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- The only boss in Conker's Bad Fur Day that is related in some way to the Panther King is the Experiment, found and fought in the War Arc chapter; and it's because it and the Tediz were created by Ze Professor so they could defeat the Panther King (Conker still has to defeat them because they are threatening the otherwise peaceful kingdom).
- Mystery G in Neo Contra. He has no connection to the villains of the game, yet he's only there as a mini-boss in Mission 2 to make sure that Bill Rizer is the ultimate soldier. He also pulls a Heroic Sacrifice halfway through the game, depending on how good your performance was throughout the game.
- Papu Papu, the first boss of Crash Bandicoot. Every other boss in the game is either a scientist working with the Neo Cortex, or an animal Cortex mutated. Papu Papu, on the other hand, is just the leader of a Wacky Wayside Tribe that Crash stumbles through.
- Dante plays this role in Devil May Cry 4 (and he is That One Boss to boot). Nero thinks he is the Big Bad at first, since the first thing he does is interrupting a sermon and killing the local pope. He's actually just here to get Yamato back and discover what the Order of the Sword (for which Nero works) is up to. Then Nero discovers that the Not Quite Dead Pope in question is the real Big Bad, so Dante sort of becomes an Aloof Ally.
- The Legend of Zelda:
- In The Legend of Zelda: Skyward Sword, Moldarach and Tentalus (both, incidentally, found in Lanayru Desert) are the only two bosses with no connection to Ghirahim.
- Gohdan from The Legend of Zelda: The Wind Waker is a creature born of the Gods' need to test the potential hero. As such, he does not appear in the refights at Ganon's Castle.
- Several minibosses in The Legend of Zelda: Majora's Mask, given the nature of the game's villain. Among them, the ancient creatures and peoples of Ikana Canyon stand out, including Captain Skull Keeta, Igos du Ikana, and all of the Garos.
- In Mega Man X6, Dynamo isn't helping Gate and his Nightmare Investigators, nor X and the maverick hunters; he's just there to gather some nightmare souls (which on this game would be something like Experience points) to make himself stronger.
- Cyborg Ninja in Metal Gear Solid is the only boss in the game that isn't a part of Fox Hound. He's a tertiary factor, antagonistic to both sides. It turns out to be Gray Fox, who left Fox Hound before the events of the game.
- The B.O.X Security Robot in Metroid: Fusion is the only boss in the game to not be infected by an X parasite. The first time, anyway, as it reappears for a second round once an X parasite infects it's organic components.
- Crocomire in Super Metroid does not seem to be affiliated with the Space Pirates at all, mostly just being a random Zebes creature until Samus shows up and attacks it.
- Metroid Prime 2: Echoes has almost all of its bosses being either Ing or Ing-possessed creatures. The exceptions are Dark Samus, who appears three times doing her own thing, and the Caretaker Class Drone, a random machine that attacks Samus.
- Of the seven sea monsters in The Ocean Hunter, five of the seven are explained to have been the creations of the seventh, Rahab the sea god. The sixth one, Midgardsorm, is implied to be a completely unaffiliated party but may have caused more death and destruction than Rahab himself.
- Benny and Clyde from River City Ransom - they're not affiliated with any of the gangs working for Slick, and it's strongly implied that they fight Alex and Ryan solely because the latter two intruded on the former two's hangout.
- All of the bosses in Sly 3: Honor Among Thieves aside from Dr. M's mutant creatures.
- The Ox in the Metropolis level in Spyro 2: Ripto's Rage!.
- In Time Crisis and Time Crisis II, Wild Dog is The Dragon to the games' respective Big Bads, but starting in 3, he works separately from the Final Boss to get revenge on the VSSE. in Project Titan, he is the Lone Wolf Final Boss operating bunches of robot projects, challengine Richard from VSSE.
- In the first Viewtiful Joe, Alastor was affiliated with JADOW, but didn't really care for their plans (even after explaining them in meticulous detail by reading the game's script aloud); he (as a Noble Demon Blood Knight) was only concerned with fighting strong opponents like the eponymous hero. In both Viewtiful Joe 2 and Double Trouble, he reappears, unaffiliated with either game's villainous organizations (GEDOW and MADOW) and is again only there to seek a rematch with Joe.
- Brady Culture in the first episode of Sam & Max: Freelance Police is the only antagonist not working for Hugh Bliss.
- Rayquaza from Super Smash Bros. Brawl, isn't allied with the other villains and is just attacking Fox because Fox entered his territory. Subverted later on when Tabuu creates a clone of him to guard the Great Maze.
- Depending on which version of the game, the first boss or most of the bosses in Donald Duck: Goin' Qu@ckers aren't affiliated with the final boss and Big Bad Merlock (the one exception being the Game Boy Advance version, where Merlock is the only boss faced in the game):
- The first boss (Bernadette the Bird in the console versions, Humphrey the Bear in the Game Boy Color version), due to being a non-anthropomorphic animal, is clearly not attacking Donald because of Merlock's orders and simply serves as an obstacle to prevent Donald from rescuing Daisy immediately.
- While the Beagle Boy faced in Duckburg and Magica De Spell appear to be attacking Donald for their own reasons in most versions, this isn't the case in the remake made for PlayStation 2 and GameCube, where the Beagle Boy trio and Magica actually mention being ordered to attack Donald by Merlock in the cutscenes prior to their boss fights.
- The Crew has Cameron Rockport. Whereas the other named opponents are members of the 510 crewnote , 'Cam' is a lone individual who serves as the boss of the South region, as his efforts are the sole reason there isn't a significant 510 presence in the region.
- Most of the enemies in the Baldur's Gate games, especially the second one, have nothing to do with the main enemy, being interested in you because of who you are or just having their own plans you wander into.
- Many of the bosses in the second half of Final Fantasy VI— Phunbaba, Doomgaze, the Eight Dragons, and Atma Weapon— don't work for Kefka, but were released from their slumber when he started mucking about with plate tectonics. In the first half of the game, Vargas has nothing to do with the Empire— he's just a martial artist with an unrelated grudge against Sabin— and neither does Dadaluma, a thug who apparently just loves to fight (and is possibly mentally disturbed).
- Fire Emblem: Battles against random bandits not affiliated with the story's main villains are ubiquitous, usually early in the game. The Blazing Blade actually somewhat subverts this by having a series of bandits stretched out over multiple chapters during Lyn's story, thus averting the "lone" aspect of it.
- Oliver in Path of Radiance, a corrupt senator with connections to slave traders, serves as the Arc Villain while the group is in Begnion, but he isn't connected to Daein or Ashnard at all. He's actually fought because the leader of Begnion has promised an alliance against Daein on the condition that Ike's group help take him out.
- Validar in Fire Emblem Awakening is a strange case. He's fought while Mad King Gangrel is the current Arc Villain and seems to have no connections to him. However, Validar is actually The Heavy of the game in reality and Gangrel is just a Disc-One Final Boss, and while this is obvious to the player from the start, the characters in-game don't know this yet. So he serves this role early on before becoming much more important later.
- Kingdom Hearts II:
- Implied with Shan Yu. He has his own army of Heartless, but is never seen making contact with Pete or Maleficent to make any sort of deal. He's trying to conquer The Land of Dragons on his own, and only battles Sora because he's in the way.
- Hades is shown working with Pete during the first visit to Olympus Coliseum on a joint venture to take care of both Sora and Hercules, but on the second visit appears to have ended the alliance to focus on Herc.
- On the first visit to Halloween Town, Lock, Shock, and Barrel are working for Maleficent and fight you to buy time for Oogie to get better from his recent resurrection. When they're encountered on the second visit, they're not working for anybody and start causing trouble in Christmas Town just because it's fun.
- On the second visit to Halloween Town, somebody is stealing presents from Santa Claus for unknown reasons. It's later discovered that the theft was caused by the Experiment, a creation of Dr. Finklestein's that went rogue. It stole the presents in a vain attempt to gain a heart, which Dr. Finklestein did not give it during the creation process.
- The MCP is unaffiliated with the other villains, and tries to take over Hollow Bastion on its own.
- Your rivals in Pokémon. They're not allied at all with the villainous team that are the main big bads of the game, but they challenge you anyway to test their strength. Sometimes they serve as the True Final Boss after the main villains are dealt with, but not always.
- King Boom Boo from Sonic Adventure 2. A ghost haunting the Death Chamber that attacks Knuckles after he finds the key to Eggman's base. Aside from living in the pyramid that Eggman turned into his base, it isn't associated with Eggman in any way, as the latter has his own Egg Golem as a guard, so it wasn't deployed by him. King Boom Boo is simply the leader of the smaller ghosts that keep appearing in Knuckles' levels.
- Super Mario Bros.:
- Belome and Punchinello in Super Mario RPG. The game actually has quite a few villains who aren't connected with the main bad guys, but these two are given the least context. There's also Booster, who indirectly causes the game's most extreme example of Giant Space Flea from Nowhere. Valentina, like Booster, is also the main villain of a story arc but is in no way affiliated with the Big Bad.
- Despite being a Koopa, Jr. Troopa in Paper Mario actually isn't aligned with Bowser. In fact, near the end of the game he even attacks four of Bowser's minions just to get a final match with Mario.
- Most Chapter bosses in Paper Mario: The Thousand-Year Door aren't affiliated with the X-Nauts, the main antagonistic force in the game. Hooktail, however, does turn out to have been affiliated with the game's Bigger Bad. Most of them, such as Grubba or Cortez, are simply bad guys who found one of the Crystal Stars and are using or hoarding it for entirely selfish reasons. Doopliss is an interesting case since he starts out as a Lone Wolf Boss but then allies himself with the Shadow Sirens after his chapter. Smorg is another odd example in that it was originally intended to have been a creature summoned by Beldam of the Shadow Sirens, but this exposition dialogue was cut in the final version, leaving its origins ambiguous.
- Super Paper Mario has Francis, the third boss. He is not allied with Count Bleck; he's just some nerd who kidnapped your Exposition Fairy.
- Several bosses from Super Mario Galaxy, such as Major Burrows and Buggaboom, have to be defeated because they're threatening innocent characters for personal reasons, not because Bowser told them to do so.
- The Bubble King and Ghost bosses from Wario Land 2, which initially start by capturing the Big Bad (temporarily). Kind of their own antagonists, considering that beating them gets an alternate ending.
- Many examples also exist in the Mario & Luigi series, like Popple from Superstar Saga, possibly Trunkle from the same game, Bowser in all three games, Durmite/whatever in Bowser's Inside Story, the Tower of Yikk (second giant Bowser boss) in the same game, Mom Piranha and the Piranha Bean in Superstar Saga, Mrs. Thwomp in Partners in Time, and Broque Monsieur in Bowser's Inside Story have no connection to the Big Bad whatsoever, and most have no connection to the storyline at all.
- In Mario & Luigi: Dream Team, you've got Grobot (which just malfunctioned), Mammoshka (who was just in the way), Mount Pajamaja (who you annoyed in the dream world), Big Massif (who you fight in the dream world to wake up his real world counterpart), Wiggler (who you fight because Popple made you think he was a security guard), Popple (who was just robbing a building at the time), the Zeekeeper, Pi'illodium and quite a few others.
- From the second X-Men Legends, Sauron. He makes it very clear he sent Apocalypse's goons packing when they came recruiting, but when the player mentions they work with Ka-Zar, he attacks out of spite.
- In the first Marvel Ultimate Alliance, the Mandarin, Mephisto, and Galactus are not affiliated with Dr. Doom or the Masters of Evil. Mandarin had previously left the group after a failed attempt at taking it over for himself, and the two immortal beings were used by Doom in his quest for power. Nonetheless, you still have to fight them.
Shoot 'Em Ups
- The first few bosses of most Touhou games rarely have much to do with the plot.
Non-Video Game Examples Include:Literature
- Harry Potter and the Chamber of Secrets: Aragog isn't a minion of Voldemort. Also Lockhart is just working to improve his own position, and has nothing to do with the heir of Slytherin.
- Harry Potter and the Order of the Phoenix: Dolores Umbridge isn't one of Voldemort's death eaters, she's just a very sadistic Obstructive Bureaucrat. She does join them in Deathly Hallows, but less because she cares about pureblood supremacy and more because they give her a convenient supply of victims to torment.
- Eureka: Most villains aren't affiliated with Beverly Barlowe.
- Gulpo (King of the Blobs), a oneshot villain from the Joe Oriolo Felix The Cat cartoon "Felix Babysits". He's not affiliated with Professor or Master Cylinder, he's just a ravenous amoeba that becomes a threat to Felix and Poindexter when the latter shrinks Felix and unwittingly enlarges Gulpo with a formula. He comes back as a boss fight in the 1992 video game, but due to the games wafer-thin plot, it's not clear if he's affiliated with Professor now or if he's just giving Felix trouble again for the heck of it.
- Young Justice: Harm is the only villain that is not revealed to have been (and is permanently defeated before he is even known about by, let alone becomes) part of The Light throughout the show's two seasons.
- Gravity Falls: Only a few of the Monsters of the Week are related to the mystery surrounding the Author of the Journals, even counting the ones that the Author interacted with in the past. (Some episodes have the Pines discover an entirely "new" anomaly, such as the two living video games or the Summerween Trickster.) None of the villains are allied with Bill Cipher except for other major antagonist Gideon (even that doesn't stick), and when Bill's true minions finally do show up, it's only for the last few episodes of the series.