Lone Wolf Boss
This is when a Video Game boss isn't teamed up or associated with the Big Bad. He's a lone wolf and isn't anyone's lackey. He's a villain on his own. This is relatively common in RPGs, where the player party often winds up just running into bosses that just happen to be at the end of caves, attacking a town, guarding MacGuffins, etc. Sometimes overlaps with Giant Space Flea from Nowhere, but while the Giant Space Flea From Nowhere comes from out of, well, nowhere, the Lone Wolf Boss is often established into the plot, and sometimes even plays a crucial role in some way, but either has nothing to with the aims of the Big Bad, or is outright opposed to them. Compare Villain of Another Story.
- King Boom Boo from Sonic Adventure 2. A ghost is haunting the Death Chamber and harasses Knuckles after he finds the key to Eggman's base. Eggman has his own Egg Golem as a guard, so it wasn't deployed by him.
- The only boss in Conkers Bad Fur Day that is related in some way to the Panther King is the Experiment; 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).
- 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.
- 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 unambiguous.
- Super Paper Mario has Francis, the third boss.
- 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.
- 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.
- Rayquaza from Super Smash Bros. Brawl, though Tabuu does later use him to guard the Great Maze.
- 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.
- 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.
- 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.
- Fire Emblem: Battles against random bandits not affiliated with the story's main villains are ubiquitous, usually early in the game. 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 Daien or Ashnard at all. He's actually fought because the leader of Begnion has promised an alliance against Daien 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 serves this role early on before becoming much more important later.
- Most of the enemies in the Baldur's Gate games 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.
- 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.
- 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.
- Papu Papu, the first boss of the first Crash Bandicoot (1996). Every other boss in the series 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.
- 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.
- 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.
- 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.
- 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.
- Brady Culture in the first episode of Sam & Max: Freelance Police is the only antagonist not working for Hugh Bliss.
- 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.
Non-Video Game Examples Include:
- Harry Potter: Aragog isn't a minion of Voldemort.
- Harry Potter: Dolores Umbridge isn't one of Voldemort's death eaters.
- Eureka: Most villains aren't affiliated with Beverly Barlowe.