The mindset is this: you see a world without fear, without anger, hate, or war. And then you go and conquer that world, because they'd never expect it.
So, the Big Bad is done for. Maybe they Never Found the Body, or maybe s/he's finally been Killed Off for Real. But for some reason, the series of events hasn't ended yet.
The Evil Power Vacuum occurs when a Big Bad is, at long last, seemingly taken down by the good guys or an outside group. The result is usually a sort of "power scramble" amongst the good guys, the bad guys, and every allegiance in between, as each group tries to come out on top. Tyrant Takes the Helm is when a revolution or a coup dethrones an old evil leader, only for a new evil to take its place.
This is sometimes the result of Nice Job Breaking It, Hero, especially if the chaos following the Big Bad's fall is worse than anything he ever did.
See also Balance Between Good and Evil, Enemy Civil War, Asskicking Equals Authority, and The Starscream.
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Anime & Manga
This happens in Melody of Oblivion whenever the Monster King is killed. Last time, it caused an apocalyptic war that more or less ruined reality (it turned Earth into a maze, which is meant almost entirely literally), and was only stopped once the killer agreed to become the next Monster King. The monsters themselves are eldritch abominations. it's rather interesting that humanity *could* fight them, even if they lost.
This is happening in One Piece. With the death of Whitebeard, piracy is skyrocketing as it did when Gold Roger was executed, now worse than ever, possibly. Apparently, the only thing keeping most possible crews from forming was the belief that there was no room at the top. That, and belief in One Piece was beginning to waiver. Whitebeard saw to that as well.
The premise for the Doryu Arc of Rave Master is that other criminal groups are trying to become top dog after Demon Card was destroyed. However, before the arc is even over, Demon Card has been revived by the new Big Bad.
A storyline in the original backstory of Magic: The Gathering involved Ertai and Crovax, both former crewmen of the Weatherlight, fighting over which of them will succeed the now-vanished Volrath as ruler of Rath. This leads to a series of brutal confrontations that sees both of them turning into figurative and literal monsters (courtesy of some Phyrexian implants) and destroys whatever good is left in them. Crovax eventually succeeds, at the cost of finally, irrevocably crossing the Moral Event Horizon.
In Runaways, the team has to deal with this after taking down their evil parents, who ran all the illegal activities anywhere within range of LA.
And in the Moon Knight series, there's a new "Kingpin of L.A." filling the void.
A running theme of the Milestone comic Hardware was that Hardware's mentor/boss/enemy (it was complicated) kept his hand in organized crime because without his influence, anarchy would be loosed amongst the criminal element of the city. Later, he died trying to save people, and it turned out he was right.
In the Spider-Man universe, when Parker helps to take down The Kingpin, it almost immediately turns worse, as less-refined, less-humane, and less-subtle underbosses scramble to take the top spot Kingpin used to occupy.
When Kobra, a long-time Diabolical Mastermind who had served as a Big Bad many times in The DCU, was Killed Off for Real by Black Adam, his Religion of Evil was wracked with power struggles. This seems to have been settled, as his good twin has been brought back to life, turned evil, and taken the reigns of the organization. And become the Big Bad in a JSA miniseries.
In The Savage Dragon, a Gang War erupts after Dragon kills Overlord, the ruler of the Vicious Circle.
In Queen Of All Oni, it's revealed that Daolon Wong was the Darkest Mage, a sort of arch mage for Evil Sorcerers. Following his loss of power at the end of season 3 and his death in-story, the spot is now open, and a couple of subplots focus on the villains trying to gain power to assume the role Wong left behind.
Films — Animation
In Transformers: The Movie, following Megatron's apparent demise and subsequent dumping into space, the Decepticons try to decide on a new leader, and their argument leads into an all-out brawl aboard Astrotrain. It turns out Megatron is Not Quite Dead, though, and after a power-up from Unicron, he returns as Galvaton in time to reclaim his title as leader of the Decepticons... by blowing Starscream to ashes mere seconds after he'd literally crowned himself the new leader.
Inverted in Megamind. Megamind "defeating" Metroman caused Megamind to make a new hero, and Music Man advises Megamind that wherever there is evil a new force for good will rise.
Films — Live-Action
At the beginning of L.A. Confidential, mob boss Mickey Cohen is arrested. A recurring subplot shows all the mobsters seeking to fill Cohen's place either being scared out of Los Angeles or riddled with bullets. By the climax of the film, Police Chief Dudley Smith is poised to seize control of L.A.'s organized crime.
American Gangster: The beginning of the film takes place after Harlem mob boss Bumpy Johnson's death, and shows Frank Lucas's rise to power out of the chaos that accompanied Bumpy's death.
In the Lone Wolf series of solo gamebooks, each time the Archlord of the Darklands is killed, the remaining Darklords fight an Enemy Civil War to determine the next Archlord.
The main danger of the One Ring in The Lord of the Rings is that powerful individuals would eventually use it to replace Sauron. Even if they resisted corruption long enough to defeat him, they'd end up becoming corrupt and replacing him in the end.
Partial example in the appendices of ROTK where Aragorn and Éomer are forced to go on punitive expeditions among the Easterlings and Haradrim to keep this under control.
Tolkien briefly considered a sequel to LotR in which Aragorn fights against a Morgoth-worshipping cult which seeks to bring back Middle-Earth's original Big Bad, but ultimately (and probably wisely) decided that it would subvert the trilogy's End of an Age / Dawn of an Era themes too much.
Anti-Villain mobster "Gentleman" Johnny Marcone maintains an iron grip on the Chicago underworld in order to avoid precisely that; sure, he's gotten rich from exploiting other people, but at least under him the most unpleasant aspects are kept to a strict minimum. If he were to go, the turf wars and power grabs would tear up the city, and lots of innocent people would get killed in the crossfire.
Also, in the short story "Aftermath", set after Changes, the destruction of the Red Court has led to a power struggle among other supernatural baddies. The only race seen in the story is the Fomor, but Gard indicates that several others have appeared. And incidentally been fought off by Marcone, who probably has every intention of filling the Red Court's void himself, at least on the local level.
This ongoing struggle goes on to be one of the two major plot threads in the next full-length novel, Ghost Story.
Partway through The Mallorean, the main characters are informed of how current Big Bad Zandramas took her position — after the death of God of Evil Torak, the Grolims (his priests) were left completely without guidance... until she had a vision, ran off into the wilderness, and eventually came back to take over the church. (The intervening period, as the heroes work out, is when the Dark Prophecy settled into her head.)
At the end of the first book of Brian Sanderson's Mistborn trilogy, the protagonists have succeeded in killing the immortal Lord Ruler, who had reigned over the Final Empire for a thousand years. Being, well, immortal, the Lord Ruler didn't leave behind any instructions on what to do in his absence, and the protagonists only have control over the capital city. As a result, the rest of the empire has quickly devolved into various warring factions struggling for power, and the capital city is looking like a big, fat target ripe for conquest...
Toward the end of Belisarius Series there was a large ammount of power jockeying between the various empires once it became clear that the Big Bad was doomed militarily.
Happens in Charmed after the Source is killed (for the third and final time). At first there is an orderly succession, but it rapidly breaks down and increasingly-mediocre contenders appear as Big Bads each season thereafter.
The entire neighborhood is united in hatred of the main characters. Hal and Lois win them over, and five seconds later the street's turned into a giant screaming match.
When Reese stops being the school bully, a dozen other bullies appear and terrorize the students. Malcolm has to persuade Reese to return to his evil ways to bring things back to a manageable level. Reese is particularly outraged when he sees people picking on Stevie (who's out of bounds due to being in a wheelchair).
Reese: I was a jerk! Malcolm: Yes, but you were the alpha jerk!
A major plot point of The Shadow Line is the power vacuum in the drug trade following the death of Harvey Wratten. In the final episode, it turns out this was specifically invoked by Gatehouse, who killed Harvey to give his protégées Jay Wratten and Ratallack a chance to rise to the top.
Stargate SG-1 has a very, very long Sorting Algorithm of Evil, arguably to the point of deconstruction. The big source of that is that the followers of a dead System Lord defect to the System Lord who killed their master. But what happens when your master was killed by someone who is not only not a System Lord but isn't even Goa'uld? Okay, let's get this party started:
Apophis. Starting with kidnapping several friends of the main characters for use as hosts he remained a threat until he, after steadily losing power and influence because of the conflict with the heroes, was defeated and killed by a more powerful System Lord late in the second season.
Sokar, having inspired the myth of Satan through his ruthlessness and evil and having a fleet of warships at his command ready to conquer the galaxy, was shaping up to be the new Big Bad when SG-1 and their Tok'Ra allies killed him by blowing up a moon. Unfortunately, before Sokar was killed he had brought Apophis Back from the Dead so that he could suffer on said moon. Apophis, true to form, survived and took control over Sokar's resources and army.
So, once again the Big Bad is Apophis. Apophis with a fleet of warships poised to take over the galaxy. He starts with attacking Teal'c's homeworld of Chulak, continues by killing several rival System Lords and, when on the brink of Galactic Domination, his fleet is vaporized when SG-1 blow up a sun. Unfortunately he survives. Also unfortunately, the nova screwed up the Faster-Than-Light Travel of the ships escaping the nova, and both Apophis and SG-1 find themselves trapped in another galaxy. To make it even worse, the writers choose this exact moment to subvert Scifi Writers Have No Sense Of Scale and Casual Interstellar Travel, meaning that even traveling at full speed, it would take over 200 years to return to their own galaxy. He's eventually killed for real when the Replicators invade his ship and it slams into another planet.
Next up is Anubis, who creates a nearly-unstoppable force of super soldiers, and has access to technology more advanced than literally everyone else except the Neglectful Precursors, who are all gone. He devastates the remaining System Lords with his immense forces, leaving our heroes as the only hope of stopping him. He is finally defeated when the fleet sent to conquer Earth is destroyed by a Lost Technology Superweapon.
Ba'al takes over the remainder of Anubis' forces and continues to take over the galaxy. He was doing a pretty good job until the replicators launch an all-out attack, starting by killing all the remaining System Lords other than Ba'al and Anubis, who's still alive and actually commands Ba'al, who defects and winds up in an Enemy Mine with the heroes. End result: Anubis is gone for good when Oma decides to spend an eternity fighting him. The System Lords are all dead, except for Ba'al, who is overthrown, and the Replicators are wiped out. Finally, with all major enemies defeated, the series ended. Everyone lives Happily Ever After...
Wait, what? Yeah, that's right, it's the Ori on their universal Missionary Tour of Evil and Doom, but at least the finale may or may not have nuked them all... and in fact did, but that left their self-created Jesus archetype Adria, newly Ascended, to take over all their power. It took brainwashing her followers into forsaking her with an ancient mind probe and falling into the same "fighting for eternity" trap that Anubis got into that the Universe was finally saved...or, at least as saved as it can be with the Wraith still bopping around the Pegasus Galaxy...
Mentioned in the background of Season 3 of Supernatural — in light of Azazel's death in the previous season finale, the Legions of Hell are left fighting each other for control, with Lilith rising as the new "Queen Bitch" in the latter half of the season.
Later seasons have Crowley as the King of Hell, and in season 9, while he's held prisoner by the Winchesters and presumed dead by his minions, Abaddon attempts to take his place.
Believe it or not this is how Triple H wound up becoming who he was. The Undertaker and The Rock both ended up injured. Trips, who was at the time thought not to be over enough to hold the spot, got moved up by default.
In the WWE, this tends to happen when someone in the main event is either out for a long time, becomes a part-timer, or retires. Edge's retirement couldn't have come at a worse time — the main event scene was already severely depleted, Shawn Michaels having retired, Triple H and The Undertaker semi-retired, and Rey Mysterio Jr embroiled in a feud with Cody Rhodes. They had to bump up the draft six weeks early because SmackDown didn't have a top babyface, so Randy Orton was hastily moved to the blue brand. The vacuum was gradually filled by CM Punk (who ascended to superstardom during the second Summer of Punk), Christian (whose feud with Randy cemented him as a possible main event player), and various younger talents such as Daniel Bryan and Dolph Ziggler. This is why building up new talent is so important — you can't risk a scenario where you don't have a big enough name to have decent, money-making feuds with.
At the end of the 2011 CHIKARA season, the rudo (heel) stable Die Bruderschaft des Kreuzes (BDK) had been forcibly disbanded. Ares, Claudio Castagnoli (Antonio Cesaro) and Sinn Bodhi were all no longer with the promotion, and Eddie Kingston and UltraMantis Black were both technicos. The opening storyline for 2012 is which of the remaining rudos is going to come out on top of the heap. Tim Donst (Ares' Dragon), Obariyon (Bodhi's Dragon) and Ophidian are all currently in the mix.
StarCraft ends with the Zerg overmind defeated at last. Then in Brood War all the factions get pulled into a struggle between Kerrigan and the cerebrates to replace it.
This is how Saika Magoichi's revenge (for the razing of the Saika village) goes horribly wrong in his Samurai Warriors 2 story; after he shoots and kills Oda Nobunaga, he comes across a number of peasants beset by raiders who've found out already that Nobunaga is gone; later Fuuma Kotarou reveals that he released the news specifically to accelerate/cause the power vacuum that Nobunaga had been preventing.
Much of the Undead plotline in WarCraft III: The Frozen Throne follows Arthas, Sylvanas, and the Dreadlords fighting over who controls the Scourge now that the Burning Legion has been defeated.
Sengoku Basara had this happen twice: Oda Nobunaga's death at the hands of Akechi Mitsuhide led to the rise of Toyotomi Hideyoshi, whose death at the hands of Tokugawa Ieyasu led to the rise of Ishida Mitsunari.
Implied to be a force at play in the expansion Awakening. The Architect existed before the Blight, but was unable to attempt to "awaken" other Darkspawn until the Archdemon arose and commanded them to the surface. However, while the Archdemon lived, it essentially put out interference, keeping the Architect's plans from bearing fruit. It was only after the Archdemon's death—a time that should have sent the Darkspawn back underground—that the Architect was able to begin his mission. Within a few years of the start of the Blight, his schemes have snowballed to the point that one NPC mentions that the Darkspawn army is greater than or equal to a Blight's strength—something unheard of in the world previously.
The Architect also created his own rival the Mother, a Broodmother that did not appreciate her newfound "freedom" since she believes that existence without the song of the Old Gods is unbearable. The plotline of Awakening is about the Warden Commander getting dragged into their Enemy Civil War.
Several characters consider this to be the fate of Caesar's Legion in Fallout: New Vegas if Caesar dies. While he does have a successor in Legate Lanius, without a charismatic leader to hold the Legion together it will inevitably crumbles back into the warring tribes that it was forged from. This is a problem, as the Legion was definitely a lesser evil, owing to the safety and discipline it brought to the formerly anarchic lands of Arizona.
In Mass Effect 2, Shepard kills the vast majority (including the leadership) of Omega Station's Blue Suns, Eclipse, and Blood Pack - the station's three major crime syndicates - to save Garrus from them. Come Mass Effect 3: Omega, it is revealed by Aria that their deaths triggered a massive power struggle by the lesser gangs. Eventually, a group called the Talons came out the victor, with a new morally-respectable leader in Nyreen Kandros.
This is what happens in the strange secret ending of Demon's Crest that you get by beating Phalanx early, before he's marked on the map. Firebrand hasn't assembled the Crest and thus lacks the power to rule in Phalanx's place, so he takes off, leaving the Ghoul Realm in anarchy.
In Valis II, Megas steps into the power vacuum created by the death of Rogles.
Batman: Arkham Knight shows two aspects to this trope. In the immediate aftermath of Joker's death, Gotham's violent crimes (and crime in general) take a nosedive. For the better part of year, it's never been so peaceful. However the Joker was actually a mitigating factor of sorts to the other criminals in the city, keeping them fighting amongst themselves. Now with that obstacle gone, the villains can unite to take down their mutual enemy. So they wreak terror on Gotham together, on an unprecedented scale, to rid themselves of the Dark Knight once and for all.
Lampshaded in The Order of the Stick, where Haley is convinced not to kill her former employer and leader of the Thieves Guild Bozzok because of this trope.
Following K'Z'K's death in Sluggy Freelance, at least two other demons have tried to fill the power vacuum. Skip is trying to find a piece of K'Z'K he can use to restore the real thing, while Meander has set up a cult to do insect based world conquest in her own way.
In The Gamers Alliance, when King Renu dies in the First Age, his kingdom becomes a battleground for rival factions until the Mullencamp cult led by Sydney Losstarot defeats the other factions and takes over. Demons take over the previously villainous Yamato Empire, rally behind four different hordes and begin fighting against each other when their master, the dark god Mardük, kicks the bucket after the Cataclysm in the Third Age.
This happens within the first few arcs of Worm, and is partly the fault of the protagonist. On her first night as an attempted superhero, she runs into a superpowered gang boss and defeats him, decapitating his gang and causing the other villains in the city, scenting blood, to move more openly. His second-in-command begins a bombing spree without him to hold her back.
After Shredder died in the 2000s Teenage Mutant Ninja Turtles, our shelled heroes had to contend with a literal city at war in the Second Season. In that case, Shredder's adopted daughter, Karai, became the new Shredder. In season four, the series was left with no central villain since the Utrom Shredder, Ch'rell had been exiled to a frozen asteroid by the end of the third season finale. This left the turtles free to take part in a variety of adventures in this Shredder-less fourth season (Karai did take up Shredder's mantle, but was defeated quite decisively in a duel with Leonardo). The power vacuum was filled again in the fifth season when the ancient Demon Shredder was resurrected again. Note that Leonardo invokes this trope almost word for word to justify aiding the leader of a former enemy faction just to get some order back in the city.
In Justice League, when Darkseid was killed by Superman by leaving him to die in Brainiac's exploding asteroid base, a civil-war erupted in Apokolips between Granny Goodness' forces and those of Virman Vundabar. This was deliberately maintained for several seasons by the Justice League to prevent a united Apokolips from threatening Earth. This came to a halt when Tala resurrected Darkseid. When Darkseid returned to Apokolips, they ended the war right then and there.
Transformers Animated actually begins with Megatron apparently dying at the hands of Optimus Prime (with a little help from Starscream) and Starscream appointing himself leader... just before everyone else abandons ship as they were about to crash. Starscream later gets Lugnut and Blitzwing on his side, but when Megatron gets back, he's pretty pissed and takes revenge on the usurper. The other Decepticons are quick to re-affirm their loyalty to Megatron. Though Lugnut's loyalty never wavered to begin with. He continued to believe that Megatron was still alive, which actually was the main cause behind Megatron's return.
With the defeat of Shen-Du and his return to a helpless statue, everything seems fine, until Jade blows Shen-Du to slag with the Dragon talisman. At this point Uncle (who of course blames Jackie) says that since Shen-Du has been destroyed a new, stronger darkness can take his place. Cue Shen-Du's extended family!
In fact, this happened at the end/beginning of every season: one threat would be destroyed, only to make room for a new threat, sometimes as a direct result of destroying the first enemy.
In one episode of The Fairly OddParents, Vicky loses her job as Timmy's babysitter only for Timmy's Too Dumb to Live parents to replace her with an arguably more evil or just as evil demonic babysitter. Gary and Betty weren't eviler. They were just so annoying Timmy would rather endure Vicky.
One Adventure Time episode had Finn defend a village of house people from an obnoxious green ogre and teach him how to feel empathy. Unfortunately, with the ogre out of the way, their much worse predators called "Why-Wolves" (like werewolves, except more intelligent and inquisitive) terrorize the villagers thanks to the ogre not releasing "Obnoxygen", which is lethal to them.
In Ben 10: Ultimate Alien, Charmcaster managed to overthrow the tyrant Adwaita at some point. Unfortunately, her fellow rebels immediately waged war among themselves in a bid to take over.