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- In Legacy of Kain: Defiance, one of the boss fights is a duel between the two protagonists, Kain and Raziel. For the first half of the fight, you control Kain trying to beat Raziel into submission, before control switches to Raziel half way through.
- In LEGO Star Wars, you play through most of the last level of Episode III as either Obi-Wan or Anakin. Come the last stage, the character not being used becomes the boss (although you can still switch control of the characters even during the duel). There's only one way it'll turn out despite who wins. Oddly, this does actually give an easy victory, activate the second player and simply kill them without them defending.
- Deadly Creatures has a few portions where the tarantula and scorpion cross paths and you have to beat one with the other.
- Beat Down: Fists of Vengeance sees the male characters who are not picked as the player character getting fought in order to join your gang, which means depending on who you select at the beginning you'll have to fight either two or three of them.
- In the Yakuza series, in the games with multiple protagonists there's a point where two of the protagonists face off against one another (typically Kiryu and Saejima). During these encounters, you're usually given the option of choosing which character you wish to control for that battle. Regardless of who wins, the battle usually ends with the characters fighting to a standstill and progressing.
- In addition to the whole "one character leaves clues, the two others find them" mechanic in Fahrenheit, there is an episode where Carla and Tyler spar at the police gym. Notably, not only can you decide whom to control during the sparring, but you can also lose (even on purpose), which is helpful because the winner gets a boost to their Sanity Meter (which Carla usually needs more than Tyler).
- Likewise, in Heavy Rain, Ethan, Madison, or Norman (whoever is alive at that point) must fight Scott a.k.a. the Origami Killer in the endgame. You control the former, but you can still lose and have your current character killed.
- Not a physical conflict, but in Dreamfall: The Longest Journey, when April and Kian meet for the first time, they engage in a heated argument over the Azadi politics in the Northlands. Notably, you can select both characters' responses, so it is possible to either convince April to reconsider her views on Azadi, or force Kian to take a good look at his superiors. Too bad it doesn't really lead to any Story Branching.
- In the single-player story mode of X-Men vs. Street Fighter, after defeating Apocalypse, the player takes control of whichever character landed the final blow and must then fight his tag partner in a one-on-one match. This turn of events goes unexplained.
- In Injustice: Gods Among Us, the single-player campaign has you swapping characters at the end of most chapters, and every so often you'll end up in a fight with a character you controlled in a previous chapter.
- In the Subspace Emissary of Super Smash Bros. Brawl, this happens numerous times:
- "Midair Stadium", and by extension the entire game, begins with a competitive bout between Mario and Kirby. The player can choose to play as either character. In any case, the fight ends with the victor and the defeated shaking hands. This fight is actually a reference to the ending of Smash Bros. 64's into video.
- After a battle against a shadow bug doppelganger of Princess Peach or Princess Zelda in "The Lake Shore", Mario and Pit face off against Link and Yoshi, after one of the teams mistakes the other for having just killed the princess. Which team is in control of the player depends on which princess was saved earlier.
- At the end of "The Path to the Ruins", Lucas and Pokémon Trainer a.k.a. Red (who at this point only has Squirtle) fight Wario in vengeance of Ness. The player only has control over the former two.
- At the end of "The Ruins", Lucas and Pokémon Trainer (who now has Ivysaur in addition to Squirtle) battle Charizard, whom Pokémon Trainer captures afterward with his Poké Ball. Again, the player has control over Lucas and Pokémon Trainer.
- At the end of "The Glacial Peak", Lucario and Meta Knight fight, which is between this and Defeat Means Playable (since it's Lucario's first appearance in the story). Just like with Mario and Kirby at the beginning of the game, the player can choose either character before the fight.
- Finally, at the end of the first iteration of "Subspace", the player takes control of King Dedede as he is forced to fight Bowser, who at this point is unaware that Tabuu is behind the entire plot.
- Happens often in Tribes: Vengeance. First is when Victoria fights and kills her lover Daniel after he is tricked into killing her father. Then subverted when Julia chases after Jericho, only to be one-upped by Mercury (who is also a player character), but played straight when she fights and kills Mercury himself.
- There is a brief level in the original Call of Juarez where Ray finally catches up with Billy and guns him down (though Billy survives).
- In Mega Man X5, if you can save Zero from going Maverick, then X and Zero get into an argument that escalates into a fight (with you playing as whomever you took into the level). If Zero goes Maverick, then you have no choice and X has to destroy Zero.
- The second ending for each character in Muramasa: The Demon Blade features the other as the final boss.
- This is actually a pretty major element of the Sonic the Hedgehog series. As most boss fights that aren't a mecha piloted by Dr. Ivo "Eggman" Robotnik tend to be conflicts between the major characters.
- At the end of Hidden Palace Zone in Sonic 3 & Knuckles, Sonic fights Knuckles the Echidna, who has been hindering him at every available opportunity after being tricked by Dr Robotnik into thinking that Sonic wanted to steal the Master Emerald. The inverse doesn't happen however, as Knuckles' story takes place some time after Sonic's.
- Sonic Adventure has Sonic fight Knuckles again, as well as E-102 Gamma. However, playing through as Knuckles and Gamma allows the player to fight Sonic, and playing as Tails puts him in the fights instead of Sonic.
- Sonic Adventure 2 has the story split into two sides; a 'Hero' side with Sonic, Tails, and Knuckles, and a 'Dark' side with Shadow, Eggman, and Rouge. Each character is matched to another, and fights their counterpart several times over the course of the game. Again, the fights are playable from both perspectives.
- Sonic Heroes has the characters split into 4 teams of 3, with two of the other teams serving as Boss Battles during the game — Team Sonic and Team Chaotix fight Team Rose and Team Dark, whilst Team Dark and Team Rose fight Team Sonic and Team Chaotix.
- Sonic Rush has Sonic vs Blaze at the end of Dead Line Zone, the one you fight again depending on which you are playing as. Bizarrely, despite the game going out of the way to establish that it's the same fight, the version of Eggman watching in the background also depends on who the player character is, sending otherwise sound plot consistency straight out of the window unless you accept both Eggman and Nega being present canonically.
- Sonic the Hedgehog (2006) has Sonic and Shadow fight Silver at least once. Again, you can play either side of the same fight, according to which character's story mode you're playing.
- In Crash Bash, if playing a two-player game with one good and one evil character, the two players must duel each other to decide whether good or evil triumphs.
- In Ghostbusters (1990) for the Sega Genesis, the player is given a choice between Peter, Ray, and Egon at the beginning. The two that are not picked will later be fought as bosses with the in-story justification of being possessed. Essentially you are fighting the demons which means that you have to avoid your friends attacks.
- In Arc the Lad: Twilight of the Spirits, you spend the game alternating between controlling two parties; a party of human characters led by Kharg, and a party of deimos led by Darc. In the final chapter of the game, both parties meet each other and you have to choose one party that you control in order to defeat the other (shortly before the Big Bad appears and forces them into an Enemy Mine situation).
- Happens repeatedly during Fire Emblem: Radiant Dawn. There's a twist in this game; when you fight an alternate team, they keep the levels and items from when you were last controlling them. If you manage to keep both teams around the same power, it's an even match-up, but if they're not balanced, you'll spend half the levels plowing through 'yourself' and the other half running away from 'yourself'.
- In Fortune Summoners, there's a brief section where you play as Stella in a flashback explaining how she got to the section of dungeon you just reached. When you reach the present, she challenges Arche to a duel, serving as a Boss Fight (something of a Curbstomp Battle, since she's a Squishy Wizard and the battle takes place in a small arena), before joining the Player Party.
- In Star Wars: The Old Republic, an Imperial Flashpoint sees you hunt down and eliminate the protagonist of the original Knights of the Old Republic. Needless to say, Darth Revan puts up a hell of a fight.
- One of the Sith Warrior story missions also has you fight it out with either a Light Side or Dark Side version of yourself (which one you fight depends on your own alignment).
- Midway through Mario & Luigi: Bowsers Inside Story, the Mario Bros. fight Bowser after finally getting out from his insides. Bowser has the attacks he learned while under the player's command. Bowser is much less competent when controlled by AI; he fails attack commands regularly and never uses defensive commands. However, his HP is much greater than he had when controlled by the player.
- Also in Super Paper Mario, after the group has been split, Mario manages to find Bowser. They have a fight due to some misunderstandings, and he comes to his senses afterwards and rejoins, of course.
- In Legend of Mana, Escad and Daena come to blows over disagreeing about what to do with Irwin. You're forced to take a side (refusing to take a side will have them choose for you), and the battle is to the death. No matter what, one party member isn't coming out of that fight alive. And then it's all made moot when Daena's third option is outright rejected by Matilda and you're driven to kill Irwin anyway.
- Pokémon Gold and Silver and the remakes have the post-Elite Four battle with Red, the Player Character you controlled if you played Pokémon Red and Blue before that.
- Digital Devil Saga has a rivalry between Serph and Heat come to a head when Mick tempts Heat with Sera, leading to a fight between the two. You can decide whether you fight back seriously or not. Heat is just faking it as a distraction, and tells Serph to play along — he's still loyal, though if you fail to trust Heat and do fight back seriously, then it can come back to bite you in the sequel.
- Kingdom Hearts:
- In Kingdom Hearts II, you spend the first five hours of the game playing as Roxas, before the player character switches to Sora. Near the end of the game, Sora fights Roxas, who's revealed to be his Nobody, in a cutscene battle, which is made an actual battle in the Final Mix version.
- In Kingdom Hearts: Birth by Sleep, you play as three characters: Terra, Ventus, and Aqua. The former two, both possessed, are eventually fought by the latter.
- Kingdom Hearts 3D: Dream Drop Distance features Sora and Riku as playable characters. At the end of the game, a possessed Sora, clad in Ventus's armor and fighting with his fighting style, serves as the Post Final Boss.
- In Tales of Symphonia: Dawn of the New World, after defeating the Big Bad, Emil ends up in a life-or-death battle against Marta and Lloyd. The reason isn't quite as clear-cut as most examples, and winning gets you the Bad Ending.
- River City Ransom has an interesting example. If you choose to go solo rather than bringing a partner character with you (since EX allows you to edit characters with the right cheats; it's not always Alex or Ryan) at the start of the game, eventually you'll run into them again where otherwise you wouldn't find anyone. If you have the right conversation, the two of you will have a fight. If you've chosen the right file save for who would have been your partner, you're easily in for the hardest fight in the entire game.
- The "Actually Ed the Undying" challenge path of Kingdom of Loathing features %playername the Adventurer as the final boss, though your quest isn't quite over when you defeat them, as you still need to recover your Holy MacGuffin, and as you'll recall from your regular playthroughs, you handed that over to the Council of Loathing who stored it in a secret warehouse.
- If the player chooses to side with a certain faction in Deus Ex: Invisible War, they must fight the protagonist of the first game - J.C. Denton as the end-game boss.
- In Eternal Sonata Chopin is your final enemy. He realizes that the game world is his Dying Dream and he attempts to survive it by trying to destroy it and everyone inside it. The game is interesting in this case since winning the fight will end up with Chopin dying of his tuberculosis in Real Life while losing it on purpose ends with everyone in the otherworld ceasing to exist, but Chopin waking up and deciding that he wants to live.
- In a couple of the Touhou Project games (Lotus Land Story and Imperishable Night), you have to fight either Marisa or Reimu as the stage 4 boss, depending on who you're playing as.
- In the (non-canon) Brutal Bonus Level of Ace Combat Zero: The Belkan War you, as Cipher, must fight the True Final Boss — Mobius One, the protagonist of Ace Combat 04: Shattered Skies. This has since become a staple in the Ace Combat series to include protagonists of previous games as bosses in the non-canon bonus levels. Perhaps the farthest callback is the bonus level of Ace Combat X: Skies of Deception, where the bonus aces were the ZOE Commander (simply identified as ZOE) in his red ADF-01 Falken and Scarface One (just credited as Scarface) in the XFA-27, which was the ultimate plane all the way back in Ace Combat 2.
- MechWarrior 4 has the player, Ian Dresari, fighting to reclaim his family's right to rule; depending on your choices he leaves his sister to die to claim a weapons cache and the throne, or claims the cache and supports his sister. The Expansion Pack Black Knight assumes the former choice, with Dresari becoming a tyrant whom the Black Knight Legion is hired to take down.
- The finale of Transformers: Fall of Cybertron involves the player selecting to control either Optimus Prime or Megatron as they have their final battle before landing on Earth.
- In the final story mission of Grand Theft Auto V, Franklin is forced to kill either Michael or Trevor. However, it's also possible to Take a Third Option where the characters team up to take care of loose ends.
- Saints Row IV has one mission where you fight and kill what can be considered a "past self" of the player character from Saints Row 2 and your character notes how it's the Stillwater default player. After killing it, you fight another version of the default player and a second person, which Kinzie says it's the co-op player. The entire fight takes place in a simulation so nothing of value is lost when the previous player characters are killed.
- Assassin's Creed: