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Anime & Manga
- Haru's father, Gale Glory, from Rave Master, due to the fact that he helped found Demon Card and when he tried to stop them, he had a Dark Bring shoved in his forehead that would mature into a powerful explosive.
- Kanon's dad in Kanon.
- Mikoto's constant references to her brother in Mai-HiME. He turns out to be much, much nearer than she thinks...
- Nadia's long-lost (and presumed dead) father in Nadia: The Secret of Blue Water.
- Sumire's father in the TV series version of Sakura Wars.
- Ahryung's mother in Gwisin Byeolgok, a powerful shaman who for some reason sold her child's soul and body to Nachal.
- Van Hohenheim from Fullmetal Alchemist. It's initially presented as Parental Abandonment, since that's how his children see it. However, the real reason for his leaving is because he's a human philosopher's stone whose blood was used to create the Big Bad Father, who then used Hohenheim as an Unwitting Pawn to destroy the kingdom of Xerxes. Hohenheim is filled with guilt, and plans to stop Father from doing the same to Amestris; this was half of the reason he left home. The other half was to somehow find a way in which he could live out a normal lifespan and die at the end of it, so he wouldn't outlive his beloved wife and their sons. (He sorts fulfills this when he dies at the end of the manga, having outlived Trisha but not Ed and Al.).
- Renton's father in Eureka Seven is revealed to be more and more involved in the main plot as the story moves on.
- Ironically, Ao's parents, Renton and Eureka In the sequel Eureka Seven AO.
- Shun's father from Gate Keepers.
- Nagi Springfield, father of Negi Springfield of Mahou Sensei Negima!.
- Also Negi's mother Arika. Justified in that she was unjustly accused of a crime, and they didn't want Negi going off half-cocked to defend her reputation, so they didn't tell him about her at all.
- Konoka's mother is said to be a super skilled Magic Knight, but she is never seen. It's believed that Mrs. Konoe is Walking the Earth to hone her skills.
- Suzuhara Shuuko in Kidou Tenshi Angelic Layer is Misaki's long-gone mother, "busy with work" and defending her title as Angelic Layer champion. This is a spoiler for the manga, but is revealed early in the anime.
- Rumors flew during the first half of the Pokémon series' run that Ash's father was really Team Rocket's leader, Giovanni. This was discredited by canon in the updated remakes of the original games. A scientist at the end of the Rocket Warehouse mistook the main character (including the new female variation) for Giovanni's child, but then corrected himself, stating that said child has red hair. This seems to match the description of the rival from Gold, Silver, and Crystal.
- The latest games confirm this. A flashback sequence shows the second generation rival (Silver) talking to his dad, Giovanni.
- Masaru's Disappeared Dad in Digimon Savers, Daimon Suguru, is second only to Hitlermo -- er, Kurata on the list of "Characters Most Instrumental in Driving the Plot." Li Jiang-Yu from Digimon Tamers may count — very important to the backstory and, eventually, the plot, but not very mysterious and definitely not missing.
- In Kenichi: The Mightiest Disciple, Miu's father is the leader of the organization of Evil Mentors YAMI and possible Big Bad of the series. He is also directly responsible for Miu's Missing Mom.
- Ken "The Eagle" Washio's Disappeared Dad in Science Ninja Team Gatchaman, also known as Red Impulse.
- In One Piece, the main character Monkey D. Luffy's father is Dragon the Revolutionary, the most wanted criminal in the world and the only one actively trying to bring down the World Government.
- Also Portgas D. Ace whose father was Gold Roger, not Dragon as previously believed. Garp adopted him, he goes by his mother's name, and he doesn't like his father because all the grief his heritage caused him, knowing that in the eyes of the world, he wasn't supposed to exist.
- Maka's mother in Soul Eater is quite possibly being setup as something like this. Reportedly very skilled as a meister, former partner (and ex-wife) of the current Death Scythe, yet she has not turned up in any capacity - or had any significant references made - in the manga while Shibusen was dealing with Asura. The anime's Gecko Ending had her send Maka encouraging postcards from her trips around the world...rather than doing anything practical for her daughter or colleagues who were trying to prevent the end of the world. Maka idolises her mother, and from her comments about the woman she is clearly trying to emulate her as a successful, strong scythe meister.
- Nube's father Jikuu in Hell Teacher Nube. We only find out about him in the manga; he doesn't appear in the anime.
- For much of the run time of Star Driver, the only things we knew about Takuto's father were that he's somewhere on Southern Cross Island, a painter and that his name starts with R. The more episodes pass, the more it becomes clear that the only character who seemed to possess most of these features is a Red Herring and Takuto's actual dad is Head, the Big Bad, who for some reason looks much younger than he actually is. In fact, if one rewatches everything with this knowledge in mind, it becomes clear that subtle hints at Takuto's father's identity have been dropped ever since the very first episode.
- In Teen Titans, Raven's mother stayed away from her until she was about ten years old. Since her Father is an inter-dimensional Demon, he doesn't show up until he's ready to use Raven as a portal to Earth.
- Another Titan with parent issues, Roy Harper knows absolutely nothing about his mother. Literally nothing, other than he had to have had one. He knows his father died in a forest fire, but his mother was just never mentioned or never alluded to anywhere. The lack of information actually helped Roy break out of a Lotus-Eater Machine situation.
- Batgirl was taken from her parents as a child by an assassin, who trained her to be the ultimate killer. As the series progresses, she learns that she wasn't taken at all. The assassin who raised her is her real father. In addition, the final arc of the series has her trying to discover the identity of her mother, and learning that she's her longtime Arch-Enemy Lady Shiva.
- Pokémon Reset Bloodlines takes Ash's father and his status of this in canon Up to Eleven. Not only does Ash realize the memories of him have become so hazy he can't even remember anything about him, but Ash also encounters a number of characters who look like him, culminating in one of these people calling Ash her brother. Outside of that, plot occurring outside of Ash's awareness builds the mystery up more and more.
- Tobias, in Animorphs, when Elfangor, the Andalite who gave the kids the morphing cube, is revealed to be his father.
- In the His Dark Materials trilogy, Lord Asriel and Mrs. Coulter are revealed to be Lyra's parents.
- Bria in The Last Dove. Though there's never really any doubt from the beginning that she's Queen Vasi's daughter.
- Halt in Ranger's Apprentice; he's heir to the throne of Clonmel and his brother is the current king.
- Pansy Osmond from The Portrait of a Lady turns out to be the product of an affair between her father and Serena Merle.
- In Vampire Academy, Rose grew up with no knowledge of her father's identity, other that he was a Turkish Moroi. He turns out to be Ibrahim "Abe" Mazur, a notorious smuggler and trader in information. He later plays an active part in her life.
Live Action TV
- The Evil Queen of The 10th Kingdom.
- Claire Bennet from Heroes. Her birth father is Nathan Petrelli.
- In the very first episode, Clara's father is perpetually on his way home from a business trip. The Reveal comes that this is the same man that has been menacing Mohinder Suresh throughout the episode and he plays himself to be a typical dad when he comes home. Not as much as a spoiler, but considering how Heroes loves the end-of-episode reveals, it's one of the first big reveals of the series.
- Alias did this most famously with the season one finale, "Almost Thirty Years", in which The Man walks into the room where Sydney Bristow has been tortured. Sydney raises her head weakly and says "MOM?!"
- A 30 Rock episode in which Liz had a really bad day culminated with her boyfriend taking her to meet his "mother" on her deathbed. After he left the room, his "mother" confessed to Liz (mistaking her for his ex-wife) that she was actually his grandmother and his "sister" was his real mother. Then she promptly died.
- Claire on Lost: a throwaway line about her "daddy abandonment crap" in Season 1 is explained in Season 3 when her father turns out to be Christian Shephard, Jack's dad.
- Narrowly averted on Battlestar Galactica when it was widely presumed that the missing Number 7 Cylon, Daniel, was Kara Thrace's missing father until Word of God denied it.
- 3rd Rock from the Sun, Dick Solomon's birth father is revealed to be The Big Giant Head played by William Shatner. Knowing this, fans realized Dick was previously married to his cousin Janet. Also note that they have no blood relation to Sally, Tommy, or Harry, even though they pretend to be siblings.
- John Winchester probably counts. Until the end of Season One, he was busy investigating the secrets of Sam's identity as an evil Chosen One, and he was basically hiding all of these secrets, as well as his whereabouts, from Sam and Dean (who were thus searching for their father without knowing why he was missing.
- Baldur's Gate: The main character's Disappeared Dad turns out to be Bhaal, God of Murder.
- Done twice in Disgaea, with both parents of Laharl. Laharl's father is Mid-Boss, or rather the Dark Adonis, working behind the scenes to reunite the Netherworld and Celestia, while his mother is Big Sis Prinny, paying penance for the sin of taking her own life to save Laharl's.
- Jade Empire: One of the Lotus Assassins sent to kill Master Li's family couldn't bring himself to kill his infant child, Dawn Star ? who ended up being raised by Master Li at his school in Two Rivers, neither even suspecting their relationship until they're told about it late in the game.
- Ace Attorney's Kay Faraday took up the thief's lifestyle after finding out that her dead father was the original Yatagarasu. She doesn't find out the major twist until later.
- Kratos of Tales of Symphonia.
- Dragon Quest V: The Hero's mother.
- Both of Ashley's parents take this role in the Another Code games. Her dad is this for the first game while her mom takes the second.
- Chris Hyde is this for Kyle in Last Window. The primary objective is to find out about his One Last Job and how it got him killed.
- Dr. Sciuridae in El Goonish Shive, who was forced to leave his 'granddaughter' Grace when the company behind Project Lycanthrope discovered that he had intentionally replaced the intended DNA source for Shade Tail with a sample of his deceased daughter's DNA.
- Nobody knows who the hell Tedd's mom is, but something to do with her had a major impact on Tedd's life.
- Linda Walkerton in It's Walky! who switched one of her twin children, Sal, at birth in an attempt to mislead Head Alien.
- Agatha in Girl Genius is revealed as the daughter of Bill and Lucrezia Heterodyne.
- In Gunnerkrigg Court, there's clearly some big secret about Antimony's missing parents, but no one's telling her anything.
- Well, we know that Surma was a famous medium, and now her nature and why she's dead and Anthony is absent is revealed. Annie was pretty unhappy to have these details discovered in a less than nice way.
- Kat didn't believe in magic and never saw her mother using a computer, which made it a rather... interesting moment when Anja mentioned the magical machine she developed years ago.
- In Drowtales Mel'arnach turns out to be the "father" of Kalki, with Snadhya'rune as the mother. Made possible with the Jaal'darya clan's Organic Technology / Bio-Augmentation.
- Played for laughs in The Order of the Stick here.
- In The Wretched Ones, Charlie and Kazuko's father disappeared right before Kazuko was born. His fate is unknown.
- In the Whateley Universe, She-Beast is now known to be the daughter of the notorious supervillain Dr. Diabolik. And she has a pretty darn good idea about her mother. It's not pretty.
- There's worse lurking around. Carmilla used to be Michael Waite, child of an unwed mother. The father eventually turns out to be a very powerful demon of lust and his mother turns out to be a descendant of Cthulhu who slowly turns into a Deep One.
- Franz Hopper in Code Lyoko.
- Morgana, Roxy's mother, in Winx Club.
- Brad Chiles and Judy Reeves, the real parents of Fred Jones in Scooby-Doo! Mystery Incorporated. Fred has gotten wise to their plans with the rest of the previous Mystery Inc. team to locate the cursed treasure of Crystal Cove and has disowned them.