"The ultimate villain of the story, who's causing the problem the heroes must solve."
Note that Big Bad is not a catch-all trope for the biggest and ugliest villain of any given story. The Big Bad is the one who turns out to be behind several other seemingly independent threats.
Berserk mainly has the Godhand, and Griffith post-Face Heel Turn in particular, as Big Bads, but several arcs of the manga have seen Guts going against other servants of the Godhand. The Lost Children arc had Rosine, and the Conviction arc had Bishop Mozgus, with the most recent arc focusing on Emperor Ganishka.
While Ichigo was recovering his lost powers after losing them to defeat Aizen, Shukuro Tsukishima and Kugo Ginjo were a temporary Big Bad Duumvirate.
The latest Big Bad, and newest one on the block, is The Emperor of the Vandenreich.
Combattler V: Empress Janera, even though she was working through pawns for the first half of story.
Vicious from Cowboy Bebop. Due to the episodic nature of the show, he's only in 5 episodes, but he's not only the central threat of those episodes, he also plays a huge role in Spike's past.
In Chrono Crusade, Aion's behind a huge chunk of the bad things that happen and is the final foe Chrono and Rosette have to face—although in the manga his morality is a little more gray than his anime counterpart.
In NORA: The Last Chronicle of Devildom, Kneel is orginally the Big Bad until Fall shows up, offically taking the role soon after Knell becomes The Starscream. With Knell driving Nora to achieve his full strength by becoming a "true" Cerberus and destroying everything, he can be considered the Bigger Bad.
That is, until the final chapter, where Knell shows up stronger than ever, nearly goes Omnicidal Maniac on all of creation, and officially replaces Fall as the Big Bad until he is consumed by the Cereberus Vortex.
At least until Lelouch kills him, at which point Schniezal takes over as the BB.
Daimos: Olban was the real Puppet Master caused the conflict in the story, manipulating everybody to achieve power.
Death Note takes an unusual approach to this trope by making the main character himself the Big Bad.
Ryuk is the Bigger Bad, since he's the one who dropped the Death Note in the first place, causing all of the events in the series. Not much would've changed if he left Light alone after dropping the notebook.
The notebook itself could be considered this as well.
Digimon Tamers first had HYPNOS, then Zhuqiaomon, and after this the D-Reaper. Impmon was originally intended to be this (which is why he's portrayed in typical Big Bad fashion in the early promotional material), but Konaka later changed his mind.
The sequel, Dragon Ball Z has Vegeta, Frieza, Cell and Buu.
Dragon Ball GT has Baby, a Big Bad Duumvirate of Dr. Gero and Dr. Myu, and finally the Shadow Dragons.
The Most popular is Frieza because he is the most recurring and the one who started the Dragon ball franchise.
Final Fantasy: Unlimited gives us Earl Tyrant, who is succeeded by Solijashy for FFU: After. A strong case could actually be made for Oscha being the true villain, as well.
Fairy Tail has at least one Big Bad per arc as is typical. Most of them are usually connected to the Bigger Bad Zeref, whether trying to unseal him or are indirectly connected to others trying to unseal him.
The Claw from Gun X Swordis a sweet old man, with a track record of crimes agains the protagonists as long as his artificial right arm. Every single bad thing in the series ultimately traces back to him.
Dio Brando in JoJo's Bizarre Adventure. Every arc that doesn't feature him as the main villain features one who is connected to him, however small. The Pillar Men (Part 2) created the Stone Mask that turned Dio into a vampire, Yoshikage Kira (Part 4) got his Stand abilities from one of the arrows that Dio once owned, Diavolo (Part 5) was directly responsible for Dio getting his hands on the arrow in the first place, and Enrico Pucci (Part 6) was Dio's closest confidante.
Kara No Kyoukai has ArayaSouren, who is responsible for pretty much everything before and after Shiki, the main charfacter, woke from her coma. Strangely enough, he is finished off in the fifth movie in a series of seven movies.
Kinnikuman has had, in terms of Big Bads that were actually dangerous, Robin Mask for the 20th Choujin Olympics arc, Warsman for the 21st Choujin Olympics arc, Buffaloman for the Devil Choujin arc, Akuma Shogun for the Golden Mask arc, the tag-team of Neptuneman and Big the Budo for the Golden Mask arc, and lastly Kinnikuman Super Phoenix for the Throne arc.
Kotetsu Jeeg: Queen Himika for the first half, Emperor Dragon for the second.
Mahou Sensei Negima! has Fate, who may or may not be the biggest threat. Although it's later revealed that Dynamis is actually running CE and he actually brought Fate back for additional muscle, making him the Big Bad and Fate merely The Dragon.
In the past, the Lifemaker was undeniably the Big Bad. And may still be the Big Bad.
Naruto initially presents Orochimaru as the Big Bad. The series becomes a Big Bad Ensemble in Part II, featuring Orochimaru, Pain, Danzo, Kabuto, and Tobi as contenders for the title. However, the series appears to have settled on the true Big Bad: Tobi, the true leader of Akatsuki and the one who instigated the events of the series.
One Piece follows this example as well through its story arcs, sit back - this take some doing.
Captain Morgan arc: Captain Morgan, a dirty Navy official with an axe for an arm.
Laboon arc: Mister 9, an agent of Baroque Works. Eventually redeems himself in an apparent Heroic Sacrifice.
Whiskey Peak arc: At first, Mister 8 seems to be in charge, but he actually answers to Mister Five, who in turn reports to Miss All Sunday who is never fought directly, though she is confronted.
Drum Island arc: Wapol, the former king of Drum Island, attempting to reclaim his kingdom after previously abandoning it when the Black Beard Pirates attacked.
Punk Hazard seems to have Caesar Crown as its top antagonist.
Fans generally speculate that an overall Big Bad for the entire series will eventually be revealed, and as of now most foreshadowing is pointing to Blackbeard.
In the Pokémon Special manga, Giovanni (or Sakaki, if you're going by the Japanese) pulls this off just like his anime counterpart should be doing in the first and fifth arcs.
The other Big Bads are Lance (second arc), Mask of Ice (third arc), Archie and Maxie (fourth arc), Guile Hideout (sixth arc), Cyrus (seventh arc), Charon (eigth arc) and Archer (ninth arc). The mysterious Sird, however, seems to be a series-spanning Big Bad, with a plan spanning several arcs.
Technically, Molly got her Reality Warper abilities from a swarm of minor Eldritch Abominations that moved into her house, but as there's no indication they're even sentient, she remains the Big Bad (for a given value of "bad," anyway, as she's really just motivated by childish desires).
The closest thing Puella Magi Madoka Magica has to a main villain is adorable but duplicitous and secretive little Weasel Mascot Kyubey, who doesn't tell the Magical Girls he creates certain key facts, including that Magical Girls are essentially liches, or that every Magical Girl is doomed to become a Witch like the ones they fight, and doesn't care one whit about humans as long as the universe itself continues to exist.
Akio Ohtori of Revolutionary Girl Utena. He loses Anthy but it could be rightly said that otherwise, he got away with everything, including being responsible for probably hundreds of deaths, if not thousands.
The first season of Rosario + Vampire had Hokuto. The second season has Gyokuro.
Rurouni Kenshin had Makoto Shishio and Enishi Yukishiro. To expand on this:
Shishio was the Big Bad of the Kyoto arc by virtue of being Kenshin's replacement as the Ishin Shishi's top assassin, a Social Darwinist whose views clashed with Kenshin's pacifistic ideals, and his desire to overthrow the Japanese government that both his and Kenshin's swords helped to set up. He had the strength, connections, manpower and weaponry to start and maintain his campaign, plus being a magnificentlyManipulative Bastard for a lot of people, both within his private army and on a wider scale; not to mention his aptitude for planning and executing strategies to keep himself two steps ahead of his enemies. What made him especially effective was that he was willing to cop to his faults whenever any aspect of his planning did fail such as underestimating Sanosuke and not anticipating he'd have portable bombs powerful enough to destroy the Rengoku battleship, he actually respected his underlings to a degree, and he proved powerful enough to stave off four of the strongest opponents he could have—while being physically impaired himself (his burns from the government's assassination attempt meant he couldn't fight longer than 15 minutes at a time or else he'd risk death by overheating).
By contrast, Enishi,the Big Bad of the Jinchu arc, has a much closer tie to Kenshin than Shishio did (both Kenshin and Enishi had Tomoe in common, and both got lasting marks from her death—Kenshin got the second half of his scar, with the first half coming from Tomoe's slain fiance; Enishi, meanwhile, had his hair turn white from the shock of seeing Tomoe die in front of him), being the only one to both physically defeat Kenshin in combat and psychologically break him.
Sailor Moon was no stranger to this concept, but it was even more fond of setting up the seasons Dragon as the Big Bad, only to do a big reveal at the end.
First season: Queen Metaria
Sailor Moon R: Ail and En in Part One, and Wiseman/Death Phantom in Part Two
Sailor Moon S: Pharaoh 90
Sailor Moon SuperS: Queen Nehellenia
Sailor Stars: Chaos (who is the original source of all the aforementioned except Ail and En)
Codename: Sailor V, the manga that began before Sailor Moon but that ended after it has Danburite as its Big Bad. Though in the scheme of things he's a small fry, being an underling of the leader of the very first Quirky Miniboss Squad.
Slayers NEXT: Chaos Dragon Gaav and Hellmaster Phibrizo.
Slayers TRY: Valgaav and Dark Star Dugradigdu
Slayers Revolution: Zanaffar (revived by Dulcis)
Slayers Evolution-R: The ghost of Rezo-Shabranigdo.
And in the final original light novel, another piece of Shabranigdo, held within the soul of a mercenary named Luke, was a Big Bad.
Sonic X has Dr. Eggman in the first two seasons and Dark Oak in the final season.
Soul Eater has one for every major story arc. In the first one, it's Medusa, the second, Arachnae, and the third, Noah(The Greed Incarnation)but actually it's the Book of Eibon's Table of Contents as the Noahs are artificial constructs created by it.. Although Medusa is notable.In that she wakes up Kishin Ashura and so far, hasn't been killed, and is still an active villain.Until she is killed by Crona in the Moon Arc Kishin Asura is often mistaken for one, but he more qualifies as a Bigger Bad.However he did make a few recurring appearances in the story arcs and like medusa is still as active villain.Now the next arc is about Asura and him as the Big Bad this time.Also Soul eater is about preventing Kishins from being born just like Asura since everybody is after him,so Asura does qualify as a big bad to the entire series.
in Soul Eater Not! Medusa's and Arachne's younger sister Shaula Gorgon can be qualified as the Big Bad in this arc.
In Umineko No Naku Koro Ni, Beatrice is this at first, until she is usurped by Bernkastel and Lambdadelta. Because of this, Bernkastel is now a Rogue Protagonist and Fallen Hero, since she was the amalgamation of all the dead Rika Furudes from Higurashi.
Lord Darcia in Wolf's Rain is not only a Big Bad, his entire family line is responsible for anything evil involved in the story... even in its "happy ending," which is anything but because of him.
Oddly enough, the original ending (the version that stops at episode 26) seems to present Lady Jaguara as the real villain, especially after Darcia's apparent death. In the OVA, Darcia takes that position back hard.
Season 1: Rex Godwin starts off looking like one, but turns out to be more of a Stealth Mentor. In the second half of the season, Rudger (Rex's brother and leader of The Psycho Rangers) seems to take over, but is soon abruptly killed off halfway through his arc, leaving the rest of it to his followers who had been Dragon Their Feet. The final three episodes of the season, however, reveal the guy behind everything: it really was Rex the whole time, playing everyone up to and including two deities for suckers.
Season 2: Z-one, who was, through his followers, responsible for Rex and Rudger turning evil, and thus could be considered the Bigger Bad for Season 1, as well.
Season 1: Dr. Faker so far, but now that the World Duel Carnival has started it's ambiguous as to whether it'll be him or Tron, the most mysterious competitor in said Carnival, who'll turn out to be Eviler than Thou.
Generally, it can be argued that the biggest bad of the original series is Bakura/Zorc, the biggest bad of GX is the Light of Ruin (while not the final adversary, and in fact beaten offscreen, it is Judai's Arch-NemesisBecause Destiny Says So and responsible for two seasons worth of strife, the other two villains only getting one), and the biggest bad of 5D's is ZONE.
And, in the world portrayed in the cards themselves, it seems that Invader of Darkness fits the Big Bad role pretty well. He even has a Badass Cape. However, close seconds would seem to go to Dark Lucius, who one could argue crossed the Moral Event Horizon in Sakuretsu Armor.
Note that the giant monster from Sakuretsu Armor is the same from the equip spell Falling Down, who is actually Warrior Dai Grepher, tainted by the dark power of the Archfiends. And yes, he later becomes Dark Lucius as he gains control over his new power.
Sakyo in Season 2. Although Younger Toguro looks like this as well, he's more the Dragon-in-Chief.
Sensui in Season 3. He is the leader of the villains, but another Big Bad could be Elder Toguro, who, seeing himself as Sakyo's successor, gave Sensui the idea for the Evil Plan.
The three main rulers of the Makai world. One of them is revealed to be Yusuke's ancestor.
In the manga, it's revealed that alot of the early villains had been pawns in an enormously elaborate publicity stunt overseen by King Enma, the true villain.
Onimaru Takeshi in Yaiba, your typical Dark Overlord. Also Kaguya and, during the Pyramid and Underworld arcs, Boss.
In the last arc, there's also the Platina Company.
In the most recent arc of Shakugan no Shanamain character Yuji becomes the Big Bad after ascending to Snake of the Festival.
Subverted. The Snake of the Festival and Yuji succeed in creating a new world for Crimson Denizens to live without having to consume humans' Power of Existence. Many, if not all of those consumed by Denizens, are returned to existence. The Crimson Lords' and Flame Hazes' fear that this destroy the world proves to be without merit, and the eternal war between the Denizens and Flame Hazes end. The Flame Hazes are now free to be actual people instead of walking weapons whose only purpose is fighting, something Yuji desperately wanted for Shana, who he does end up in a relationship with. Everything went exactly according to the Snake and Yuji's plans.
Windaria The king of the Shadowland appears to be this but its actually Lagado.
Sekidousai in Inukami! whose inventions form the basis of early plots and those Evil Plan drives the second half of the show.
The Pope, a.k.a. Gemini Saga, in the Sanctuary Arc of Saint Seiya , Hilda in the Asgard Arc, and the respective titular villains of the Poseidon and Hades Arcs. The movies have their own Big Bads as well.
Rain Devila in Wedding Peach is behind all the demons who attack Momoko and her friends until her own Heel Face Turn in the end.
Kenichi: The Mightiest Disciple presents us with Saiga Furinji, the eponymous One Shadow in the Yami organization's One Shadow Nine Fists group—essentially, the strongest martial artist in the organization—who is also the son of the series' Big Good, Hayato Furinji, and the Disappeared Dad to Hayato's granddaughter Miu. However, it seems Saiga may be a complicated case of this, as he's been shown to still be a Martial Pacifist despite being the leader of a group that advocates murderous martial arts.
