more level headed in his pursuits. Leon is a cruel and cocky jerk without any standards, who will do anything in his power to be the strongest and get rid of those who will stand in his way, even if it meant sending them as a sacrifice to Abel's plans. He even desires to challenge Sho to achieve his goal.
Subverted in the Bayonetta franchise, the titular character's magical order called the Umbran Witches are a female-only group of magic-users who have contracts with infernal demons and can slow down time. By all accounts they should be the evil counterparts to the the male-only group of magic-users who work with angels and can speed up time, the Lumen Sages, except in the first game the Lumen Sages tried to exterminate the Umbran Witch order in order to steal their half of a god's power, the Eyes of the World, which would make themthe evil counterparts. Of course, this gets fully subverted in the sequel when its revealed the Lumen Sages weren't really evil, they were led down a path of destruction by the angels lying to them in an attempt at a power-grab for the Eyes of the World, coupled with the Lumen Sage leader, Balder, being corrupted by housing the pure evil half of the soul of the former God of Chaos in his body. Additionally, despite the Umbra Witches serving demons, the demons are played straight, meaning they could deceive the titular character into doing something bad..
In Breath of Fire IV, Fou-Lu is an Evil Counterpart to Ryu. He's superpowerful. (It's implied by various reactions to them that they are actually also Evil Twins, but the sprites don't actually look that similar, especially since Ryu has short blue hair and Fou-Lu has long silvery hair.)
Akuma is Ryu'sBlue counterpart in various Street Fighter games and their adaptations. The brother of Ryu's master, Akuma was a student of the same martial art and was also driven by the desire to be the most powerful martial artist, deciding that he was willing to kill those he defeated in the pursuit of true strength, while Ryu ultimately rejects killing. (The exception being in Street Fighter Alpha 2 and 3, where there's an Evil Ryu Secret Character. There, he turns out even worse than Akuma. Whereas Akuma has a sort of moral code, even if it falls heavily under Blue and Orange Morality, Evil Ryu is just a cold-blooded killer who ends up slaughtering the entire cast.)
Ultra Street Fighter IV gives us Decapre for Cammy. Aside from being the her twin, the former also represents what the latter could have become had she not broken free from her brainwashing.
City of Heroes: Going Rogue has this in spades. In the Mirror Universe of Praetoria; players will encounter familiar names and faces, sometimes in the most unlikely places. But due to the game's fluid alignment system, they can be your allies, or your enemies. Among them are:
Emperor Cole, counterpart to Statesman, single-handedly saved the world in the Hamidon Wars and now rules the world with a gold-plated, iron fist.
Praetor White (aka Marauder), counterpart to Back Alley Brawler, runs Praetoria's Powers Division.
Praetor Tilman (aka Mother Mayham), counterpart to Sister Psyche, is in charge of the Seers, Praetoria's Thought Police.
Praetor Sinclair (aka Chimera), counterpart to Manticore, is Emperor Cole's personal assassin.
Praetor Berry (aka Neuron), counterpart to Synapse, has made hundreds of scientific advances singlehandedly.
Metronome, counterpart to the Clockwork King, behaves much like his Primal Earth counterpart, including his obsession with Penelope Yin.
Penelope Yin, counterpart to herself, is a Resistance spy in Mother Mayham's mental hospital.
The franchise has the obviously titled Evil/Nega Crash, his alternate universe equivalent from the Tenth Dimension. Fake Crash (a goofy lookalike created from "an experiment gone horribly wrong") interchanges between being an antagonist or occasional friend of Crash, similar to Wario.
Crash Bash plays this straight, having two teams (good versus evil). Former villains Tiny and Dingodile become part of the good team, with Koala Kong and Rilla Roo representing their counterparts for the evil team.
Nina Cortex was recreated into one for Coco Bandicoot in the Radical Entertainment developed games. Both act as right hand girls and Kid Sidekicks to Cortex and Crash respectively, however while Coco is bubbly, altruistic and looks up to her older brother, Nina is snide and conniving, and considers herself superior to her uncle.
Bryce Cousland and Loghain Mac Tir, as well. Both are immensely loyal, powerful figures in Ferelden and heroes of the war against Orlais. They are also the only two Teyrns left in Ferelden. In personality and actions, however, they are entirely different, and have diametrically opposed views on the Grey Wardens.
Inverted somewhat in the Dungeon Keeper series as most of your minions are evil counterparts to the forces of good, with the biggest example being Black Knight and Knight. Other examples include Warlock/Wizard, Dark Elf/Elf and Vampire/Monk.
In EarthBound, Ness is approached by a time traveler, Buzz Buzz, and learns that he's the hero who saves Earth from an alien invasion. Unbeknown to him (and the player, until the end of the game), Porky — your initial guest character who is totally narcissistic and useless — has been approached by the alien leader, Giygas, to be his right hand man.
Throughout the series, at least for the average denizens of Tamriel, the Daedric Princes are seen as this toward the Aedric Divines. Anyone who worships a Daedric Prince is typically seen as evil, or at the very least, as dangerous lunatics. Ultimately played with significantly, as the Daedra are not inherently evil (and the Aedra are not inherently good), and even within the different cultures of Tamriel, some are seen as good to certain groups that are seen as evil by others.
Likewise with the Morag Tong and the Dark Brotherhood. Both are assassin's guilds, but the Morag Tong is government sanctioned within Morrowind and its members are honorable Professional Killers. The Brotherhood is a fully criminal offshoot of the Morag Tong, popular elsewhere in the Empire, who are much closer to Psychos For Hire and worship Sithis, a borderline God of Evil. Dealing with the Dark Brotherhood is a major part of the Morag Tong questline.
Necromancers in Tamriel have always been portrayed in a "dark grey" light. The Order of the Black Worm, however, show just how evil and depraved they can be if they want to. It doesn't help that the Order's leader is an Omnicidal Maniac. Dealing with them is a major part of the Mages Guild questline.
The Thieves Guild have somewhat become this to the Dark Brotherhood, maintaining a working relationship with the Brotherhood. When the Thieves Guild needs someone (outside of the Thieves Guild itself) dead, they'll contact the Brotherhood. When the Brotherhood needs something stolen or an item appraised, they'll go to the Thieves Guild.
The Dragonborn DLC reveals that the Dragonborn has one in the First Dragonborn, an undead Dragon-Priest who once ruled over Solstheim and now seeks to return to life.
Several classes in Everquest II have good and evil counterparts. The Paladin, Swashbuckler, Conjurer, and Mystic, have evil counterparts in the Shadowknight, Brigand, Necromancer, and Defiler, respectively. Previously, the Monk, Ranger, Illusionist, and Templar had evil counterparts in the Bruiser, Assassin, Coercer, and Inquisitor, respectively, but these eight classes are now neutral (taking the number of neutral classes to seventeen).
Inverted with Three Dog from Fallout 3, who sees himself and his radio station, Galaxy News Radio, as the good counterpart to the Enclave's propaganda station, telling the brutal truth about current events and encouraging people to "fight the Good Fight."
Caesar can also be considered this to a good-aligned Courier. Both want to shape the future of New Vegas, both can potentially own Rex and befriend Arcade Gannon, and both can gather a group of followers. The similarities end there, however. A good Courier encourages rival groups such as the NCR, the Brotherhood and the Followers to retain their identities and co-operate peacefully for the benefit of all like a Guile Hero, whereas Caesar violently crushes opposing groups and eliminates their identities, then absorbs their assets into the Legion. A good Courier's relationship with Arcade is built on mutual trust and respect and helps him overcome his internal conflicts, whereas Caesar's friendship with Arcade is one of forced compliance and causes the troubled man to eventually commit suicide. Caesar orders for the annihilation of entire communities over minor slights, whereas a good Courier can be kind and forgiving enough to come to the rescue of a man who shot them in the head.
Final Fantasy IV has Cecil and Golbez. It's revealed that they're blood brothers, and Cecil thinks when he finds out that it could easily be him, that was possessed by Zemus to act as the villain. In the sequel they have mirror movesets, Cecil having White Magic while Golbez has Black Magic, and their Cover and Taunt abilities both draw attacks from allies in different ways.
There is also a clear contrast drawn between Kefka, a Bad Boss who harasses his troops and is generally a menace, to the honorable and beloved General Leo Cristophe.
Final Fantasy VII builds up Sephiroth as Cloud's, but while the link starts as fairly concrete at the start of the game, the reveal that Much of Cloud's backstory was a lie and was, in fact, the tale of his friend Zack pushes this aside.
If you compare how they react to revelations about themselves; Sephiroth thought he was special and awesome, only to learn that he was a laboratory monster. Likewise, Cloud thought he was this epic super-soldier, only to learn that everything he remembered about that was a lie. But where Sephiroth desperately tried to restore his pride through godly delusions, Cloud managed to (with Tifa's help) restore himself to a state free of delusions.
Spin-offs instead treat Sephiroth as more an Evil Counterpart to Aerith — he thinks he's the last Cetra, she actually is; both had fathers involved in the Jenova Project; Aerith has the White Materia to call Holy, Sephiroth seeks the Black Materia to call Meteor; Aerith is a benevolent protector of the planet, Sephiorth is more in line with an eco-terrorist. Word of God has said they were intended during development to be revealed as siblings, which is why they have similar hairstyles and both have Green Eyes. In a novella set before Advent Children, it's implied Aerith could have created avatars of herself like Sephiroth did, but she felt it more important to let Cloud handle things on his own.
Cloud and Sephiroth's appearances in Kingdom Hearts play this totally straight with them, with Sephiroth sporting a black angel's wing on his right shoulder and Cloud having a black demon's wing on his left shoulder. In the same series, it is even heavily implied, if not outright stated, that the Sephiroth in that game was actually Cloud's Enemy Without, an embodiment of his inner darkness.
There's also Dyne in relation to Barret. Both are men from Corel who lost their arms in a Shinra attack and got Arm Cannons to replace them. Also, they are both violent, but Barret directs his anger at Shinra while Dyne snapped and became an Omnicidal Maniac. It shows that Barret could have followed a very similar path to him.
On a lesser note there's Hojo against Gast Faremis. Both were scientists working for Shinra, but Gast was a kind man who used science to obtain wisdom when Hojo is an immoral Mad Scientist. Futhermore, Hojo is the father of Sephiroth, which is the evil counterpart to Aeris, Gast's daughter.
Subverted with Cloud Strife and Rufus Shinra. Cloud ends up becoming the leader of AVALANCHE just a little after Rufus ends up taking over the Shinra Corporation, both because of Sephiroth's murder of President Shinra. Rufus and Cloud have similar colouring and facial features, as well as similar mannerisms; both are stylish, rude, self-important showoffs with strategic minds. They have a dual on the roof of the Shinra Building in which Cloud is unable to kill Rufus, and suggests to the others that they'll have to fight again. At that point, the focus shifts to Cloud and Sephiroth as rivals; Cloud and Rufus remain as similar personality types on opposite sides, but their relationship is never futher explored.
In Dirge of Cerberus, all of the Tsviets share something in common with Vincent. Shelke is immortal, Nero wields Darkness, Rosso has similar attire (red clothes, metal gauntlets) and fighting methods, Azul has the same shapeshifting powers, and Weiss is trying to attain the power of Omega, the antithesis to Chaos. Furthermore, he's the vessel for Hojo, who turns into monsters like Vincent, but has no morals or physical prowess to call his own. Oh, they also all use a combination of guns and martial arts, leaning towards guns. Except for Shelke. Rosso and Vincent lampshade this with their discussion on each other's "humanity."
Final Fantasy VIII. Seifer was an evil counterpart to Squall, both using gunblades and been trained at the same Garden. Although Seifer was more ambitious than evil.
Final Fantasy IX had Zidane to Kuja - both created by Garland to lead Gaia to war. Zidane is horrified when he thinks that if things had gone differently, he could be the one doing all the evil Kuja has been doing.
The Final Fantasy X and Final Fantasy X-2 duet has Tidus and Shuyin; one died while failing to protect his beloved, while the other gave his existence and succeeded. They even look alike, and fans speculate the fayth deliberately modeled Tidus after Shuyin in their dream-Zanarkand.
Both Yunalesca and Seymour are evil counterparts to Yuna.
Given his status as Unsent, Seymour was pulling double duty as the counterpart to Yuna and Auron.
The endgame quests from the Heavensward expansion of Final Fantasy XIV has the Warriors of Darkness, a group of five warriors siding with the Ascians against the Scions and the Warrior of Light. Subverted in that they Warriors of Darkness are not evil so much as desperate to save the world they came from and are willing to do whatever it takes, even if it means destroying another world.
Final Fantasy Tactics A2 has Illua, the Big Bad of the game and evil counterpart to Luso. Luso and Illua both have grimoires that have blank pages and are filling up with words as they go on their adventures. If Luso fills out his book, it will give him the power to return home, but if Illua fills out her book, then she gets to summon a great evil demon from another dimension to terrorize Ivalice with. Whether Illua succeeds in defeating Luso or not doesn't matter since once she is slain, her last efforts get recorded in the book and the demon gets summoned anyway.
First Encounter Assault Recon2: Project Origin, Sergeant Harold Keegan eventually becomes this to the Player Character Michael Beckett. He's a member of Dark Signal like Beckett, and matches or possibly even surpasses Beckett in terms of psychic potential, but has questionable mental stability. After Alma possesses and Mind Rapes him, he learns that Beckett is (completely unwillingly) Alma's favourite, and becomes a Crazy Jealous Guy obsessed with killing Beckett, and capable of using Beckett's Bullet Time powers.
FEAR: Perseus Mandate has the Nightcrawler Elites, who possess the Point Man's Bullet Time abilities through unknown means. They will usually "teleport" when taking damage.
"Starkiller" from The Force Unleashed has been described as the "photo negative" of Luke Skywalker, and is what Luke may have become had he been trained by Vader instead of Obi-Wan. Starkiller falls more in line with Luke's story after turning to the light, ultimately engaging in a self-sacrificing battle against Vader and the Emperor aboard the half-completed Death Star... For bonus points, in George Lucas's original draft, Luke's original name was "Luke Starkiller."
Azel in God Hand has the left God Hand, while the main character, Gene, has the right. It is said that he who possesses a God Hand may be either god or devil; Azel chose the latter route, dubbing himself "the Devil Hand". He wiped out his entire clan (protectors of the God Hands) to test his power, and then sided with the demons plotting to raise Angra.
In Guild Wars, to progress beyond a certain point in the plot you have to defeat your own character's evil twin in single combat. The doppelganger has the same skills as your character and higher stats, so you can't defeat it by simple brute force; you have to win by outsmarting the AI.
Halo 4 introduces The Didact for Master Chief, a heavily armored Forerunner commander who was the lover and protector of "the Librarian" similar to Chief's relationship with Cortana. The Librarian also imprisons The Didact for his crimes like how Cortana freezes Chief for his protection, Chief wants to protect humanity while the Didact seeks to destroy it in revenge.
In Hitman: Blood Money, Mark Parchezzi III is this to Agent 47. Even though 47 can be viewed as a villain, he is shown to have a set of values and morality, while what little is seen of Parchezzi shows him to be completely without scruples. Plus, while 47 performs rather indiscriminate hits, Parchezzi works for the Franchise, a clandestine government group with the goal of keeping human cloning illegal so that nobody else may benefit from it.
The Heartless might be Evil Counterparts of either people or Nobodies.
Donald and Goofy have entire races of Heartless counterparts in the first game - the shield-using Defender for Goofy, and the sorcerous Wizard for Donald. On the very rare occasions one drops its weapon (each has a 0.2% chance), the corresponding hero can pick it up and use it immediately.
Looking at the backstory revealed in Birth By Sleep, the case can be made that Xehanort is an Evil Counterpart to Sora. They both grew up at Destiny Islands, they both became Keyblade weilders, they both became a sort of composite being (Xehanort through Grand Theft Me, Sora through absorbing others' hearts), they both became a Heartless and a Nobody. Sora is a Naive Hero and increasingly portrayed as a Messianic Archetype, while Xehanort is a Magnificent Bastard who has recently showed some Fallen Angel symbolism.
A character known as Shadow Kirby also appears in Kirby: Triple Deluxe as the final boss of Kirby Fighters single player mode, although it is unknown whether it's the same one or not.
Meta Knight has Galacta Knight. Both have very similar appearance, attacks, and movesets. The primary differences between the two are that Galacta Knight lacks Meta Knight's sense of chivalry, and Galacta has a more angelic appearance compared to Meta Knight (White feathered wings and brighter colors compared to Meta's bat wings and dark colors).
Knights of the Old Republic possibly has an Evil Counterpart to the Jedi Exile in the form of Darth Nihilus; both were presumably present at Malachor V during that final battle there, and where the Exile survived all the death and destruction there by cutting themselves off from the Force entirely - thus becoming sort of a Force black-hole - Nihilus instead chose to sustain himself by feeding on the energy of other beings, essentially becoming a Force vampire. This is more or less the (in-story) trick to beating him when you confront him near the end of the game, convincing him to try to feed off of the Exile and instead weakening him severely.
And potentially Bastila to the player in the first game.
Hanharr is Mira's evil counterpart. Both are bounty hunters with intrinsically different reasons and methods of going about their business - whereas Mira is more about the credits and prefers bringing people in alive, Hanharr does it simply for the thrill of the hunt and will kill his targets regardless of what he's paid for it. This is most prominently reflected in that, when the two end up pitted against each other on Nar Shaddaa, which one of them you play as for that fight and incorporate into your party afterwards depends on the player's alignment, with light-side players playing as Mira and dark-siders as Hanharr.
Visas Marr is another one of these, to the Handmaiden. They're both disciples of essentially the biggest names on either side, the Handmaiden to Atris and Visas to the aforementioned Darth Nihilus. Interestingly, however, is their different approaches to combat - the Handmaiden is entirely melee-focused, not even having been trained in the use of the Force by Atris, while Visas is a more traditional dark Jedi - and that both have doubts about their masters that make it rather easy to convince them away from that cause - the Handmaiden can be trained as a Jedi mostly by sparring with her, Visas turns primarily because you chose to spare her after the initial fight against her. The two were even originally meant to join the party based on the player's alignment as with the above, Handmaiden joining light-siders and Visas dark-siders.
Malefor from The Legend of Spyro trilogy'' seems to be this to Spyro. Both are Purple Dragons, both were, according to Chief Prowlus and the statues of him all over the place, heroic in their youth, and both were trained freely by their elders in the Dragon Elements. The difference is Malefor let his power go to his head and went mad with power while Spyro remained good hearted (though Spyro was raised by dragonflies which may have had something to do with it). Malefor is aware of this and worked it into his Not So DifferentHannibal Lecture.
DarkLink. In some games, Dark Link is just a mid level boss and in other games, he's a full fledged villain. Dark Link uses a sword and shield in exactly the same way as Link and frequently mirrors Link's attacks to block them.
Also, The Legend of Zelda: Skyward Sword'sGhirahim as Demise's sword to Fi as Link's sword. His persona was carefully crafted to be Fi's polar opposite. Fi is fairly emotionless and speaks in percentages.Ghirahim is flamboyant to the extreme, and very open and dramatic. Once his true form is revealed, his text boxes look similar to Fi's, albeit black. Demise's weapon even looks like a dark version of the Master Sword- even down to an upside-down Triforce on the blade.
Zig-zagged with Princess Hilda from The Legend of Zelda: A Link Between Worlds. She looks like an evil version of Princess Zelda— what with her red eyes to Zelda'sInnocent Blue Eyes, her purple attire to Zelda'spink attire, and her dark hair color to Zelda'sblonde hair. Still, she is morally ambiguous and even helpful towards Link. Until the final boss that is, where it's revealed she is working with the Big Bad. Then again double subverted when it turns out she isn't evil, she is a Well-Intentioned Extremist who would risk another kingdom for her own. Hilda was being used and after the boss battle she makes up with Zelda.
In Lollipop Chainsaw, Swan is this trope to Juliet Starling. Both were motivated by 'love' to pervert the natural order of life and death: he raised an undead army to punish Juliet for not requiting his feelings, she crippled her boyfriend as part of a magic ritual to prevent his death. Notably, Juliet can only defeat Swan by allowing Nick to pass on (rather than forcing him to continue living in his extremely dependent, painful state)- essentially acknowledging that "life is about more than what we want", something Swan was too angry to do.
Many of the Guilds of Lusternia have counterparts in the form of foils, but only the Celestine priesthood have a straight-up Evil Counterpart in the form of the Nihilists: the former are white-winged priests granted angelic companions by extradimensional incarnations of virtues, while the latter are bat-winged priests granted demonic companions by extradimensional incarnations of sins.
The Mass Effect 2 DLC Lair of the Shadow Broker takes it even further with Tela Vasir, an asari Spectre and agent of the Shadow Broker. She even delivers a Not So Different speech to Shepard, who for all intents and purpose, is working for the equally shady Illusive Man.
Shepard is being targeted by Cerberus assassin Kai Leng, who was first introduced in Mass Effect: Retribution. Before Kai Leng worked with Cerberus, he was an Alliance N7 Operative (like Shepard) who was imprisoned for murdering a krogan in a bar while on leave (with nothing but aknife). Also after Shepard was killed s/he was given many cybernetic implants to help rebuild him/her, and Kai Leng now also has cybernetic enhancements.. Finally, they're both the best and most skilled fighters of their specific sides: Shepard for the Alliance and Council, and Kai Leng for Cerberus.
Another evil counterpart to Shepard in Mass Effect 3 is The Illusive Man. While Shepard is willing to sacrifce himself/herself for the greater good, and reluctantly sacrifices others for the same, TIM forcibly sacrifices others to achieve his goals and acquire power. While Shepard's sacrifices bring humanity closer to victory, TIM's sacrifces brings humanity closer to destruction.
Achieved in the Multiplayer, with the Phoenix classes, biotic Cerberus defectors, and the Dragoons, which is what would have happened if the Phoenixes had stayed loyal. Same suit? Check. Same attack, different only in color? Check. The Phoenix gets it better, since at least it gets shields.
Also in Multiplayer, the N7 Shadow and Slayer classes are the Good Counterparts to the Phantoms. Skilled in battle ballet? Check. Wicked sword? Check. Invisibility cloak? Hand cannon thing? Check and check, for the Shadow and Slayer respectively.
In the Mega Man games, Bass (AKA Forte in the original Japanese versions). The TV show had Proto Man (Blues in Japan) in this role, despite him being a good guy in the games. This may be because in his first appearance in Mega Man 3, if you didn't know the plot (which, as was common for the time, wasn't actually in the game), it was very easy to mistake him for a villain unless you beat the game. Most likely, though, they just wanted to have a clear cut Evil Counterpart to Mega Man, and Bass hadn't been invented yet.
Zero's own evil counterpart is Ax-Crazy Omega Zero, considering that Omega possesses Zero's original body and uses the same attacks Zero himself uses in Mega Man X. Plus, Omega is what Zero himself would have become if Zero had followed Wily's plans for him.
Originally, Zero was intended by Dr. Wily as the Evil Counterpart to Mega Man X. However, after his defeat by Sigma (who later ironically becomes the Big Bad of the series), Zero was cured of the virus and became X's Lancer instead.
Both have earlier Evil Counterparts: Mega Man has Quint and Zero has Sigma.
In Mega Man Battle Network, MegaMan no longer has a direct counterpart; Bass is considered one to MegaMan because both are the only Navis who always have distinctive humanity among NetNavis, with Bass being an experiment and MegaMan being's Lan's dead little brother brought back as a Navi, but aside from said trait there is nobody who has similar powers to MegaMan. There is another pairing introduced, though, Baryl and Chaud as well as Colonel and ProtoMan. Both star in 5 depending on the version, and both are leaders who think more logically. Baryl, however, is adopted by Wily and in the 6th game he becomes one of the main villains.
Messiah: In the final boss fight, Bob the cherub meets Satan's imps, who too can possess people and who look like babies, though demonic ones.
Liquid Snake from Metal Gear Solid is one of the few literal examples. He and his twin Solid Snake were cloned from the same man, and although Liquid was (supposedly) genetically superior than his brother Solid, Liquid grew up believing the opposite and wanted to kill his father Big Boss to prove his worth. When Solid takes away that chance from him by defeating Big Boss first, Liquid decided to take his aggression to Solid instead.
Big Boss himself counts. Both he and Snake have been put through the wringer and seen just how horribly soldiers are treated by their governments that claim to respect them. Big Boss crosses lines that Snake refuses to. Right before his death, after finally realizing how far he had fallen, Big Boss commends Snake for not going down the same path that he did.
The SA-X from Metroid: Fusion is stated by Samus herself to be the embodiment of her potential for evil. It has all of her EXACT abilities, but no heart or conscience, which makes sense, as it is a clone of her created from X-Parasiteinfection.
Dark Samus from the Metroid Prime Trilogy also fills the role of evil counterpart to Samus. Dark Samus has abilities quite similar to Samus' abilities, though her moves are a slight variant of Samus' moves plus she has her own abilities as well. The games' scan logs state that Dark Samus is quite intelligent and can manipulate other races to benefit her own agenda, which is to spread the corruptible Phazon across the galaxy. Ironically enough, chronologically, Samus ends up becoming Dark Samus's own Good Counterpart; in Fusion Samus has Metroid DNA integrated with her body to save her from the X and Dark Samus was born when the Metroid Prime integrated Samus's Phazon Suit and DNA into itself at the end of the titular game.
In Millennia: Altered Destinies, McDonald's Evil Counterpart is an alternate timeline version of McDonald who was recruited by the Microids instead of the Hoods. The other McDonald flies an identical XTM but uses the ship to undermine the player's actions. Unlike the other examples, there is no way to get rid of the other McDonald.
The gnomes introduced in Overlord II are a good counterpart to your minions. Unfortunately for them, in the setting, "Good" means either "self-serving Jerk Ass using their supposed virtue as free license to do whatever they want" or "obnoxious, ineffectual idiot", and they got stuck with the latter version.
Still, another example of a Good Counterpart for the Evil OverlordVillain Protagonist would be Queen Fay, leader of the Elves and the reigning being of Light Magic (you being Dark Magic). She still ends up coming to you for an Enemy Mine against the Anti-Magic Empire in which she ends up sacrificing her energy to power the Overlord's Tower Heart, ending with her corruption and becoming a Fallen Hero.
In Overlord I, your Evil Overlord character comes up against an Eviler Counterpart in the form of the Wizard who was possessed by your predecessor.
Neverwinter Nights 2: Ammon Jerro, who, like the player character is collecting the shards of the Silver Sword of Gith to reconstruct it, aims to vanquish the King of Shadows, and has collected a group of (involuntary) allies to aid him. Possibly subverted in that the player can be just as evil as either character - or potentially more so.
The Mask of the Betrayer expansion has Arraman, who isn't really 'evil' as such but opposes your character at every turn, unless you give up on the Crusade.
Neverwinter Nights has Maugrim for Aribeth (for a while), Haedraline for Drogan in Shadows of Undrentide, and Sabal for Nathyrra and the Valsharess for the Seer in Hordes of the Underdark.
Various community expansions have examples. Alex / Mordred for the player in the The Bastard Of Kosigan and Vico for Bran (and in part Anden, though his role is more of a Foil to Vico) and Arto Benthur (something like that) for the player in A Dance with Rogues are probably the best, though those modules are also the ones with the best reoccurring characters.
NieR: Automata has A9, an android similar to 2B and is wanted by YoRHa for subverting humanity's attempts to retake earth from the machine lifeforms.
The Gengar line has been set up as this for the Alakazam line. Both are powerful squishy wizards who must be traded to reach their final forms who share similar stats and are capable of Mega Evolving, and where the stoic Alakazam is described as being intelligent but benign, Gengar is a malicious Slasher Smile-sporting curser who steals the life force of humans.
The Mandibuzz line is this to the Braviary line—the latter consists of Always Malewarrior eagles who are said to be powerful and honorable fighters, while the former consists of Always Femalevultures with an appetite for bones, including human ones (in fact, Vullaby, Mandibuzz's baby form, wears a human skull as a diaper). To drive the point home, the Mandibuzz line is outfitted with the Dark-type, meaning that they fight dirty.
Alex Mercer from [PROTOTYPE] has to contend with Blackwatch Super Soldiers who have controlled exposure to the same virus powering him It IS him, but that you won't find out for a while, as well as the Hunters who have similar powers - all the way up to the Supreme Hunter also being able to shapeshift - but are clearly inhuman. It's not so much Good Counterpart versus Evil Counterpart as it is Evil Versus Evil though.
In Robopon, Sun-Zero is this to Sunny, and Negapon is this to Gigapon.
The RPG, Sailor Moon: Another Story has a set of evil counter parts for Moon and the Inner Senshi known as the Opposito Senshi. Each is named for a Babylonian god or goddess that is roughly equivalent to the powers and role of the Sailor Senshi. Moon has Sin, named for the Moon god. Mercury has Nabu, named for the god of wisdom. Venus has Ishtar, named for the fertility goddess. Jupiter has Marduk, named for king of the gods, and Mars has Nergal, named for the fire god. The Ayakashi sisters mentioned above also make a short appearance.
There are a couple present in the Soul Series. The most direct example is Lizardman to Sophitia; both are Greek warriors chosen by Hephaestus, but while Sophitia succeeded (sort of) in her mission and returned home, Aeon Calcos failed, was transformed into a horrible lizard monster and swore revenge on the god that had abandoned him.
Astaroth and Rock share this dynamic, because Astaroth is an Evil Knockoff of Rock.
Samurai Shodown has Rasetsumaru who is the Bizzaarro counterpart of Haohmaru.
Claudia of Silent Hill 3 was raised in the same nightmarish cult as Alessa Heather by a similarly abusive parent and may also possess the ability to summon the series' iconic Dark World, however she embraced the cult's teachings and their plans of resurrecting "God" while Alessa Heather rejected them.
Shadow the Hedgehog was introduced as Sonic's Evil Counterpart. Since then, though, he's become more of an Anti-Hero Counterpart.
Then Shadow got his own evil counterpart in the form of Mephiles the Dark, the main villain from Sonic the Hedgehog (2006) whose form is a copy of Shadow's own shadow.
Sonic's original Evil Counterpart is Metal Sonic.
In a somewhat rare example, the villainous Dr. Eggman has an Evil Counterpart as well, in the form of his dimensional counterpart/descendant Eggman Nega. Where Eggman is Affably Evil with a skewed but nonetheless present sense of morals and heroism, Nega unabashedly loves fear, chaos, and suffering — essentially, he's what Eggman would be without his human qualities.
In Sonic Forces, Infinite is depicted as the Evil Counterpart to the Avatar. Both characters are motivated to better themselves after their teammates are killed by a more powerful being that dismissed them as a weakling. And while Infinite wants to increase his power for his own sake, the Avatar wants to become stronger to protect his friends and save the world.
In the original Persona, there's Ideal Maki/Mary and Mai/Mae vs. Pandora and Aki/Maggie, with the former two representing Maki Sonomura's ideal self and ego and the latter two representing Maki's nihilism and id. There's also Kei/Nate (good, if a bit of a jerk) vs. Kandori/Guido (definitely evil), being wealthy businessmen who took different paths, which becomes even more apparent if you have them meet each other again in Persona 2.
The main cast of Persona 2 actually have to fight their Shadows, manifestations of their dark sides created by Nyarlathotep. Before they fight their Shadows, the cast of Persona 2: Innocent Sin also have to face the Masked Four: Leaders of the Masked Circle chosen by the Joker, whether intentionally or only subconsciously, because of their parallels with the main four party members. Of the three fought during the game, two of them even wield modified versions of their counterpart's initial Personas.
Strega of Persona 3 are the Evil Counterparts to SEES; where as SEES seeks to save the world because they and their loved ones all have something to live for, Strega seeks to destroy the world because they believe all life is pointless. Specifically, Strega's leader Takaya is the Protagonist's Evil Counterpart, though he's more against your team in general than you specifically.
The tradition continues in Persona 4, where fighting the Shadows of your soon-to-be party members is a major part of the game, generally after the original screams "You're not me!", causing the Shadow to become berserk. The true killer, Adachi, also serves this role for the protagonist. In fact, he even has the same US voice actor and a modified version of the main character's first Persona.
In Persona 5, the traitor, Goro Akechi, is this to the protagonist. In fact, the deity manipulating everything specifically choose the two to be rivals in its twisted game; Akechi and the protagonist even have the same "Wild Card" power that allows them to use multiple Personas. This is also inverted with Shadow Futaba, who represents Futaba's positivity.
Wario was once an evil rival of Mario, complete with evil versions of Mario's powerups. Then he shifted to a greedy Anti-Hero who stole from other villains, soon replacing his dark powerups with the gimmick of Nigh-Invulnerability and bizarre transformations based on how he is injured. On a couple of occasions Wario has actually helped Mario however, both with and without selfish motives.
Later on, Nintendo gave Luigi his own Evil Counterpart in the form of Waluigi.
It's interesting to note that the prefix "wa", originated from the word "warui", means plenty of things, including "evil" in Japanese. Hence, Wario and Waluigi are, literally, "Bad Mario" and "Bad Luigi". However, their names can also mean, based on the meanings of the word "Warui", " Wrong Mario/Luigi", "Poor Mario/Luigi", "Hateful Mario/Luigi", "Abominable Mario/Luigi", "Wrong Mario/Luigi" or "Inferior Mario/Luigi".
Furthermore, Waluigi´s name in Japanese is an anagram of the word "Ijiwaru". Which means his name has extra meanings such as "Ill-tempered Luigi" or "Sadistic Luigi".
Bowser gets one in Mario & Luigi: Bowser's Inside Story when the Dark Star becomes Dark Bowser, the final boss. Bowser has evolved into one to Mario as well—similar fire powers, similar stomping abilities, their powerups have numerous parallels...
A more direct example is Lemon Browning, who is the Alternate Universe version of heroine Excellen Browning. The split came in a shuttle crash. The original Excellen survived without a scratch, while the other died and was rebuilt by her parents into a cyborg.
Similarly, there's the Shadow-Mirror equivalents of Kyosuke Nanbu and Sanger Zonvolt, especially the latter.
And Z adds Asakim Dowin to the family of evil counterparts (in this case, of Masaki Andoh), and unfortunately there won't be a white Paladin Shu to stop him.
Tales of the Abyss elevates this to an art form. Every single member of the party has an evil counterpart in the Six God-Generals, and the Big Bad, Dorian General Van Grants, is pretty much an Evil Counterpart to half the party:
Luke's evil counterpart is Asch, as he's Asch's clone
Tear's evil counterpart is Legretta, who trained her to fight.
Anise's evil counterpart is Arietta, who was a Fon Master Guardian before Anise took over her job.
Natalia's evil counterpart is Largo, who seems to have her sense of honour and dedication, and is also her father.
Jade's evil counterpart is Dist, who grew up with Jade and idolized him; they created fomicry together. Well, more like Jade created fomicry and Dist was there when it happened.
Guy's evil counterpart is Sync; or at least, the game would have you believe that. This is a Red Herring - Sync is counterpart to Guy in terms of their Lightning Bruiser fighting style, but story-wise, he's another clone of the original Fon Master Ion, making the current Ion his Good Counterpart.
Big Bad Van is personally connected or mirrored by about half the main party. Luke is his student and the product of his fomicry experiments, and both are primarily seeking a way to avert the Score. Guy is, like Van, a survivor of the sinking of Hod; initially, they both want revenge for their painful childhoods, but Guy manages to overcome his bitterness while Van takes it...wayyyy too far. Tear is Van's sister, obviously. Jade is also a practitioner of fomicry, but while even he realizes fomicry is amoral, Van sees it as the way to recreate the world and save it from the Score. He and Anise had ulterior motives for joining the Order of Lorelei.
Yggdrasil aka Mithos the Hero in Tales of Symphonia could be considered as such to Lloyd, both of them starting out as well-intentioned Determinators, though while Lloyd eventually learns when to back down and think things through, Mithos remains stubborn and unwavering to the bitter end, which causes his Start of Darkness (his last words even have him calling Lloyd "my shadow" and proclaiming that he "stands at the end of the path I chose not to follow.") He also has a lot in common with Genis, both being disillusioned half-elves and having to suffer the persecution that comes from being such, though Genis eventually learns to accept the humans who persecuted him, while Mithos continues to be bitter and resentful towards them.
In the early Tekken games (more so the first one), there would be 8-10 default characters, and consequently 8-10 sub boss characters, specifically designed to match up with their corresponding default character and vise versa, as a 'rival' (i.e. one would always fight the other on Round 8). Most of these were actual counterparts of the default character, and in the first game, they were literally clone characters too. Examples would be what Anna is to Nina, as well as what Armor King is to King, or what Kunimitsu is to Yoshimitsu. Their Evil Counterpart nature was due to most of their intentions and/or employers i.e. Nina was sent as an assassin to take down the Big Bad where as Anna was working for them. Or King wanting to use the tournament winnings to fund an orphanage, where as Armor King didn't care about King's orphanage and just wanted to prove he was better (as well as being generally quite a dark and mysterious character). Yoshimitsu was the leader of a clan who wanted to steal from the rich to give to the poor, but Kunimitsu wanted to steal from the poor to give to herself (and even stole from her own clan). Later Tekken games kept all these characters, but from Tekken 3 and onward, they had scrapped the sub-boss system associated with it.
Tenchu 2 had Lord Toda for Lord Gohda and the Burning Dawn ninja for the Azuma ninja.
Vasteel Original in Thunder Force V is prototype of player's Vasteel fighter. Also Vasteel Nocht from Thunder Force VI which is large fighter that utilise weapon similar to player fighter from previous three games.
Rafe Adler in Uncharted 4: A Thief's End is a rival treasure hunter who acts as a much more violent and sociopathic version of Drake. He is just as much a capable climber, explorer, and gunman as Drake, and even shares Drake's fondness for dry humor at times. It is revealed over the course of the game that one of his primary motivations is to outdo Drake, who he is incredibly jealous of.
In the Ultima series, Lord Blackthorne is this to Lord British. The Virtues have evil counterparts as well.
The Guardian ends up usurping the Avatar in his long absence, replacing the doctrine of the Virtues with his own propaganda, the "Fellowship".
In Um Jammer Lammy, Lammy has Rammy, although it's something of a parody as Rammy has no real relationship with Lammy at all, and Lammy seems to have very little idea who Rammy even is. Rammy can also be quite helpful in certain game modes.
Colonel Noodle and PaRappa in PaRappa The Rapper 2 - both are obsessed with avoiding a certain food that has become boring (burgers for the former and noodles for the latter), both have eccentric scientist fathers and missing mothers, and both use their rapping talent to deal with life's troubles. Colonel Noodle even uses PaRappa's "I gotta believe!" before his stage.
In World of Warcraft you actually get to beat up your own evil counterpart. Or technically, your "inner turmoil" (or for casters, it has often been identified by players as your inner idiot - it only uses melee attacks).
The Warlock class is, lore-wise, the Evil Counterpart to the Mage, as they are usually former mages fallen into the temptation of resorting to demonic energy to make them stronger.
The Lich King's Death Knights, both as a hero unit in Warcraft III and a class in World of Warcraft, serves as an Evil Counterpart to the Paladin (they're even referred to as such) in both games.
Another example is the boss battle Herald Volazj, who actually drives you insane and makes you fight evil twisted versions of your party members. Though, after you beat them, you may help your real party members kill their evil selves.
Shadow Priests are in themselves the evil counterpart to their Light and Holy brethren.
There have been plenty of non-playable evil counterparts to every class, such as the Druids of the Flame for Druids.
Deathwing firmly establishes himself as an evil counterpart to Alexstrasza, being bent on the destruction of life and twisting dragons into genetically-engineered monstrosities.
Mutons of XCOM: Enemy Unknown have been described like this, an alien SEAL Team Six to fight your own troops.
In the XCOM: Enemy Unknown expansion Enemy Within, an evil organization called EXALT is revealed to be secretly in league with the aliens, although they have their own mysterious goals. Their operatives use the same tactics as your own XCOM soldiers, and their weapons are identical in stats (but less boxy) to your own firearms and laser weapons (EXALT never develops plasma). Like your soldiers, EXALT uses Meld to enhance their operatives, although they never build MEC Troopers. Even their HQ's location is opposite to yours. The XCOM base is deep underground, while the EXALT HQ is on top of a skyscraper. When storming it, your soldiers find a hologlobe identical to yours but red in color, although their HQ is more aesthetic than functional in stark contrast to the XCOM base. There are some subtle hints that EXALT may have evolved out of the original XCOM project in The '60s.