In Code Geass this is Emperor Charles zi Britannia's raison d'etre. He has children by 108 different wives and believes the best way to choose a successor to the throne is to pit them all against each other, encouraging backstabbing and assassination at every turn, so that the last one standing will be the strongest and most fit to lead.Prodigal prince Lelouch blames the death of his mother and the crippling of his sister on the Emperor's ruthless parenting style, and he launches a worldwide rebellion against Brittania so he can put an end to this system of sibling rivalry forever. Though, for most of the series, the Emperor doesn't consider Lelouch much of a threat and takes a hands-off approach towards dealing with him.
The irony in all this is that it's revealed that Lelouch and Nunnally are actually the children Charles loves the most. This is mainly by virtue of the fact that they are the only children he had with the only one of his 108 consorts that he loved: Marianne vi Britannia, who is revealed to be alive (albeit via Grand Theft Me) and in on his Assimilation Plot.
The Fourth Kazekage from Naruto. He placed a known dangerous tanuki-demon into his unborn child Gaara to create a Tyke Bomb for his ninja village. He used his own wife as a Human Sacrifice to complete the act, all without her consent. When he couldn't train the aforementioned Tyke Bomb to control his powers well, he tries to kill Gaara. Ironically, Gaara isn't the one who kills him — Orochimaru is. Though they do eventually have their fight after the Fourth is revived via the Edo Tensei during the Fourth Great Shinobi War, where the truth about Gaara's mother and Yashamaru is finally revealed. The two make their peace before the Fourth is sealed away, entrusting the village to his son and successor.
In Yu-Gi-Oh! Gozaburo Kaiba is an Abusive Dad and Jerk Ass whom adoptive son Seto Kaiba disposed of in the backstory. In the anime he returns as the Big Bad of the Virtual Nightmare Filler Arc to make one final attempt at revenge. Trapping Kaiba and his allies in his virtual world, Gozaburo uses his biological son, Noah, and his former employees, The Big Five as the muscle in a plot to permanently trap his son and escape back into the world in his body. Defeated by Kaiba, Gozaburo makes a last attempt at Taking You with Me, but is stopped when Noah pulls a Heel-Face Turn and sacrifices himself to destroy them both.
Vinland Saga: Now that King Sweyn is sure that his older son Harold will be able to succeed him on the throne, his younger son Canute becomes a liability. Canute doesn't like it.
A Cruel God Reigns: Jeremy is repeatedly beaten and raped by his step-father, which is the main source of his angst for the rest of the series... but can you blame the poor kid?
The primary goal of Brad Burns, and later his brother Luke, in Green Blood is to track down the man who murdered his mother: his father Edward King.
The Big Bad of Count Cain is Cain's father Alexis, who transitioned smoothly from beating his children when they were small to manipulating them into pawns in his Evil Plan now that they're grown.
Inverted with Spider-Man. His Arch-Enemy, the Green Goblin, is not this, but a major development of the last decade or so is that he more or less imagines he is, seeing Peter- a smart, brave, capable self-made man- as a better son than his own child, Harry. On an older level, Peter's search for a father figure is one of the underlying themes of the comic, and the idea that Osborn- as well as other enemies like Doctor Octopus- are twisted inversions of this has been around for a while.
This is also played with in Ultimate Spider-Man, where Osborn's military research (including pieces of Peter's parents' research) leads directly to Peter gaining his powers. And Miles Morales, the new Ultimate Spider-man, got his powers from a stolen spider from Osborn's lab. Osborn keeps unintentionally birthing spidermen.
A similar situation exists between Batman and Ra's Al-Ghul. He, too, sees Bruce almost like the son he never had, and he actually plans on making him both his heir and his son-in-law by marrying him to his daughter Talia, something both Bruce and Talia are seriously tempted to do.
Played straight and then subverted in the Black Glove story arc, where it is implied that the eponymous villain is actually Bruce's dad Thomas, who was really an evil psychopath. Neither allegation turns out to be true, though the real Black Glove, one Doctor Simon Hurt, nonetheless claims to be Thomas Wayne to both Bruce and Alfred's face, even though both men obviously knew he wasn't. It is implied that Hurt is actually Satan himself, though for a moment Batman accuses him of being an actor who used to impersonate his father, which would make this yet another inversion. Hurt denies this and claimed to have killed said actor and wore his skin to a party. So it's a triple subversion, with Hurt being a guy pretending to be a guy who pretended to be Bruce Wayne's dad, and pretending to be Bruce's Wayne's dad. Phew!
Return of Bruce Wayne suggests that Hurt is Dr Thomas Wayne. Just not that Dr Thomas Wayne...
In Fables, the Adversary is revealed to be Geppeto, thereby making him Pinnochio'sArchnemesis Dad. Though, this is less explicit, because his son is conflicted about opposing his father explicitly.
The android superhero Red Tornado and his creator T.O. Morrow have this dynamic. Several storylines revolve around Morrow's attempts to destroy/manipulate/reprogram his prodigal son.
In Secret Six Scandal Savage has a hatred for her father of such intensity that even mentioning his name is often enough to drive her to violence. When your dad is the immortal psychopath Vandal Savage, who can blame you?
The Pride in Runaways is made up of six pairs of Archnemesis Dads and Evil Matriarchs. In a mild subversion, The Pride honestly believe that they are doing the best they can for their children: by destroying the world and allowing the Gibborim to remake it, they will be handing their children paradise. With one exception the kids don't agree, and their interference ultimately leads to the deaths of all The Pride's members.
At the end of the war between New Genesis and Apokolips, rulers Highfather and Darkseid exchanged their baby sons as part of the peace treaty. Darkseid's son, Orion, was raised a hero (albeit one with anger issues), who plays this about as straight as possible, sometimes going after Darkseid even against the wishes of his adopted father.
In Heroes story Fearless, Bob is a variation because in the particular universe Elle has never met him but he is very evil.
Another example is the Big Bad of the Tangled Roots trilogy. Babs Seeds's (The Protagonist) father, he's a crime lord, ruthless businesspony and not above trying to kill his own subordinates... that's not all though...
More implied in the Hotel Transylvania fic How to Zing. Martha starts out Human, but Drac turns her into a Vampire so they can be together. Her father then swears vengeance on all Vampires for what happened. Said father is Abraham Van Helsing.
Films — Animated
In The Hunchback of Notre Dame, Frollo takes Quasimodo in after killing his mother, but only to save his own soul and keep Quasi for later use. He raises his erstwhile son to hate himself, that the world is dark and cruel, and keeps him locked away from sight to prevent being associated with him. When Frollo's atrocities increase Quasi realizes the man's evil, calls him out on his abusive parenting, and saves Esmeralda from the murderously insane Frollo.
Films — Live-Action
Dreverhaven in the Dutch movie Character has such an antagonistic relationship with his son that said son is the prime suspect when Dreverhaven is murdered.
Bruce Banner's father, David, in the 2003 Hulk. After performing dangerous tests on himself, some of it was passed on genetically when Bruce was conceived. He attempted to murder Bruce but failed, striking down his wife in the process. Thirty years later, following his release from prison, he tracks down Bruce and attempts to rebuild their relationship while secretly plotting to drain Bruce's powers and alter-ego in order to rebuild his own decaying cellular structure and gain his revenge on the military. A very, very bad dude, though not without his sympathetic moments.
One could hardly be a worse father than Georges Leon, the quasi-immortal gambler of Tim Powers' Last Call. He schemes to live on by stealing other people's bodies, including that of his son and the book's hero, Scott Crane. Scott's older brother Richard has already fallen prey to Georges.
In Ship Breaker, Nailer's dad, Richard Lopez, takes Abusive DadUp to Eleven. He starts out as an alcoholicdrug-addicted ex-pit fighter who regularly beats his son and threatens to maim or kill him. As the story progresses, he takes over as the main antagonist, seeking to kidnap Nita, whom Nailer has placed under his protection. This culminates in Richard capturing Nita (and plotting to sell her organs on the black market) and a Knife Fight between him and Nailer, who Richard fully intends to disembowel. In the end, Nailer is forced to kill Richard and is left guilt-ridden over the fact that he doesn't feel bad about it. The story does imply that while he was never a great dad, he was once a better person than he is now, and Nailer does have memories of better times that the two of them had, but his actions in the present far outweigh anything he may have done in the past.
Tigerstar of Warrior Cats is the Big Bad, with his son Brambleclaw as the hero during the New Prophecy arc. However, while Tigerstar seeks to rule the world, Brambleclaw wants to stop him and says he'd rather die than join him.
Clear Sky was this for Thunder in Dawn Of The Clans until his Heel-Face Turn in The First Battle.
Ulcis of Deepgate Codex tried to hang his daughter Rebecca aka Carnival shortly after she was born, then gave her to his henchmen to be raped and tortured. Years later, when she and several others descend into the Abyss, he takes a perverse delight in tormenting her with the memory of what happened, trying to break her all over again.
El Internado: Iván's father is the bad guy the main characters know the best, because he is the one who delivers the threats and the medicines.
Leverage: Jimmy Ford, the father of team leader Nathan Ford, was a Loan Shark (among other things) who worked for the Three Families that controlled organized crime in Boston. Jimmy raised his son to enter the family business, but as some point Nathan rebelled; he first studied for the priesthood, then became an insurance fraud investigator, and finally emerged as the leader of a group of (more or less) heroic Con Artists who Pay Evil unto Evil to Corrupt Corporate Executives, Just Like Robin Hood. Eventually, Jimmy became one of Leverage's targets, causing Nathan's teammates to worry that he was going after his father with a little too much enthusiasm. This doesn't stop Jimmy from dying to protect his son and Nate from nearly killing to avenge him.
John Locke's father abandoned him until well into his adult life, at which point he stole his kidney, re-abandoned him, used him as a courier, abandoned him again, and pushed him out of an 8-story window.
Locke was too much of a wuss to actually kill him when he had the chance.
Revolution: Tom Neville acts as this to his son Jason Neville. Jason reveals in "The Song Remains The Same" that he did everything his father asked him to do, which included hurting and killing people for him...but Tom just kept looking straight through him. The first season finale has Tom taking over the Monroe Republic. Jason is working with him, but he hasn't actually agreed to anything. That's a good thing, because it's already becoming clear that things are going to break down between them sooner rather than later.
In Season 10, this is revisited when Clark travels to the Alternate Universe of Earth-2 and encounters that world's Lionel, who not only abused Lex and his illegitimate daughter Tess, but also managed to find and raise his reality's Clark and transform him into a Psycho for Hire known as Ultraman, whom he allowed to murder Earth-2 Lex. By the end of the episode he has attempted to beat our Clark (whom he believes to be his Clark) to death for not having killedhim already. He later escapes to Earth-1 where he steals LuthorCorp from our Tess and spends several episodes trying to manipulate Lex's unstable clone Alexander/Conner, whom he doses with Red K. When that fails, he kidnaps Tess and tries to cut out her heart for use in resurrecting Lex (though only after discovering that Conner's is unavailable); he is shot by her for his trouble. Interestingly, his last act before he dies is to make a deal with that season's Big Bad, Darkseid, in order to bring the real Lex back, ensuring that he has a proper heir. Phew.
The X-Files: C.G.B. Spender to both of his sons. He shoots one of them and attempts to foil the other's plans at every turn (and steal his brain, at one point). Not exactly Father of the Year.
Though he's not as much of an antagonist as Regina or Cora, King George certainly causes his fair share of problems in Prince Charming's life. It's fairly complicated, as George got Charming's brother first in a deal with Rumplestiltskin, and got Charming (James) as a replacement because he needed a son to kill a dragon after the first boy died. He did initially want to be a father to James, but couldn't handle it when the boy that he gave "everything" to objects to an Arranged Marriage and runs off with Snow White. He poisons Snow White so that she can't have children (she gets better), kills George's mother, teams up with Regina to wage war on James and Snow, and finally tries to get Charming ousted from his job as Sheriff in Storybrooke.
Justified: Crime boss Bo Crowder, towards his son, Vigilante Man Boyd Crowder. It climaxes when Bo has Boyd's entire gang of followers massacred.
In Greek Mythology, Cronos had his children fed to him in order to ensure that a prophecy which stated one of his sons would overthrow him would never come to pass. Until Cronos' wife fed a stone to Cronos instead of baby Zeus. Zeus then proceeded to free his brothers and sisters from Cronos stomach and promptly kicked Cronos ass.
Cronos's father Uranus (the sky) wasn't much better. He feared and hated all of his children so much that he forced them back into Gaia (the earth). Naturally, being forced to keep all of her full grown children inside her at once pissed Gaia off so much that she helped her son Cronos, the youngest and boldest Titan, get revenge on dear ol' dad. She forged a sickle which Cronos used to castrate his own father when Uranus was in the mood for some earth lovin'.
In some versions of myth he did not trapped and "was not in the mood" but rather hadn't stopped it in the first place.
Fear of the new generation overthrowing the old one is a major running theme in Greek mythology, so there are a lot of examples of fathers becoming enemies of their children. In some tellings of the story, the entire Trojan War was a Batman Gambit by Zeus, who wanted to find a way to kill off his demigod children so they wouldn't overthrow him. This is despite the fact that the closest relative of his was either Zeus' great-nephew or his second cousin (Achilles' mother was Thetis the sea nymph, whose father was either Poseidon, Zeus' brother, or Oceanus, Zeus' uncle). Although most of the heroes did have some percentage of divine blood, it was really no more than any prominent person would have.
Zeus's son Sarpedon dies fighting for the Trojans, but he seems to be genuinely upset. And Aeneas, the one surviving Trojan, is Zeus's grandson in some versions of the myth. Seeing what happens to Aeneas afterwards...
Zeus and Poseidon were unique in that they averted this trope. While they didn't do much in the way of actual parenting, they went out of their way to give gifts and support to their demigod progeny. (Zeus had a lot of children due to his philandering but he did try to do his best to take responsibility for them.) Poseidon in particular was a Papa Wolf to his son Polyphemus and made Odysseus' journey home a living nightmare for blinding his son.
Every generation of Tekken's Mishima clan starting with Kazuya has this issue. Jinpachi was a nice enough guy, but Heihachi hated him anyways, starting a vicious cycle of hate with his own son Kazuya. In fact, the main plot of the Tekken series exists because the Mishimas all hate and fight their fathers until they turn corrupt themselves. So far, the only exception to this rule seems to be Heihachi's bastard son Lars.
Jecht from Final Fantasy X is an abusive, alcoholicJerk Jock of a dad. The nemesis relationship between himself and his son Tidus was heightened by the fact that both played the same sport, and Jecht went for the Drill Sergeant Nasty method of teaching and was too vain to admit his son might ever be anywhere near as good as him. Later, he was transformed into the Eldritch Abomination that terrorizes the entire world. Surprisingly, the trope is somewhat subverted, because Jecht becomes increasingly sympathetic as the game goes on, especially as Tidus comes to realizes that some of his FreudianIssues are his own problems and not his father's fault. Though Jecht does admit at the end he was a pretty crappy father too.
In Malicious, before the main game proper, the backstory has King Eldrake as one hell of an evil father, he is a corrupt king who imprisoned his own wife, Queen Ashlelei, for being against the turn of their kingdom into a corrupt one, despite the fact she was the one who brought victories and success to their kingdom; their two children Valeria and Erica could not stand their father's evil ways so they freed their mother and plotted a rebellion, only for King Eldrake to ally himself with foreign barbarians and kill his own two children without any remorse leading to the Queen's madness and the slaughter of the King and his followers by her hands.
In BlazBlue, one of the main villains of the game is Carl's father and personal antagonist Relius Clover, who turned Carl's sister into the machine known as Nirvana. Relius used the knowledge from that experiment to make a new and improved version of Nirvana, harvesting Carl's mother in the process. When Carl finally finds and confronts him in Continuum Shift's story mode, Relius tries to kill him for calling him out. Needless to say, they aren't on good terms.
This happens to Tiltyu and Lex in Fire Emblem: Genealogy of the Holy War, since their fathers Leptor and Langobalt are members of a conspiracy led by Alvis. Or better said, by Manfloy from the Lopto Sect.
For a series built on parent/creator issues, it's surprising that Mass Effect doesn't have more examples.
Urdnot Wrex's father, Jarrod, though Wrex killed him (in self-defense) long before the game started.
Miranda Lawson's father is obsessed with creating the perfect legacy through Designer Babies. We don't now how many he's gone through, but Miranda wasn't the first one he made, just the first he "kept" - and he was already working on a replacement for her when she was in her teens. She escaped, taking her clone baby sister Oriana with her. Miranda's efforts to keep Oriana out of her father's reach make up the bulk of her character arc.
Lemeza and Shawn Kosugi's relationship before and during La-Mulana is pretty rocky. Shawn essentially dumped his son on his own father to look for the fabled ruins of La-Mulana, and when Lemeza grew up and took up archaeology, they became bitter professional rivals, which was not helped by Shawn poaching Lemeza's work. This animosity manages to get the game started - Lemeza's original main reason for coming to La-Mulana was because his father taunted him about finding the ruins first - and carries on to the ending wherein Shawn waits for Lemeza to do all the hard work involved in getting the greatest treasure of the ruins and then steals it from his own son.
Ivy Valentine in the Soul Series. She despises her demonic father Cervantes (given the fact that her cursed existence is his fault), and he did try, more than once, to consume her soul to gain power. Before the events of V, however, she finally defeated him, not only reclaiming her own soul, but also all the souls he had ever devoured. But he still lives. (Well, not "alive", since he's still an undead being, but he's still around.
Royce, the King of Asgard in Heart Core and the father of Ame, is not only a horrible parent, considering how he almost killed both Ame and her innocent sister, but he is also the main villain of the series.
In Less Than Three Comics' Brat Pack, Firestorm's father abused him through his entire life, but the rest of the world only knows him as Napalm, one of America's greatest superheroes.
Jobe of the Whateley Universe seems to be developing this relation with his father, supervillain Gizmatic, also known as King Wilkins of Karedonia.
YAY-OK on Rocket Monkeys has an Omnicidal Maniac for a father who is obsessed with destroying everything in sight and oblivious to his son's desire to be close to him, though he is shown to genuinely enjoy spending time with him.
The Big Bad of Tenjho Tenge is Souichiro Nagi's father Sohaku. The guy stole his ex-wife's (Souichiro's beloved mother Makiko) eye for its power, chopped off her arm when she tried to stop him, and later implanted his own eye into Souichiro as part of his plan to take over Souichiro's body and powers. That's not even getting into his other victims — it's a long list.
Y: The Last Man. Dr. Matsumori to Dr. Allison Mann. After Allison dies, Yorick notes that it was her hatred of her father that drove her to be brilliant, and her post-gendercide clones didn't have that.
While not really a spoiler anymore to anyone even remotely familiar with Star Wars, Darth Vader is an archetypical example toward both Luke Skywalker and Princess Leia Organa, though he does, eventually, get better.
In Shocker, the psychotic killer Horace Pinker reveals during his execution that Jonathan is actually his son and that he killed his mom. For trying to stop him, Pinker has apparently made it his life's goal to destroy his son and brutally murder everyone he loves, including his adoptive family and his girlfriend.
Toklo's Jerkass father in Seeker Bears appears in Toklo's Story and returns in Forest Of Wolves. He had kicked Toklo and his family out when they were younger, so he fights him for his territory to return home.
Andrew Ryan from BioShock, but it comes as a surprise to him too and he stops trying to kill you when he finds out.
Miang, revealed to be the mother ofall humanity,is also the story's Big Bad. And as a BodySurfer who can awaken in any human woman, one of Miang's incarnations was Fei's own mother Karen. Fei and Karen were not technically adversaries, but Miang's consciousness was in control most of the time. Karen resurfaced in the end to be a Heroic Sacrifice to save young Fei's life. Miang simply surfed to another new body somewhere else in the world.
Fei's father got some of this too. Grahf, a mysterious and dark adversary of Fei for most of the game, is not only actuallyhimselffrom a previous life incarnation who survives as a BodySurfer, but it's Fei's own father Kahn who turns out to have been Grahf's host for years already. Though Kahn and Fei are also not technically adversaries, Kahn does all he can just to stay in control of his own body, though Kahn appeared to have even more periods of useful self-control than Karen did.
Rico's archnemesis Kaiser Sigmund is actually his father, andneither of them knew they were related.
In Jade Empire, not only is Master Li your character's father figure, it's also possible to find out that he's Dawn Star's father. In a subversion, absolutely nothing changes with his reactions to Dawn Star.
Tekken: In the first two games, Kazuya's #1 archnemesis is his father Heihachi. In Part 3, Kazuya "died" and Heihachi was an Archnemesis Granpa to Jin. From Tekken 4 onward, Heihachi is still the archnemesis to both Jin and Kazuya (who is Back from the Dead) and Kazuya is an Archnemesis Dad to Jin, who hates them both.
In Assassin's Creed III, Connor Kenway's father Haytham is the Grand Master of the Colonial Templars and a major antagonist, though Connor considers Charles Lee to be his personal nemesis.
Tarquin wants this for himself and Elan in a bizarre way. He clearly cares about his son and would like him to rule with him, but since Elan won't ignore his atrocities, Genre Savvy Tarquin figures that them eventually fighting to the death will at least make an excellent story that could have them live forever in legends. Elan is... somewhat less keen on this plan.
Tarquin and his other son Nale seem to also share this dynamic in an Evil Versus Evil way. They were also former allies, but Nale seems to have betrayed Tarquin at some point, and the two hated each others' methods (Nale being Contractually Genre Blind and always eager to show his superiority). Tarquin still tries to give Nale a chance to be a villain on his side, but it doesn't work out. Finally, Nale shouts that he doesn't want anything from Tarquin, including his favouritism, not realising that with the special favour withdrawn, other motives give Tarquin reason to just kill him on the spot.
In Codename: Kids Next Door, Numbuh One / Nigel Uno is quite understandably freaked out when he realizes that Big Bad Grandfather is his grandfather. This also makes Father his uncle. Inverted with his father who was once the legendary KND operative Agent Zero.
In The Powerpuff Girls, it is eventually revealed that Mojo Jojo, nemesis of the titular characters was once Professor Utonium's monkey assistant Jojo and it was through his tampering that Chemical X was introduced into the formula that created them. Mojo is left speechless at the realization that this technically makes him the creator of his greatest enemies.
Not only that, but due to a time-travel episode, he inadvertantly caused a young Utonium to actually want to become a scientist to "create the perfect little girl" after being saved by the Powerpuffs. This means that Mojo created the means for his & the girls' existance, but also the original desire which lead him to be adopted by the Professor as Jojo in the fist place.
Ninjago has Lloyd and Lord Garmadon. In this case, Garmadon actually loves his son, and neither wants to fight him or for him to be evil. But they're still destined to fight each other.
Gender flipped in W.I.T.C.H. where Nerissa is revealed to be Caleb's mother.