Revchi is the Starter Villain, trying to steal Yuno's four-leaf grimoire, which provokes Asta to manifest his five-leaf grimoire. Later Heath Grice, who's trying to steal a magic stone from a village for the Eye of the Midnight Sun.
The Dungeon Exploration Arc has Mars, a mage from the Diamond Kingdom who comes into conflict with the Black Bulls and Golden Dawn.
Rades Spirito in the Royal Capital Assault Arc, with his corpses attacking throughout the Capital.
The Eye of the Midnight Sun Encounter Arc has Baro and Sally trying time kidnap children from Nean, with Licht then appearing.
Vetto in the Underwater Temple Arc, leading members of the Eye of the Midnight Sun to obtain a magic stone.
The Forest of Witches Arc has Fana attack the forest for a magic stone, and Mars and Ladros lead an army to conquer the forest. After these threats are dealt with, the Witch Queen establishes herself as this for the rest of the arc.
The closest thing the Royal Knights Arc has to one is Langris, whose near-murder of Finral puts him into conflict with the Black Bulls.
Bleach: Kageroza Inaba is a villain created for the anime's last filler arc. In canon, Ichigo sacrifices his powers to defeat Aizen after training in the Dangai as a result of Aizen destroying the Janitor that prevents Soul Reapers lingering too long there. Kageroza takes advantage of the loss of the Janitor and Ichigo's powers to enact his plan to destroy the Gotei 13 by manipulating the power fluctations within the now-unstable Dangai. The key to defeating Kageroza flees to the human world and falls under Ichigo's protection, bringing him into direct conflict with Kageroza. Ichigo helps her to gain the power she needs to defy Kageroza; she is later able to use this strength to help Ichigo and the Gotei 13 defeat Kageroza for good.
The "Deep Blood" arc has rogue alchemist Aureolus Izzard.
The "Sisters" arc has Accelerator, the one at the center of the "Level 6 Shift" experiment.
The "Angel Fall" arc has Misha, a fallen angel looking to get back to Heaven.
The "Three Stories" arc has Etzali for the first story, Ouma Yamisaka for the second story and Ao Amai for the third story.
The "Hyouka Kazakiri" arc has Sherry Cromwell, the one after Hyouka Kazakiri.
The "Orsola Aquinas Rescue" arc has Agnese Sanctis, the leader of the warrior nuns sent by the Roman Orthodox Church to retrieve Orsola.
The "Tree Diagram" arc has Awaki Musujime, whose out to retrieve the core remnant of the Tree Diagram on behalf of her employers.
The "Daihasei Festival" arc has Lidvia Lorenzetti, an official of the Roman Orthodox Church seeking the Croce de Pietro in order to use it to force all of Academy City to convert to Roman Catholicism.
The "Queen of the Adriatic Sea" arc has Bishop Biagio Busoni of the Roman Orthodox Church, the one in charge of the La Regina del Mare Adriatico battleship.
The "Academy City Invasion" arc has a Big Bad Ensemble of Vento of the Front and Amata Kihara, the former being a member of the Roman Orthodox Church's God's Right Seat.
The "Document of Constantine" arc has Terra of the Left, the second member of God's Right Seat to take center stage.
The "Battle Royale" arc mainly has Teitoku Kakine, leader of SCHOOL, and Shizuri Mugino, leader of ITEM, though members of MEMBER and BLOCK also appear as enemies.
The "Acqua of the Back" arc has the eponymous Acqua of the Back of God's Right Seat.
The "British Royal Family" arc has Second Princess Carissa, the one leading a coup to take over England.
The "DRAGON" arc has the Spark Signal terrorist group, Board member Shiokishi's faction, and Shizuri Mugino.
The "World War III" arc has Fiamma of the Right, who was also active in the previous few arcs as well. He's not the only player involved in the war, but every other faction was really being manipulated by him.
Eternity Devil arc: The titular Eternity Devil, the devil embodying humanity's fear of eternity, who puts the characters in a Time Loop Trap as part of its plan to kill and eat Denji.
International Assassins arc: Doll Woman, Tolka's master and the true identity of "Santa Claus", who ultimately comes out on top as the most dangerous of the various assassin parties, as well as the last one the characters face.
Justice Devil arc: Yuko, Asa's First Friend, who makes a contract with the titular Justice Devil to lead a massacre at Asa's school in order to eliminate the bullies at the school under the belief that what she's doing is right.
The "Birth" arc features Skull, leader of Black Ghost.
The "Assassins" arc has Skull again, though he only appears at the very beginning, with Cyborgs 0010, 0011, 0012 and 0013 one-by-one going up against the protagonists.
The "Man or Machine" arc has the Neo Nazis, the first villains not to be connected to Black Ghost (although the anime changes them to a cell of Black Ghost based in the arctic).
The "Mythos" arc has a Big Bad Duumvirate between Dr. Gaia and Dr. Uranus. Apollo, the leader of the Mythos Cyborgs, serves as their Dragon-in-Chief as the main foe 009 must contend with.
The "Underground Kingdom of Yomi" arc has Skull once again at the helm, although his cohort Van Vogt is equally as proactive as he is, if not more so. It's later revealed both of them really answer to a mysterious being lurking inside of their ultimate superweapon, the "Demon Statue".
The "Monster Island" arc has the five Monster Island scientists, who are really remnants of Black Ghost, leading our protagonists to discover that traces of the organization still remain.
The "Middle East War" arc has Moses, who turns out to be the leader of another remnant of Black Ghost.
The "Immigration" arc has the Commander.
The "Lorelai's Song" arc has a mysterious Black Knight terrorizing a German village, who turns out to really be a witch desiring revenge on them for their past persecution of her and her mother.
The "Bottom of the Sea" arc has the Underseas People, although at the end of the arc Bii, a Black Ghost Cyborg who spends most of the arc in an Enemy Mine with 009, betrays him and becomes the Final Boss.
The "Angels" arc has the titular "Angels", who are really a race of Winged Humanoid aliens who claim to have created humankind.
The "Battle with the Gods" arcnote which serves as a continuation/retelling of sorts of the "Angels" arc after it was Cut Short has a race of Sufficiently Advanced Aliens who may the "Gods" who created humankind and/or the angels from the previous arc.
The "City of Wind" arc has Kabrakan, a giant gold robot created to guard the titular city by a race of Ancient Astronauts.
The "Edda" trilogy of chapters has Chieftain Tekk who is really a Mad Scientist obsessed with Norse mythology named Odin.
The "Snow Carnival" one-shot has the "Snow Witch", who turns out to be a Cyborg, and not really evil so much as a victim of her Mad Scientist father's experiments.
The "Deinonychus" one-shot has Dr. Keeley, a Black Ghost operative who coerced Dr. Ross into helping him bring back the organization's reign.
The "Ghost Island" one-shot has Dr. Friedkin, a vengeful Mad Scientist seeking revenge on 009.
The "Undersea Pyramid" arc has the M organization, a criminal gang of "international tomb raiders".
The "Golden Triangle" arc has Neo Black Ghost, a reforged successor organization to the original Black Ghost.
The "Arctic Ghost" arc has Neo Black Ghost executive Julia Manoda.
The "Comp-Utopia" arc has the Sphynx supercomputer or rather, the Virtual Ghost possessing it.
The "Pharaoh Virus" arc has an unnamed Mad Scientist working for Neo Black Ghost who seeks to get his hands on the titular virus so he can pull a Poison and Cure Gambit.
The "Aphrodite" arc has Neo Black Ghost executive Aphrodite, who runs their base on Aphrodite Island.
Demon Slayer: Kimetsu no Yaiba: Except for the ''Sunrise Countdown'' arc (that shows the defining battle against Muzan and his subordinates) and two other training arcs, each arc has a major antagonist that Tanjiro and his friends must defeat, with Muzan as the overarching main villain of the series.
Final Selection arc: Teoni, a huge and monsterous demon obsessed with killing the students of Urokodaki who participate in the final election in revenge for defeating and trapping him on the Fujikasane mountain.
First Mission arc: The Demon in the Bog, a demon divided into three personalities who kidnaps and devours teenage girls. He ends becoming the first enemy that Tanjiro confronts as an official demon slayer.
Asakusa arc: Muzan Kibutsuji debuts, but he ends leaving the task to kill Tanjiro to Yahaba and Susamaru, two faithful demons that aspire to join the Twelve Kizuki and end up targeting Tamayo too.
Drum House arc: Kyogai, a former member of the Twelve Kizuki who lost his ability to become stronger by eating humans and wants to regain his former glory by eating Kiyoshi, a human with rare blood.
Natagumo Mountain arc: The Lower Rank Five Kuzuki Rui, a tyrannical and cruel demon who forces his followers to act out familial roles.
Mugen Train arc: Enmu, the Lower Rank One Kuzuki and the Sole Survivor of Muzan's slaughter of the Lower Ranks, who is tasked by his master to kill Tanjiro and Flame Hashira Rengoku by infiltrating a train and planning to kill their wills with his dream-controlling abilities. After his death, Upper Rank Three Akaza takes the role as the main villain, wanting Rengoku to join Muzan due to his impressive abilities and ultimately killing him.
Red Light District/Entertainment District arc: The Upper Rank Six Kuzuki Daki (along with her stronger older brother Gyutaro), a childish and vicious demon posing as a prostitute in the red light district, who caused the mysterious deaths of some people and the disappearance of Uzui's wives.
Swordsmith Village arc: The Upper Rank Four and Upper Rank Five Kuzuki Hantengu and Gyokko, who travel to the Swordsmith Village to cripple the Demon Slayers by killing the people tasked with forging their swords.
Infinity Castle arc: A Boss Bonanza where all the remaining Hashira and the main cast have to take on all of the remaining Upper Ranks of Kokushibo, Douma, Akaza as well as the new Uppers Ranks, Nakime and Kaigaku, as the toughest and most personal battles in the series by far. Which will all lead towards the finale of taking down Muzan once and for all.
Death Note had the Yotsuba Group, specifically Kyosuke Higuchi, as the third Kira who became the main threat for a handful of episodes during Light's Memory Gambit.
Devimon in the Black Gears/File Island Arc. He infects good Digimon with Black Gears, corrupts Leomon, and gets Ogremon to work for him.
Etemon in the Dark Network Arc, being the leader of the Dark Network.
Myotismon in the Eight Child Arc. He seeks to find and kill the eighth child and rule both worlds.
The Dark Masters in the Spiral Mountain Arc, who have taken over the digital wold (and this arc is divided into four arcs, one for each of the Dark Masters), with Apocalymon serving as the True Final Boss of the last two episodes.
Yamaki in the Wild Ones arc. While the Wild Ones are the primary threat, Yamaki seeks to exterminate all Digimon. By the Deva arc he is demoted to secondary antagonist, and does a Heel–Face Turn midway through.
Zhuqiaomon in the Deva arc, as the Devas sent to take over Earth, kill or enslave all humans, and capture Calumon are working for him.
D-Reaper in the D-Reaper arc, who seeks to assimilate all humans and Digimon, and can be considered the Big Bad of the series, as both Yamaki and Zhuqiaomon are now united with the Tamers against it.
Merukimon for the first arc. He wants to take revenge on humans for Kurata's invasion
Akihiro Kurata for the second arc. His plan is to destroy all Digimon and the digital world and rule Earth. He can, however, be considered the Big Bad of the whole season as his actions led to the threats of both Merukimon and King Drasil.
King Drasil for the third and final arc, intending to kill all humans after Kurata's threat.
While EDENS ZERO does reveal who its Big Bad truly is halfway through, most of the series' individual story arcs consist of standalone villains who provide one-off obstacles for the heroes to overcome.
The Norma arc has Sibir, a local gang leader who finds an android from the future, Pino, and tries to use her technology to get rich, forcing Rebecca and Shiki to stop him from messing with the future.
The Skull Fairy arc switches the formula up. The Arc Villain appears to be Elsie Crimson, a Space Pirate who takes an interest in Shiki Granbell due to her own personal history with Shiki's grandfather, Demon King Ziggy. She captures Aqua Wing, Rebecca's ship, and says she intends to sell Shiki, Rebecca, Happy, Weisz, and Pino all off to human trafficers on the planet Guilst. Shiki challenges her to a fight for possession of her ship, which she accepts. But in a twist, it's not only revealed that the Elsie that fought Shiki was just a copy, but that Elsie never planned to harm the heroes to begin with and always intended to give the ship to Shiki, she just enjoyed making them uncomfortable and didn't think it'd be as fun if she just handed it over to them. That ship in question was not the real Skull Fairy, but instead Edens Zero itself, Ziggy's ship which he tasked Elsie with giving to Shiki. This puts her firmly in the camp of Aloof Ally rather than a villain, Ambiguously Evil though she may still be.
The Guilst arc adds another twist to the formula. Illega, a Fat Bastard who prides himself as The Collector of beautiful women, commissions the kidnapping of Rebecca Bluegarden, but he is a Non-Action Big Bad who's barely even a danger to normal people, let alone those who use Ether Gear, and instead it's Fake Sister, an identity thief hired by Illega to kidnap Rebecca, who serves as The Heavy due to her connection to the real Sister Ivry, who Shiki and Rebecca are searching for due to Ivry's connection to the Edens Zero.
The Digitalis arc has Jamilov, an Ax-CrazyGriefer who hunts down players and slaughters NPCs in Rogue Fantasia, the virtual planet Hermit Mio ran to escape the world that tormented her. Jamilov's real name is Spider, a two-bit tech support guy who can't get enough of himself, and "Jamilov" is simply his Digital Avatar, a reflection of his Small Name, Big Ego. He's taken out pretty easily once Hermit finds the motivation to do so.
The Sun Jewel arc has Madame Kurenai, Homura's mother, a cruel tyrant whose every act of cruelty on the planet Sun Jewel is born from her insatiable Greed and mountain-sized ego. She serves as the Climax Boss for the anime's first season, as she is responsible for Valkyrie Yuna's disappearance, she's responsible for everything happening on the planet Sun Jewel, and she holds a very personal stake in Homura's character arc.
Eyeshield 21, as a series about a football team, lacks an overarching villain, with most of its conflicts being settled over the course of individual matches. During the Kanto Regional Tournament Arc, however, the series gains a temporary Big Bad in the form of Reiji "Marco" Maruko, captain of the Deimon Devil-Bats' evil counterparts, the Hakushu Dinosaurs. While the Devil-Bats still play against other teams, Marco's scheming drives much of the plot on and off the field, as various teams attempt different strategies to stop him and his monstrous centre, Rikiya Gao. After grinding their way through Deimon's former adversaries in the Taiyo Sphinx and Seibu Wild Gunmen, Marco and his Dinosaurs become the final team that the Devil-Bats have to face to claim the Kanto Regional Championship and move onto the Christmas Bowl.
Though characters like Zeref, Acnologia, and E.N.D. (all of whom are depicted as The Dreaded), all seem to be building up towards the Big Bad, since they are ultimately responsible for many of the events that transpire in the story, or at least had a hand in it.
Food Wars! lacked one during the early Story Arcs, though Erina Nakiri came the closest, fitting The Rival role to the eponymous protagonist Soma Yukihira. Certain members of the Council of Ten Masters would sprinkle in some antagonism for Soma and his classmates in later arcs, but weren't truly villains themselves, at least not until the Tyrant Takes the Helm by recruiting certain members of the Ten Masters and oust the Big Good from power, forming a "Central" organization and eliminating all dissent against their rule. From this point on, Central's leader becomes the established antagonist for the "Central saga".
Gintama: Whenever the serie get into serious arc, and sometimes for a comedic one as well, a character specific to this arc will appear and serve as it's main antagonist. Kamataro Ito for the Shinsengumi Rebellion arc, Otohime for the Ryugujo arc, Hosen for the Yoshiwara, Kintoki Sakata for the Kintama arc, and so on... This character may also double as a Knight of Cerebus depending on how serious the situation get.
Yoko Minamino for the Nanno arc, though he gets flanderized into a Butt-Monkey afterwards.
Takezawa and the Idaten gang for the Idaten arc.
Junya Akutsu for the Midnight Angels Revival arc. Supporting arc villains are Yasha and Kamishima (though Kamishima is a case of The Only One Allowed to Defeat You towards Akutsu).
The Yokohama Cavalry, Nakagaki and Mauchi, for the Yokohama Cavalry arc.
Yagyo Atsuki (revealed to be Tamaru) for the eponymous arc.
Kashiya and Joey for the Dead End Junkie arc.
Henkyou no Roukishi Bard Loen: Kaldus Coendera is a persistent threat to Bard Loen and the Tersia Family for the first three volumes. He and his family are sending men to attack Bard after a seal and the "Double Whirlpool", which are parts of a decades-old plan involving the royal family.
The Dark Continent Arc: While a central villain has yet to be revealed that arc has built up several different villains thus far. Those being the Kakin Royal Family whose succession war threatens everyone trying to reach the Dark Continent, the Phantom Troupe now that Chrollo has his Nen again and Hisoka as a Wild Card.
JoJo's Bizarre Adventure is divided up into different Parts (8 so far), each with both its own Big Bad and main protagonist.
Diamond is Unbreakable has Yoshikage Kira, who's more of an interesting example in that he's completely unrelated to the events of the first half of the storyline (where Keicho Nijimura and Akira Otoishi would be closer to the main villains).
JoJolion has the Locacaca organization as a whole, lead by Satoru Akefu, or rather his Stand user Tooru. In addition, Jobin Higashikata also serves as an antagonist .
As each Story Arc of Lyrical Nanoha covers a specific incident, all installments have their own Arc Villain.
Miss Kobayashi's Dragon Maid has Ilulu, who acted as the main antagonist for Volume 4 of the manga, and Azad for Volume 8. The series otherwise lacks recurring villains since it's primarily a Slice of Life.
Mob Psycho 100 features a different villain during almost every arc, with some exceptions if certain arc decides to focus on things that don't need an established antagonist.
Separate Ways Arc: While the main conflict between Mob and Reigen was caused by the later's selfishness, is Kirin Jodo who sets up as the antagonist during the second half of the arc, trying to ruin Reigen's life and reputation as a revenge for striking him in the stomach.
Season 1 is divided into several mini-arcs, each with their own lead antagonist.
CGS Arc: Haeda Gunnel, the abusive leader of the CGS First Group who the Third Group revolt against to found Tekkadan.
Iron-Blooded Arc: Coral Conrad, the corrupt head of Gjallarhorn's Mars Branch, who's being paid by Nobliss Gordon to kill Kudelia.
Teiwaz Arc: Maruba Arkay initially, having enlisted Teiwaz and Naze Turbine's help to stop Tekkadan. After Naze has a change of heart, the rest of the arc has No Antagonist and is instead about Tekkadan becoming a subsidiary of Teiwaz.
Brewers Arc: Brooke Kabayan, leader of the Brewers, a group of Space Pirates who've been employed by Gjallarhorn to stall Tekkadan. Although Brooke's second-in-command Kudal Cadel is the lead threat.
Colony Arc: Nobliss Gordon, who seeks to assassinate Kudelia to incite unrest and riots in the Dort Colonies, so he can profit off of it.
Earth Descent Arc: Carta Issue, who heads the forces pursuing Tekkadan all throughout the arc.
Earth Arc: Iznario Fareed, a member of the Seven Stars of Gjallarhorn who seeks to bolster his power in the Earth Sphere by using underhanded tactics to ensure the prime minister election in Arbrau goes in favor of his preferred candidate.
Season 2 can also be divided into several mini-arcs.
#26-29: Sandoval Reuters, leader of the Space Pirates group Dawn Horizon Corps. He starts off under the employ of Allium Gyojan, but is a much bigger threat and soon breaks off from him to keep fighting Tekkadan on his own.
#30-33: Galan Mossa, a mercenary employed by Rustal Elion to start a proxy war between Arbrau and SAU, with Rustal himself serving as the Greater-Scope Villain.
#34-38: The Hashmal, a rampaging Mobile Armor inadvertently awakened by Gjallarhorn commander Iok Kujan.
#39-42: A Big Bad Duumvirate between Iok Kujan, who's looking to get revenge on McGillis and Tekkadan for humiliating him in the previous arc, and Jasley Donomikols, the treacherous and power-hungryNumber Two of Teiwaz.
The remaining stretch of episodes has Rustal Elion, who was pulling the strings behind many of the enemies Tekkadan battled all throughout, before fighting them directly when Tekkadan joins McGillis in his revolution against Gjallarhorn.
The U.A. Sports Festival Arc: While The Unfought, Endeavor (with his son Shoto Todoroki as a proxy).
The Field Training Arc: Stain terrorizes Pro Heroes he deems "fake", but It's Personal for Tenya Iida, whose brother is forced to retire after Stain injures him.
The End of Term Test Arc: The U.A.staff plays as villains to test the Class 1-A students, who are tasked to treat them as such. Justified with this being a school setting, although some of them did go a bit too far.
The School Trip Arc: Dabi was the most active villain, although Muscular was part of the arc's main subplot and fight, but Shigaraki was a Greater-Scope Villain as the plan to capture Bakugo was all his.
The Hideout Infiltration Arc: Shigaraki started off as a Red Herring until All For One showed up.
Provisional Hero License Exam Arc: Gang Orca deliberately served this role for the second half of the exam itself, but Inasa is the closest thing the arc had to an actual antagonist.
The Internship Arc: Kai Chisaki takes this trope as an especially dangerous villain who one-ups the League of Villains... until the end. He plays this straight against Deku and many other heroes as he has a superpowered child for them to rescue.
Cultural Festival Arc: Gentle Criminal and La Brava attempt to disrupt the titular event, with Midoriya attempting to stop them.
Gato from the Land of Waves arc is great example. He is the central antagonist of the Land of Waves arc, but he is of no importance to the overarching story and is just there to be the first villain. After his death heroes quickly forget about him and continue their adventures to the next arc.
Although Gato is the driving force behind the antagonism, Zabuza Momochi serves as the main threat as a hired hitman of the "Land of Waves" arc.
Zaku Abumi only appears during the Chunin Exams, and briefly as a corpse during the Sound-Sand Invasion. Never mentioned again afterwards.
Furido (Kazuma) for the Sora filler arc of Shippuden.
The Akatsuki leader, Pain, serves as the main antagonist of the Pain's Assault Arc. He was also given a major role in the Itachi Pursuit Arc. For filler, he was the biggest threat in the Tsuchigumo Kinjutsu Arc.
Mitsuki, the very first enemy Naruto has encountered at the start of the series, is the main antagonist of the "Mizuki Strikes Back" anime Filler arc.
The New Seven Ninja Swordsman of the Mist, lead by Shizuma Hoshigaki, are the main villains of the Field Trip arc in the Boruto anime.
A [1] between Victor and Deepa in Kara Actuation Arc.
Lysandre (of the Evil Mentor kind, that Arc Hero Alain doesn't know of) for the Mega Evolution Specials, before his organization, Team Flare follows Team Plasma's lead as the main villains of XYZ.
Sailor Moon R: Filler Arc: Ali and En, the Maikaiju aliens
Sailor Moon R: The Black Moon Arc: The Black Moon Clan
Sailor Moon S: The Death Busters
Sailor Moon Super S: The Dead Moon Circus, though Nehellenia bled into the first arc of Sailor Stars
Sailor Moon Sailor Stars: Shadow Galactica
The manga technically has a similar progression, though the arcs referred to each other and the final story arc reveals that each arc's Big Bad is in reality a reincarnation of the final enemy in the series.
Shinzo: Both seasons had a different Big Bad, but Season 1 also had the so-called Enterran Generals who were essentially mini-bosses working for the first Big Bad.
Soul Eater has Arachne in the Arachnophobia arc and Noah/The Tables of Contents in the Book of Eibon Arc.
In the anime, Medusa is the villain of the first arc, seeking to awaken Asura, the Kishin. Arachne becomes the villain of the second arc who gets Asura on her side in an attempt to rule the world, though Medusa continues to have a significant presence. After both witches are killed, Asura becomes the final antagonist, though he is constantly mentioned thoughout the series as the ultimate enemy.
Inushan Crisis Arc: Keith Kepler, the leader of an isolationist terrorist group trying to kickstart a war between Ostania and Westalis, by assassinating Minister Brantz.
Great Adventure Cruise Arc: Snoops, an information broker and assassin.
Red Circus Arc: Billy Squire, the leader of the titular terrorist group.
The Tamagotchi television series is composed of four installments.note Actually five, but the fifth is literally just already-existing episodes with new segments in-between and thus is often not counted as a proper part of the series. The third installment, Miracle Friends, introduces Smartotchi a.k.a. Kamen X as the villain who is after the Dreambakutchis that Miraitchi and Clulutchi need to return to the future. Smartotchi does not appear at all in GO-GO Tamagotchi!, the arc that follows Miracle Friends.
Brilliant Dynamites Neon, or BDN for short, in Trigun.
Yu-Gi-Oh!: The Spirit of the Millenium Ring (aka Dark Bakura) is the series' recurring antagonist and overall Big Bad. However, he is only the central villain of two arcs, and over the course of multiple story arcs he's regularly relegated to scheming in the background as the heroes are forced to confront more immediate threats:
Trial of the Mind: Shadi
Death-T: Seto Kaiba
Monster World: Dark Bakura
Duelist Kingdom: Pegasus J. Crawford
Dragons, Dice & Dungeons: Mr. Clown (manga-only)
Battle City: Marik Ishtar -> Dark Marik.
Millennium World: Dark Bakura, Akhenaden, and Zorc Necrophades
The Yu-Gi-Oh! anime adds its own via filler arcs, and skips the first three arcs above (or adapted them into really short non-arcs).
Unlike the other sagas of the series, which feature an overarching antagonist throughout the saga's story, each of the arcs of the Spirit Detective saga focus on their own individual antagonist:
Retrieval of the Three Artifacts of Darkness arc: Hiei, the ringleader behind the theft of the Artifacts of Darkness, as well as the most dangerous of the trio and the last one Yusuke faces.
Disciple Selection Trials arc: Rando, a demon who poses as a human so as to enter Genkai's tournament in an attempt to become her apprentice and learn her Spirit Wave technique. Yusuke's entire reason for entering the tournament is due to being assigned to stop Rando.
Maze Castle arc: Suzaku, the leader of the Four Saint Beasts, as well as the one who controls the Makai Insects and leads the Insects' attack on the Human World.
Chapter Black saga: Shinobu Sensui, the leader of the Sensui Seven and the ultimate mastermind behind the group's plan to open a portal between the Human and Demon Worlds so as to bring about The End of the World as We Know It.
Three Kings saga: Yomi. While at first, all three of the titular Three Kings are of equal prominence in terms of their threat status, by the end of the saga, Yomi comes out on top as the biggest threat of the three, and ultimately ends up as the final opponent Yusuke faces in both the saga and the series as a whole.
