Mysterious Parent

When the reason for Parental Abandonment of a character is revealed, and the parent is someone important to the world of the story, or at least the events. Occasionally alluded to constantly but vaguely for maximum surprise. This is often coupled with some startling revelation about the child too, such as if the parent was/is a scientist and the child was created in a lab experiment, or are following in a Secret Legacy of the family.

In anime, said parent is usually the same sex as the child.

This trope can also apply to more distant relatives or siblings, although their existence isn't as intuitive.

Interestingly, real-life relationships can be just as tortuous and surprising as the fictional ones; for a famous example, Jack Nicholson learned just days before the premiere of Chinatown that his recently deceased "sister" was in fact his natural mother, and that the parents who raised him were in fact his grandparents (similar switches occurred in other people's lives, such as singer Bobby Darrin).

Compare with Luke I Am Your Father. Also compare Chekhov MIA, when the missing person actually shows up in the flesh.

Anime & Manga

 * Haru's father, Gale Glory, from Rave Master, due to the fact that
 * Kanon's dad in Kanon (by Chiho Saito).
 * Mikoto's constant references to her brother in Mai-HiME.
 * 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 Taisen.
 * 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 depends on whether you're reading the manga/watching the Brotherhood anime adaptation or watching the first anime.
 * In the manga and the Brotherhood anime, Van Hohenheim.
 * In the first anime, Hohenheim Elric
 * Renton's father in Eureka Seven is revealed to be more and more involved in the main plot as the story moves on.
 * Shun's father from Gate Keepers.
 * Nagi Springfield, father of Negi Springfield of Mahou Sensei Negima.
 * Also Negi's mother, 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.
 * Precia Testarossa, the abusive mother of Fate in Magical Girl Lyrical Nanoha, is the one that's ordering her to get all the Jewel Seeds.
 * in Kidou Tenshi Angelic Layer 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.
 * 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 History's Strongest Disciple Kenichi,  father is heavily implied to be   and possible Big Bad of the series. He is also directly responsible for   Missing Mom.
 * Ken "The Eagle" Washio's Disappeared Dad in Science Ninja Team Gatchaman,.
 * In One Piece, the main character Monkey D. Luffy's father is
 * Also
 * 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.
 * 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.

Comics

 * 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.
 * 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.

Films

 * Darth Vader, most famously.
 * Bootstrap Bill Turner in Pirates of the Caribbean, who manages to be vital to the plot of the first movie without actually appearing in it.

Literature

 * In the His Dark Materials trilogy,
 * Tobias, in Animorphs, when Elfangor, the Andalite who gave the kids the morphing cube, is revealed to be his father.
 * Bria in The Last Dove. Though there's never really any doubt from the beginning that she's 's daughter.

Live Action TV

 * of The Tenth Kingdom.
 * Claire Bennet from Heroes.
 * 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
 * A Thirty 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
 * 3rd Rock From the Sun, Dick Solomon's birth father is revealed to be . 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.

Video Games

 * Baldurs Gate: The main character's Disappeared Dad
 * Done twice in Disgaea, with both parents of Laharl. Laharl's father is, while his mother is
 * Jade Empire: One of the Lotus Assassins sent to kill Master Li's family couldn't bring himself to kill his infant child,.
 * Ace Attorney's Kay Faraday
 * of Tales of Symphonia.

Web Comics

 * Dr. Sciuridae in El Goonish Shive,
 * 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!,
 * Agatha in Girl Genius is revealed as the daughter of.
 * Note: that accounts for
 * Gilgamesh grew up not knowing who his parents are. Readers still don't know about his mother, though there are plausible theories.
 * 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 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 Drow Tales Made possible with the Jaal'darya clan's Organic Technology / Bio Augmentation.
 * Played for laughs in Order of the Stick, here

Web Original

 * 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.

Western Animation

 * Franz Hopper in Code Lyoko.
 * , Roxy's mother, in Winx Club.