Crossovers, more than almost any other kind of story, can get audiences excited based on little more than the idea alone. While that may be a good thing for publicity, a really good crossover can be extremely hard to write. Since you're already working with established characters that have their own stables of fans, you're already dealing with the baggage of fan expectations, and the pressure to get each of their beloved characters just right.
That alone can derail an otherwise promising tale, but one must also consider the more fundamental questions: when you've assembled a nigh-unbeatable squad of heroes, what can you possibly give them that would present them with a credible threat? The simplest, or at least most obvious, answer may be "an equally powerful, united gang of villains." But that raises yet another question: who is going to lead this group of overpowered, antisocial backstabbers? Oftentimes, one villain out of the group gets promoted to Crossover Villain-In-Chief.
A Crossover Villain-In-Chief is a previously established villain that, for whatever reason, becomes either the official or de facto leader of most or all of the other villains in the crossover. There may be a clear reason why they were raised to this position: they may be the most intelligent and/or best strategist, they could have the best (or only) leadership skills of the group, they may be the most skilled in combat, or they may just be so scary that none of the other villains dare challenge them. In more lighthearted or comedic works, they may just be the the least stupid or incompetent of the bunch. Sometimes, however, they may become the leader for no other reason than being the most popular villain, or even the writer's favorite of the bunch. In rare cases, this role may be filled by a Big Bad Duumvirate, ideally representing characters from more than one universe.
However, the Crossover Villain-In-Chief need not be the ultimate evil entity of the overall story; they only need to be the leader of a group of other villains. It's not unheard of for the Villain-In-Chief to be controlled, manipulated, or otherwise employed by a greater malevolent force, be it knowingly and willingly or not.
Sister trope of Crossover Combo Villain, which takes all of the villains (or elements thereof) and rolls them into one character. Related tropes include Villain Team-Up, Legion of Doom, and Monster Mash. Contrast Original Generation when the writers choose to create a new character (in this case, as the main villain).
- In JLA/Avengers, Krona fits this role, summoning all of the villains of the DC and Marvel universes as troops to toss against the heroes (and he has the power to make them obey — the climax happens in his personal palace, made out of Galactus' corpse).
- Crisis on Infinite Earths has an alliance of practically every villain from five different Earths being led by the Superman villains Brainiac and Lex Luthor.
- In DC's Crisis Crossover events that involve a lot of villains, like Salvation Run and Forever Evil (2013), the Big Bad Duumvirate of Lex Luthor and The Joker are usually the ones in charge.
- Marvel Comics 12-issue crossover series Secret Wars (1984) has the godlike Beyonder abduct many of Earth's mightiest heroes (Fantastic Four, Avengers, the X-Men, Spider Man) and likewise Earth's most dangerous villains (Absorbing Man, Ultron, Galactus, Enchantress). The two groups are deposited on a distant world, and set to a Goodies versus Baddies free-for-all. The Goodies decide upon Captain America as their leader; the Baddies settle upon Doctor Doom as their chief, though only after Doom orders Ultron to slay Kang the Conqueror as an object lesson.
- In Spider-Men, Mysterio's portal is responsible for Peter getting sent to Miles' universe. He also serves as their primary opposition in getting Peter home.
- In Spider-Verse, the Spider-Men from the Multiverse fight against Morlun and his family, the Inheritors, before this villain murders every version of the friendly neighborhood.
- In Sonic the Hedgehog/Mega Man: Worlds Unite, Sigma quickly establishes himself as the crossover's primary villain, as he merges Sonic and Mega Man's worlds together, pushes aside both Dr. Wily and Dr. Eggman, turns the Deadly Six into his servants, and sends an army of Mavericks into multiple universes.
- In Amazing Fantasy, Mysterio forms a Big Bad Duumvirate with the Greater-Scope Villain of the My Hero Academia universe, All For One, supplying superpowered weaponry to the local Villains to wreak havoc on Japan. Unbeknownst to him, All For One doesn't see him as an equal at all, and just wants to use him to further Shigaraki's ascension.
- In Dimensional Links, a crossover between all the The Legend of Zelda games, Demise quickly establishes himself as the most dangerous of all villains, and the others are forced to follow his orders.
- In The Dimensional War, Ganondorf is definetely this. Though Kylo Ren has some independence, it's clear Ganondorf is the dominant of the two.
- Iron117Prime's fanfics tend to have only one villain faction come out as the primary villain during the latter parts of the story.
- Frozen Turtles: The Shredder (his 2012 incarnation) proves himself as the more formidable villain, outright killing Hans (having also terrified him) and growing obsessed with obtaining Elsa's power. By Into the Unknown, he's effectively gained ice powers of his own and, once again, becomes the most dominant force everyone has to face.
- Tangled with Ninja: The Overlord becomes the main antagonist after he resurrects Mother Gothel so he can gain Rapunzel's power to restore himself to his former glory. When Gothel attempts to go after Rapunzel on her own, the Overlord is less than happy, and instills a huge amount of fear in her.
- Worlds Collide (TMNT): The Shredder (his 2003 incarnation) quickly establishes himself as the more formidable villain. Right when he encounters Aang, he brutalizes the young hero in a complete Curb-Stomp Battle. Later on, he exterminates Long Feng and the Dai Li in order to keep his position and prevent any usurpers from undermining his schemes. On the Day of the Black Sun he launches Operation Dragon Slayer, in which he kills Ozai, orders the Foot Clan to dispose of the War Council, and effectively drain the Fire Nation's resources to unleash Sozin's Comet like an extinction-level asteroid impact. Even Azula is terrified by him, so much that when she learns of Ozai's death by his hand, she loses it and hands it to the heroes to finish him off.
- Fairy May Cry: By being the Greater-Scope Villain of the fanfic, Mundus has taken this position, though not as much as the others. He's the one who provides Zeref's immortality curse and coerces Precht to turn to the dark side. He isn't as active as some of the other villains listed here, though the impact he has on the story is measurable by those characters and their deeds.
- Code Prime: Megatron is bar-none the biggest threat for the Autobots and the Black Knights to deal with. He's responsible for the problems plaguing Earth as he served as a mentor to Charles zi Britannia during the latter's childhood, allowing him to rise to power and become Emperor of Britannia. Megatron fully cements this by killing Charles and sacking Pendragon because he was disappointed about Charles' ulterior motive in the Ragnarok Connection. This effectively decapitates Britannia, and the Decepticons emerge as the predominant villains of the entire series.
- J-WITCH Season 1: The Jackie Chan Adventures villains take center stage in this fic. Daolon Wong is a servant to Phobos, but he proves to be a far more vile villain than him. Then Shendu takes the helm...for a grand total of a chapter, but still kills Cedric and nearly kills Miranda.
- Though it should be noted that unlike Hans, Gothel, Ozai, or Charles, Phobos manages to survive (albeit depowered).
- Avengers of the Multi-verse: General Modula is the head of the Cabal and the one who brought all the villains together and makes the plans to beat the Avengers. However, it's a tenuous position at best, as all the other villains include the likes of Vilgax, Vlad Plasmius, Van Kleiss, and the Dark Dragon, who are predictably vying for some leverage over each other for when the heroes are defeated.
- In Shattered Skies: The Morning Lights, Chaos is the force behind Dead End, but as it can't take physical form, it uses Joker as its Heavy and public face.
- The Marvel Gems Universe story Steven Universe: Secret Wars features Thanos bringing together multiple villains to fight the Crystal Gems and The Avengers for him, and becomes the Final Boss after they're all defeated.
- Gravity Soul features the respective Big Bads of Gravity Falls and Soul Eater, Bill Cipher and Asura, teaming up to exact revenge on their enemies by Asura making a deal with Bill. This causes the two to merge into Kishin Cipher, which makes the two more powerful and they begin bringing together antagonists from both shows to serve them.
- Rise of the Brave Tangled Dragons works often cast Pitch Black as the central antagonist, owing to his status as an immortal representation of fear itself.
- Equestria Girls: A Fairly Odd Friendship: Once the Dazzlings arrive on the scene, they quickly establish themselves as the main threat, proving to be more cunning, powerful, sadistic, and overall more dangerous than any other antagonist in the setting.
- There Was Once An Avenger From Krypton: The entire Krypton-verse exist because Doctor Doom and Reed Richards have been fusing other worlds with the Marvel Cinematic Universe, bringing not just heroes but also villains like Vilgax, the Horde, the Galra Empire, and the Diamond Authority. All of this is for the purpose of creating a strong enough force on Earth to defeat Thanos and prevent the Snap that devastated Doom's and Reed's timeline.
- Gokaiger Goseiger Super Sentai 199 Hero Great Battle sees the Black Cross Fuhrer assuming leadership of the revived Super Sentai villains. Which is rather appropriate, since he is the original Super Sentai Big Bad.
- Kamen Rider × Super Sentai: Super Hero Taisen reintroduces Dai-Shocker from Kamen Rider Decade and introduces a new Legion of Doom of Super Sentai villains called Dai-Zangyack. Their leaders, bizarrely enough, aren't past villains but two past heroes gone astray - Tsukasa Kadoya/Kamen Rider Decade and Emperor (formerly Captain) Marvelous/Gokai Red respectively. Except it later turns out they're really puppets for the true masterminds - Narutaki and Bio Hunter Silva. Of all villains to helm a Legion of Doom, those are two pretty bizarre choices considering the former was just Decade's annoying Arch-Enemy for the first half of his series and the latter was the Wild Card in Choudenshi Bioman.
- Spider-Man: No Way Home brings supervillains from the Spider-Man Trilogy (Green Goblin, Doctor Octopus, and Sandman) and The Amazing Spider-Man Series (Lizard and Electro) into the Marvel Cinematic Universe due to a botched spell by Doctor Strange. By the midway point, the Goblin quickly establishes himself as the biggest threat of the visitors, convincing the others to reject Peter's cures and killing Aunt May just to make sure that It's Personal between him and this world's Peter. After that, he serves as the Final Boss after all the other villains (except Doc Ock, who did a HeelFace Turn earlier in the film) have been Brought Down to Normal.
- Kamen Rider Decade: Apollo Geist is the one leading Dai-Shocker, an alliance of numerous past villains and monsters. Technically, the original leader of Dai-Shocker was a pre-amnesia Tsukasa Kadoya, but he's out of the picture by the time the story begins and Geist seems to be the one who's taken over as acting leader.
- Legends of Tomorrow: Season 2 has the Legends battling the Legion of Doom, a team up of major villains from its parent shows Arrow and The Flash (2014). As the only one with powers The Reverse Flash pretty firmly establishes himself as the leader of this villain pack, much to the others' annoyance, as they don't like being treated as lackeys.
- Ganondorf is the de facto leader of the enemy forces in Hyrule Warriors, where he is leading past Zelda villains such as Zant, Ghirahim, Yuga, and original villains developed specifically for the game. Some new villains were arguably necessary, as the Zelda franchise hasn't featured very many villains not named "Ganondorf" or his beast form, "Ganon."
- JoJo's Bizarre Adventure: Eyes of Heaven: Heaven Ascension DIO, an alternate version of Part 3 DIO that defeated the Stardust Crusaders, is the master of the various villains from across the eight parts of Jojos Bizarre Adventure.
- Super Smash Bros. Brawl: while not technically the leader, Ganondorf is still The Dragon to Canon Foreigner Tabuu, putting him at the head of an army that includes other franchise villains Bowser, Wario, King Dedede, Petey Piranha, Ridley, and Porky Minch.
- While she isn't the Greater-Scope Villain of the Kingdom Hearts series, Maleficent certainly fills this role at various points throughout the series. In the original game, she's leading Hades, Jafar, Ursula, Oogie Boogie, and Captain Hook (and Pete wandering about off-screen) in an effort to find the Seven Princesses of Heart and unlock the gate to Kingdom Hearts, a vast repository of knowledge and power.
- Ganondorf heads the Legion of Doom in Rakenzarn Tales and serves as the Big Bad overall for the game.
- Captain N: The Game Master has Mother Brain as the series' primary head villain. This is mostly Played for Laughs, as calling her henchmen — King Hippo and Eggplant Wizard — incompetent would be a gross understatement. It's saying something that the character who's little more than a brain in a jar is a bigger threat than either of her able-bodied underlings.
- In Phineas and Ferb: Mission Marvel, Dr. Doofenshmirtz tries to team up with the other many villains of Marvel Comics to take over the Tri-State Area, but Red Skull takes one look at Doof's utter lack of threat and, after stealing Doof's latest "-Inator" gadget, and putting him out of the game (non-lethally, of course) leads the rest of the Marvel villains to raise some hell.