Parental Abandonment, by its nature, usually excludes the parent from having much of a role in a character's story. If the backstory involves a child wallowing in angst because of having no parents, to bring them back and treat everything as being hunky-dory sort of dilutes the origin story's dramatic impact.
Sometimes, though, a parent can be brought back through use of a proper excuse. A parent who we have seen or heard nothing of in some time may suddenly re-appear and explain that there was, in fact, a very good reason for the abandonment- but for various reasons, the details could not be revealed until just this moment. This is particularly important if child is going to follow in their parent's footsteps, since we would normally expect them to be bitter if this is the career that caused them to get abandoned in the first place.
Frequently the reason turns out to be Mum never informed Dad of their baby's existence for reasons that can range from not being sure which partner was the father (a My Two Dads scenario), a desire to keep said infant all to herself, misguided 'kindness' of the 'a baby will ruin his life' nature or unresolved hostility towards him or all men.
This trope straddles a thin line - it can come off as extremely contrived unless said excuse is very, very convincing. In order for it to work there must be an explanation as to why no one bothered to bring it up until just the last minute. See also Glorified Sperm Donor for a form this can take when it's handled badly.
Sounds like but has nothing to do with taunting someone about having some real or imagined flaw which leads to the parents not loving them enough.
See also Tell Me About My Father, Turn Out Like His Father. Sometimes related to Give Him A Normal Life, and may overlap with Because You Can Cope in certain instances. If the info is specifically withheld to increase tension even though there's no good reason to withhold it, see the Rule of Drama.
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Anime and Manga
Jolyne Kujo from Part 6 of JoJo's Bizarre Adventure resents her father, Jotaro Kujo, for being absent for most of her childhood. Although partly due to work reasons, Jotaro also didn't want her getting mixed up in the supernatural troubles that he's frequently a part of.
Ranma's mother in Ranma ½. Nodoka claims that she agreed to not be around Ranma to make him a stronger man, and that she received constant letters from Genma all throughout Ranma's childhood, which stopped just about the time he and Ranma headed for China — and their absence is why she went personally to the Tendo home. This makes readers realize that this makes Genma an even bigger bastard because he deliberately kept Ranma unaware of his own mother despite writing to her regularly.
It is played straight with Kenzo. His sons, Kouji and Shiro grew up believing their parents had died cause a laboratory experiment that went wrong. However, Kenzo's father saved his son's life by turning him into a cyborg. However, neither of them told Kouji and Shiro he was alive because Kenzo was going to build a Humongous Mecha to repel the Mykene invasion they predicted, and train its pilot. And both his father and he wanted to shield Kouji and Shiro from danger and psychological shock. It was not a bad reason, even if it was somewhat weak because Juzo was also building another Humongous Mecha and he raised them, even if he hired a maid because he was nearly always absent. When Kenzo revealed the truth to his little son, it took a long while for Shiro forgiving him. Though Kouji forgave him right away.
It is subverted with Kouji and Shiro's mother. In episode 90 from Mazinger Z, their mother appeared in the Institute, revealing she was alive and asking meeting her sons before telling them why she let them believe she was dead during years. Shiro was happy of getting his mother back, but Kouji was distrustful. It turned out that Kouji was right. Their mother was truly dead and that woman was a cyborg had fabricated Dr. Hell to infiltrate in the Institute and destroying Mazinger from within. So her "good reason for abandoning them" was false.
Done with Hohenheim in Fullmetal Alchemist, where he figured out the Big Bad's evil plan and set out to stop him. He was also trying to become mortal again, however, since he wanted to die with Trisha, though ironically he didn't want to die at the end because Edward finally called him dad and Alphonse got his body back. He still dies next to her tomb, a bittersweet smile on his lips.
Played mostly straight in Code Geass with Kallen Stadtfeld and her birth mother, who is actually the incompetent family maid Miss Kouzuki. Kallen assumes her mother stayed on to continue to be her father's mistress, and treats her poorly and puts a sticker over her face on a family photo. Cue the dramatic moment when she discovers her mother actually remained out of love for Kallen, but didn't want to give away the fact Kallen is a half - "breed", and as her mother is jailed, she swears to make Miss Kouzuki her Morality Pet, later taking the sticker out of the photo. Thank God, in the Grand Finale we see Miss Kouzuki free and in her path to recovery, living modestly but happily with a Kallen who's now back to Ashford Academy.
Played with in R2, where Lelouch discovers his father's reason for abandoning him and his sister in a foreign country was to protect them from his brother, who had murdered Lelouch's mother out of jealousy. On the other hands, Lelouch immediately points out that Parental Abandonment is Not Cool, and that if his parents had really been as concerned about the well-being of their kids as they claimed, they would have figured out a way to protect them without heavily traumatising one and crippling another, and then invading the nation whose leader had him and his sister as a political hostage... thus nullifying any need for living hostages.
In Samurai Champloo, Fuu's father, the Sunflower Samurai, has a very good excuse - as a Christian in isolationist Japan, if he had stayed home, his entire family would be executed.
In the Star Village filler arc, Sumaru's parents attempt to steal the star in order to stop the star training that kills most of those who use it, but get discovered by the Hoshikage, who has them leave the village in order to watch over the star from afar and intervene if someone plans on using it again. Sumaru grows up thinking that his parents died defending the star; his father does die from the lingering effects star training, and his mother indicates that she can't stay with him if she could die at any time. His mother returns to steal the star when the star training resumes after Akahoshi kills the Hoshikage, and dies trying to recover the star.
Even though Luffy would probably not face the same situation: while his father is a VERY wanted man, his grandfather Garp is a legendary Marine hero, and the one famous for fighting Gold Roger. Concidering how Garp had wanted Luffy to become a Marine, the show indicates this would overshadow Dragon's situation. Then again, considering how Akainu acted towards Luffy during the Marineford Battle...
Usopp's father abandoned him and his mother and never returned. Luffy then convinces Ussop that his father had a good reason for leaving him, since he was doing some pirate-stuff, up to the point where Usopp gets proud of him.
In The Vision Of Escaflowne, Failure Knight Allen Schezar was badly traumatised by his sister's kidnapping and his mother's Death By Despair, and hates his Disappeared Dad for leaving the family. When he does have a chance to call him out, Allen finds out that Leon Schezar was Dead All Along, having been murdered by The Empire because he didn't give them the information he had about the Dragonkin; Mrs. Schezar was depressed to death because she knew her husband was dead since the beginning. Allen then manages to posthumously forgive his dad, and later in the series he gets his still-alive but badly fucked up younger sister back. How badly messed up is she? It turns out that she was captured by Emperor Donkirk and turned over to his wizards, tranforming her into the Axe Crazy (and male) Captain of the Dragonslayers; Dilandau.
Played straight as an arrow in Mobile Suit Victory Gundam at least twice. Hangelg Ewin, the father of series protagonist Üso Ewin, was actually Jinn Gehennam, the leader of the League Militaire. Likewise, Üso's mother, Mueller Miguel, was also involved in League Militaire, in her case as a mobile suit engineer and spy. This rather neatly explains why Üso was practically left alone with his best friend Shakti Kareen, whose own mother, Zanscare's Queen Maria Amonia, had abandoned her to Earth to protect her from Zanscare's rabid factionalism, to practically raise themselves during their early teenage years.
Also more or less used in Gundam F91, where Monica Arno is the mobile suit engineer that creates the Gundam in the title. Her youngest daughter Reese seems to understand it, but her eldest son Seabook is understandably pissed off at her. The fact that the patriarch of the family, Leslie, has just kicked the bucket doesn't help.
In Pokémon Special, Ruby has a deep resentment for his father, Norman, for leaving the family for five years. In reality, a frenzied Salamence assaulted Ruby and Sapphire, and the injuries inflicted by Ruby caused it to careen into the Weather Institute. Norman covered it up and was disqualified from his gym leader certification trial as a result. The change in Ruby's behavior left bad blood between both of them. Norman gave Ruby the go-ahead with his Contest campaign after a prolonged battle at the ruined Weather Institute five years later (would have been a birthday gift if Ruby stuck around). Then Ruby found out the motives for Norman's actions. Oops.
Gale, from Rave Master left his family when Haru was one in order to find the Rave stones, which is revealed fairly early on in the manga (or 15 years after he left. Why did no one tell Haru sooner?) This explanation alone is still unacceptable to Haru. When he actually meets Gale and learns that he left to find Rave in order to stop his Big Bad Friend, the leader of Demon Card, Haru accepts him as a father.
It kinda helped that Gale thought that the Dark Bring implanted in him by King could have created a second Overdrive at any moment, and thus wanted to be as far away from anyone as possible, especially his beloved children.
Averted in Neon Genesis Evangelion. It seems like they're setting Gendo up for this one when, right before he gets sucked into Instrumentality aka The End of the World as We Know It, he explains his reasons for ignoring his son for like a decade, mainly that he believed he would have been a horrible father and that Shinji would do better without him. Considering how badly Gendo screwed up his son when they did meet, he might have had a point. It's averted because: 1) It's way too late by then, and 2) his Freudian Excuse and subsequent apology to his son don't really fly very well with anybody, and he seems well aware of the fact as he dies.
Bokurano. Jun Ushiro and his mother, Misumi Tanaka. That's all. Each medium gives a different reason, but they're all pretty good.
Goku from Dragon Ball Z spends most of Gohan's and pretty much all of Goten's childhood's dead or off training.
Though when he is around/alive, he really does try to be the best father he can to them. Points for effort, though his Spirited Competitor causes issues in what he thinks are good parenting decisions — he learns his lesson when he goes too far during the Cell saga, just in time to realize his folly and sacrifice himself for his son. Until then, though, his former archenemy comes off as a better parent to his son than he is.
In Yu-Gi-Oh 5Ds Yusei's father sacrificed his life during the Zero Reverse disaster to ensure that his son would survive.
Although we don't know the exact circumstances involved with Hinagiku and Yukiji's being abandoned by their birth parents in Hayate the Combat Butler, Hinagiku firmly believes that they had a good reason for leaving them behind. Yukiji doesn't seem to agree.
Doctor Kentarou Go aka Prince Lagour in Voltes V. That's what happens when your dad is a a fallen nobleman from an alien planet with a massive Break the Cutie-like past, who leaves you and your siblings to work on putting an end to the tyrannical rule of Emperor Zambajil, his evil cousin and the one to blame for his banishment.
Kotetsu is a corporate-sponsored superhero, who is unable to take days off to visit his hometown to see his 9-year-old daughter. He does, however, speak to her on the phone regularly, though he never sees through on his promises to see her. The one time he does have a day off, a new Big Bad appears and screws it up. It is revealed that he left after his wife died and hasn't come back to visit his family for over 5 years; when he finally does go back, his daughter is 10 years old and hates him for absndoning her.
Nobuchika Ginoza's father, Tomomi Masaoka, left his family because, according to the system that governs their society, Tomomi was a latent criminal who could have snapped at any moment.
Renton Thurston in Eureka Seven AO wasn't there for Ao and Eureka due to being stuck fighting Scubs and Secrets in the original Eureka Seven universe. And had Eureka stayed, the trapar would have killed Ao like it did his stillborn older sister.
As reasons go, Jor-El's is pretty damn good: the planet was blowing up and the one rocket he had was just large enough to safely carry his son Kal to Earth.
In The DCU, the Persuader's father left her mother because she was abusive towards both him and the young Persuader herself. However, her threats to rough herself up and say he did it if he even thought about taking their daughter convinced him that leaving her with that monster was a better alternative to living on the run with him. They eventually get reunited in a Crowning Moment of Heartwarming before the Persuader's boss kills her father just for kicks.
Cyclops of the X-Men: Daddy had been kidnapped by aliens, and was too busy being a Space Pirate, growing a kickin' stache and seducing his felinefirst mate to find his way back to Earth. Well, we said he had a good reason for abandoning you, not necessarily for staying away.
Cyclops' father assumes both of his children have fallen to their deaths, because their parachute was on fire. That is the last thing he sees before the aliens beam him off his plane. He does not learn Scott and Alex are still alive until they have both reached adulthood. So up to that point, he has a good reason not to be there for them. However, as soon as he finds out they are alive, he asks Jean Grey not to tell his children, because this would supposedly be for their own good. When Scott finds out anyway a few months later he is mightily pissed off.
Sinestro left his family to spare them from being associated with an intergalactic criminal.
In Whispers in the Dark, a popular Percy Jackson and the Olympians fanfiction, Taylor is told that her father is dead only to find out that all this time, he's been alive and on Kronos' side. Somewhat justified in the fact that Luke didn't even know that he had a daughter until he saw Taylor and noticed that she had his blue eyes.
Nobody Dies Mommy had a good reason for abandoning Shinji...a basement full of Eldritch Abominations out to kill him (although why she didn't kill them instead of abandoning her son and possibly endangering the planet is a question unasked).
That would require a mother of a young child to murder several children the same age as her kid.
All too often handwaved in the "Adopted Hermione" subgenre of Harry Potter fanfic: Hermione learns that she's not only adopted, but "really" a Pureblood. In roughly nine such stories out of ten, no reason is ever given for her birthparents' relinquishing her — except possibly a vague assertion that it was "for her own protection".
My Enemy My Friend shows Gendo's canon motivations for abandoning Shinji to the reader, and doesn't let them forget it.
ADAM as well for the Angels. You know, considering he's been kidnapped and is held hostage by SEELE and all.
In the Ah! My Goddess story "Ah! Archfall!",Lind's farther is actually the Almighty One. She was never told who her farther was though and thinks that she was disowned by her mother for having just one wing. The actual reason for the abandonment was that she was his BASTARD daughter via one of his bodyguards but being a little older than Belldandy and a pure goddess unlike Urd, Lind was set to become the next Almighty One. To have the bastard daughter as the Almighty would have been a major embarrassment for Heaven and so the Almighty was sworn to secrecy or he would have been stripped of his title and powers, while Lind and Valmeyar would both have been killed .
Natural enough subject matter for Pirates of the Caribbean fanfic, where two generations of Turner fathers accidentally abandon their sons. Bill Turner was (at least supposedly) working away and never came back, whereas Will eventually finds himself in a Her Heart Will Go On situation, though with a twist that he may be able to come back eventually. It's a good source of Issues.
Also, Anakin didn't even know Padme had twins, so he was surprised to learn that Luke had a twin sister.
Invoked in The Truman Show, where the writers decide to bring back Truman's father after he'd "died" at sea. This is explained through Easy Amnesia, and his just then getting over it.
In Beverly Hills Chihuahua 2, Delgado gets to see his sons...who act very distant and aloof towards him, remarking that "he's never watched out for us". But Delgado tells the Chihuahuas this, who later tell this to his sons: When he and the local officers arrested some criminals, they were going to hurt Delgado's puppies. So he takes them over to Los Angeles to make sure they're safe since he couldn't do that anymore. After hearing this, his sons apologize for not understanding him and make up, letting him tag along with their police force for a while.
This is the main theme of the King Arthur myth, where the young Arthur is abandoned by his father Uther Pendragon to be raised by Merlin. The reason for this varies depending on which version of the Arthur myth is read, but, canonically, it is because as a bastard son of Uther the succession would be in doubt and/or Arthur's life would be in danger if Uther produced a later legitimate son with Ygraine.
Played with in the second book, The Wizard Heir, of Cinda William Chima's The Heir Chronicles. Because Seph's mother, Linda Downey, was fighting the system of the Wizard Guilds at the time he was born, she knew he would be in danger if anyone ever found out his parentage, and thus leaves him to a foster mother to keep him safe. Seph's father, Leander Hastings, didn't even know Linda had Seph because she disappeared on him after finding out she was pregnant.
Susan Cooper's The Grey King. Bran Davies is in truth the son of King Arthur: he was brought forward in time and left in the 20th century by his mother Guinevere after she betrayed his father. She had to leave him because she was going to find sanctuary in a convent.
In the Warchild Series, Captain Azarcon isn't around to raise his son Ryan (boy do people in fiction have tough parental issues with that name) because he's busy fighting a war against pirates and aliens.
In Harry Potter, Dean Thomas's father was an example of this. He was asked to join the Death Eaters, but refused and ran away to protect his muggle wife and baby son. (The Death Eaters didn't know he'd married a muggle.) He ended up getting killed. Dean never finds out about this.
Neither do most readers, because this info is Word Of God. It was going to go in but didn't really fit anywhere in the plot, leading J.K. to build up Neville's subplot instead. (Which also sort of fits this trope, if not perfectly.)
Also, Remus Lupin attempts to invoke this trope with his as yet unborn son, Teddy. The prospect of his child having to grow up discriminated against because of his werewolf father and the way in which his marriage to Tonks has essentially made her an outcast leads him to try to abandon them in the belief that they will be better off without him. His fears are completely justified, but his response is not, and Harry is quick to call him out on this.
In Dinoverse, the rebellious graffiti artist Janine resents how her mother is often not at home, forcing her to miss school in order to prepare the hotel for guests herself. As it turns out, her mother is keeping Janine from getting in trouble over the graffiti - she never confronted her daughter because she feared Janine would run away.
The father of Demon Princess's protagonist was first in line for the throne, which also carried the responsibility of making sure nothing bad gets through portals to the human world. The way it's run is that when the current demon king/queen dies, the heir is immediately transported to the castle and can never leave. While he was with the protagonist's mother, his father died and he was called back, giving him no time to explain or say good-bye. He decided that she wouldn't even believe the explanation, so never made contact with his family until he learned about his daughter and her latent powers.
In Animorphs Tobias's father, Elfangor, had to leave him because he was being sent back to the Yeerk War by the Ellimist. The timeline was changed back to what it should have been, but Tobias still remained.
His mother, too: she was in a car accident that left her blind and gave her amnesia of the non-laser-guided variety (i.e., it took her years to learn to take care of herself, let alone a child). She put off tracking him down because she thought she would just disrupt his life.
In The Historian the primary narrator, a young woman in the 1970s, was raised by her diplomat father because her mother died when she was an infant. You find out that her mother only faked her death to escape getting bitten - and therefore turned into a vampire - by Vlad "The Impaler" Tepes a.k.a. Dracula himself. The mother then spent the entirety of the narrator's childhood researching when and where Vlad would next appear so that she could kill him without endangering her family.
In Michael Flynn's Up Jim River, the harper, having heard the story in The January Dancer, knows that her father had an excellent reason — but points out that her mother didn't know it.
Tales Of Kolmar has Lanen's mother leaving her with her uncaring father when Lanen was tiny. Turns out this happened after a demon attack. Maren thought her Farseer was attracting them. By the time it turned out this wasn't true, years had passed, and she was afraid to go back.
There's a variation in A Brothers Price. Halley was the natural leader of the surviving princesses, but she wasn't the eldest - and by the traditions of this world, the eldest has to rule the family; especially this family, which will come to the thrones and has a recent tradition of turning into a Civil War over this point. Halley disappeared Because You Can Cope and to try and force her eldest to step up and take more responsibility.
Live Action TV
In Alias, Sydney has a rocky relationship with her father, Jack. It's implied he wasn't around much while she was growing out. Turns out he's a CIA agent fighting to save the country. And he was also in prison for part of time. Her mother, Irina, wasn't around because she faked her death and defected back to Russia.
Variant in Bones. Cam, it turns out, was an honorary stepmom to the daughter of her very serious boyfriend, but left the relationship (and, by proxy, the girl) when it turned out he had cheated on her. When the man was murdered and the team put on the case, the daughter is now a teenager and very annoyed at Cam who ends up adopting her.
Also in Bones, both of Brennan's parents were being hunted by the gang of criminals they used to work with.
Played with on Brothers and Sisters. Adulterer-patriarch William sired a bastard son with a married woman. The boy, Ryan, doesn't know this until both of his bio parents are dead. William couldn't be part of his life because both he and Ryan's mother were married to other people and weren't willing to destroy their marriages for the sake of their son. Here it's not really even a justification, but rather an explanation. Everyone still thinks William is a dick after this is revealed.
The sisters father was kept away by a spell cast by grams.
Paige was given up because of the believe her existence would screw up destiny. Some can't help but wonder whether the issue was more fear about the wrath of the elders (which would also be a valid reason, just a bit more selfish).
In Chuck the reason Chuck's and Ellie's father left was to protect them from the spy agencies that wanted to use him for research on the Intersect.
And the reason their mom left them? She was a CIA agent working undercover and an insane international weapons dealer fell in love with her. She had to leave because she was afraid of what would happen if the guy found out about her family.
Further along the plotline, the initial reason she left them was to bring the guy back to the CIA, since he was the initial Intersect, that had failed.
The episode "Family" on Cold Case the girl's father was killed the night she was born and her mother, who was distraught over what she thought was dad's abandonment, also abandoned the girl.
And the episodes "The Thin Blue Line" and "Into The Blue" reveal that Lily's dad abandoned her because he was a recovering alcoholic and felt that his staying married to Lily's mom (also an alcoholic and refused to get sober) would jeopardize his sobriety. Lily's mom threw him out and refused to allow him to have contact with her or her sister.
Happened on Criminal Minds with Reid's Disappeared Dad, whom everyone assumed left due to his mom's mental problems. When a case involving abducted childrens awakens long-buried memories and leads Reid to suspect that his dad sexually assaulted and murdered a neighbor's child, we get the real story. It turns out that a local man named George Michaels was the real murderer. When Reid's mother realized that, she told the murdered boy's father, who killed Michaels; in the process, Reid's mother fell over the body and got blood on her. Reid's father burned her clothes and helped to cover up the murder, but he was so guilty about it that he lost all confidence and had to abandon Reid to take care of his schizophrenic mother. Six years later. Or something like that. You're on your own to decide whether that's a good reason or not; Reid accepts it as a reason, but it's not clear that he thinks it's a very good one.
In season 4 of Desperate Housewives, Lynette's stepfather shows up and tells her that the reason he left her family when she was a kid was because he's gay. Lynette's mother never told her because she was embarrassed about it.
Used in season three of Gossip Girl when Chuck Bass' supposedly dead mother shows up. Serena desperately wants to believe that her reason for leaving would play into this trope, since that would make Serena feel less horrid about having been abandoned by her own father. Chuck's maybe-mama crushes Serena's hopes and fantasies however by simply explaining "I didn't want to have a kid and I never regretted giving my child up."
Subverted in Season 2 of Heroes with Maury Parkman. After Matt tracks his father down, Maury hugs him and pretends to be sorry he left. However, Maury then uses his telepathic powers to trick Matt and Nathan into fighting each other.
Unsubverted during Season 3 when Maury performs a Heel Face Turn and works for Arthur Petrelli in exchange for his son's safety.
Done very sympathetically on an episode of Lie to Me where the team investigates a congressman who has spent 80 grand on a prostitute. However, they find out that he's never had sex with her, and was giving her the money to get her out of that business. She doesn't know that he's her father, and he is portrayed as someone who gave up his child for adoption but regretted it. The fact that he has no hesitation to sacrifice his reputation and political career in order to protect her from the scandal counts a lot toward making him so sympathetic.
Then there are cases where the other parent forces your hand, as with Michael on Lost.
Or Miles, whose father makes his mother take him off the island to save their lives.
An episode of MacGyver gave us a variation: Jack Dalton's mother gave him up for adoption to protect him from a mobster that was targeting her.
Married With Children: Seven's folks stick the Bundys with the kid, but for a good reason: They felt Al/Peggy would be better parents. Of course, he ended up on the side of a milk carton, so...
Victor with Adam on The Young And The Restless. Here, Adam's mother specifically asked Victor have no part in Adam's life, but charged Victor to take care of Adam on her deathbed. Not really sure why- it's a Soap Opera so her reasons for this were probably explained like, ten or twenty years ago.
Same with Paul and Heather. He was asked to stay out of Heather's life completely at her mother's request.
On Once Upon A Time, the Evil Queen cast a curse on Fairy Tale Land, forcing Snow White and Prince Charming to put their baby daughter Emma into a portal that carried her to the real world in order to save her from the curse. Emma herself has very mixed feelings on the matter. The original plan was for them to go with her, but circumstances and another character's motivations led to neither of them making it.
In Supernatural, the protagonists' father John lived his entire life believing that his father had walked out on him. Sam and Dean learn that their grandfather had actually travelled to the future in order to keep a valuable artifact out of demonic hands and died before he could return home.
In the first episode of Stargate SG-1, Teal'c turns against Apophis and escapes to Earth with SG-1. We later learn that he left behind a wife and son, both of whom are understandably bitter with him for his abandonment. They eventually come to understand that he left for the greater good because he realized that the Tau'ri would be valuable allies in overthrowing the Goa'uld.
In the Johnny Cash song A Boy Named Sue, the dad doesn't explicitly mention just why he left at all. He does, however, justify naming his son Sue:
And he said, "Son, this world is rough/and if a man's gonna make it, he's gotta be tough/and I knew I wouldn't be there to help you along..."
Manowar's song Defender opens with the reading of a letter explaining this.
Inverted in Annie: optimist heroine Annie assumes that her parents abandoned her for a very good reason and they will one day be reunited. Unfortunately, it turns out she is really an orphan, and Miss Hannigan never told her, which enables the baddies to pull a con job.
In the movie version of the musical, her parents did intend to return for her, but they were killed in a fire before they could, and, again, Miss Hannigan keeps the information from her — as well as all of her parents' possessions, which should have gone to her.
In Jade Cocoon, Ricketz leaves his family and abandons his position as Cocoon Master of his village, because staying on would cause his wife to eventually die of a magically-induced cancerous disease, as the wives of all Cocoon Masters are women of the Nagi tribe who have a sacred duty to purify the demon-capturing cocoons their husbands inevitably accumulate in their role as magical protectors of their villages. He also tries to discover a cure, in the process becoming the catalyst for the entire plot of the story.
In Growlanser III, one of your party members had a father who disappeared one day; being half human and half Featherian, this lead to some Fantastic Racism among her relatives. (You eventually learn that the Big Bad killed him.)
Subverted in Disgaea 2 Cursed Memories with Adell's parents. They left to defeat fake Overlord Zenon and failed. The subversion is in how they intended to return (assuming they won).
James in Fallout 3 had what he thought was a pretty good reason for abandoning the main character. However, it turns out he made a grave miscalculation: his disappearance sends the Vault into anarchy and gets his son/daughter marked for death by the Overseer. Of course, James makes a fairly impressive series of well-meaning miscalculations as the game goes on...
Final Fantasy X has Jecht, who spends most of the game a distant and apparently horribly abusive father to Tidus, who's reasonably pissed off that his father abandoned him and his mother. Turns out that Jecht was swept to another world and sacrificed himself for the hope of peace. Since Tidus is, at the time, in a similar situation...
In Arc The Lad, Arc's father had a good reason to leave his wife and son for more than ten years He tried to Set Right What Once Went Wrong after the elemental spirits granted him the ability to time travel. But, because Arc The Lad is... well, Arc The Lad, he failed to save the world and only came back to die in front of his son and let him angsting
In Another Code, Ashley's father left her with her aunt to pursue research on memory to find out about his wife's death.
Pretty much all the Earthbound/Mother games where your father is only seen at the other end of the phone providing you with money and gifts the entire adventure.
Final Fantasy Legend II opens with a scene where your father is last seen leaving through your bedroom window. Throughout the game, you wind up bumping into him repeatedly, finding out he's trying to save the universe just like you are. (And you try to convince him to come home more often.)
In Xenogears, Jessie claims to have a justifiable reason for abandoning his wife and children. In the game itself, the trope is subverted, as the explanation is not very thorough and the player is left with the impression that he's making excuses. After reading the explanation given in Perfect Works, though, it becomes clear that he had to leave in order to protect them and the trope is played straight.
And don't forget Palmer, the Tower Tycoon from Pokemon Diamond And Pearl/Platinum. He is the rival's father and while he claims to remember you as his son's friend, he is never once seen outside of Battle Tower.
The reason Kratos abandoned Lloyd was because he saw him, Noishe, and the monster version of his wife fall over a cliff, and after fending off the nearby Desians, found nothing but half-eaten corpses at the bottom. He thought they had died.
Genis and Raine got abandoned because Raine was so intelligent, the Imperial Research Academy wanted to kidnap her and keep her imprisoned with other half-elves to work on science projects for them. Their parents sent them through a magical portal to the "mythical land" of Sylvarant, where they hoped the children would be safe from Fantastic Racism. They had no way of knowing that Sylvarant was poor and mana-starved, and suffered from just as much racism as Tethe'alla...
Mass Effect 2 gives us Thane Krios who left his son Kolyat, Thane didn't want Kolyat to be influenced by his fathers job as an assassin, either by becoming one himself or being connected to him for his enemies to find. Also, he found everyone involved in his wife's murder and killed them. Slowly.
In Quest For Glory IV, the Burgomeister's grandfather disappeared shortly before he was to marry the Burgomeister's grandmother, leaving her alone and pregnant. This resulted in the child and grandchild becoming rather bitter individuals. When playing as a paladin, you end up finding the grandfather's sword in a wraith's barrow, proving that his abandonment was not intentional - Piotyr had been killed before the wedding.
In Baldur's Gate2 Cernd left his wife and unborn son to pursue his calling as a druid. He thinks his commitment to maintaining the balance of nature is a good reason for abandoning his family. Nobody else does. Even the evil wizard who is about to sacrifice the baby to a lich calls him out on it, asking if Cernd even knows the kid's name. To be fair, he didn't know his wife was pregnant at the time.
Really bites Cernd in the ass; in Cernd's epilogue, his constant favoring of his druidic calling over his son leads to his son becoming an evil wizard, leading an army, and eventually forcing a showdown that results in a Mutual Kill.
Airi's father in Devil Survivor 2 had a very good reason - his investigations had ferreted out a highly dangerous Ancient Conspiracy (JP's), and it's implied that had he not faked his death and disappeared, JP's would have killed him.
In the case of Kyle and Julian Brennan in the X-Universe series, it's because Mom took Julian halfway across the galaxy after the divorce and never told Kyle where they went.
In Ever17, Tsugumi had a good reason for abandoning her son and daughter: if she didn't, they'd be captured and researched upon in the hopes of finding a way to immortality, or at the very least would never be able to attend school or have friends due to constantly being on the run. It didn't really work out, but they did get more normal lives out of it. Oddly enough, she's the only one who really has a problem over it. The kids don't care in the slightest.
In the backstory of Fate/stay night, Kiritsugu had very good reasons for abandoning his Ilya. It's also not completely his choice: his father-in-law got really pissed off that he destroyed the Holy Grail in the Fourth War, and forcibly cut off all contact between him and his daughter. All of his efforts to retrieve her failed, and he eventually dies a broken man, his only comfort his adopted son Shirou. It's not completely clear how much Ilya knows about his motivations - the Ilya path which would have focused on her was cut out of the final game, but she's still a lot less naive than she appears - but she angrily spent the ten years after he left plotting revenge. Irritatingly, Kiritsugu was dead by the time of the Fifth War, so she focuses her attentions on the adopted Shirou, whom she hates for getting Kiritsugu in her stead. Shirou, though, being the involuntary Chick Magnet that he is, turns out to actually be pretty likeable once they actually meet properly, which deflects her motivations from "torture him for the remainder of his natural life" to "be rather friendly and spend time with him in the park". This is not good news for Shirou though, as Ilya tends to make people she likes into her "Servants"; which generally involves sticking their souls into inanimate dolls so they can never ever leave her. Ever.
This is only true in Fate, though. In HF, she doesn't make any attempt to put his soul into a doll (once she meets him properly), except as a method for stopping Sakura, and she clearly regrets having to do this.
Except in the last panel of the same comic, she says "Perhaps I did something to displease him... or he wants nothing more to do with me." Both of which are definitely not valid excuses for basically orphaning your only daughter, soon after her mother died in a hospital.
Chapter 31 reveals that Antimony's mother literally gave her "fire" (A.K.A. life force) to her, and wasted away after the birth, ever so slowly, while Annie grew up. Reynardine implies even her soul "vanished". Not only that, but EVERY adult near Annie knew it would happen, if Surma ever had a child. Also, Coyote reveals that Annie isn't 100% human, but part Fire Elemental. Coupled with his wife's death and his inability to save her, it's a bit more understandable why Anthony left.
In the webcomic Bizarre Uprising, Mitsu's father (secretly a vampire) abandons him and his mother when he was young. He did this beause He's the vampire Messiah and if the other vamps found out he was still alive, they'd try and drag him back, almost certainly killing Mistu and Biana in the process. He stayed in Mitsu's life as "The Pig", the school mascot, turned Mitsu's mentor in the ways of vampireness.
In Drowtales, Ariel comes to see her mother Quain'tana as this. She is quite aloof towards her children, leaving them for months or even years at a time at boarding schools or under the care of a slave or older sibling. Quil'yate explains to Ariel that this is not because the drow are evil, but because the clan believes that it is best for young nobles to learn to prove themselves, so that they can be strong leaders. This however should be taken with a grain of salt, since it also turns out that Quain isn't really Ariel's mother, but rather her grandmother; Ariel is the daughter of her 'crazy sister' Mel'arnach, and Zhor, an elf magically turned into a spider; Quain forced the unlikely couple to give up Ariel (including an apparent attempt to kill Zhor while they were at it), thinking the two could not provide a proper environment for a future clan matriarch and wanting to take the credit for herself. Quain is also unable to have children, and it's strongly implied that the desire to have a suitable heir is part of her motivation as well.
In the Paradise setting, in which people get turned into anthropomorphic animals, this is addressed. In the early days, a man gets turned into a polar bear, but doesn't realize it's happened to others (Since he lives out in the frozen boonies of Canada) and tries to live a normal life... until while on a Seal Hunting trip ends up mauling a seal with his bear hands, at which point he becomes terrified of what he'd become and runs out into the frozen tundra to live as the beast he had become, leaving his wife and two sons behind. Years later one of his sons changed into a wolf, realized what happened, and went looking for him.
In The Gamers Alliance, when Omaroch is reunited with his son Refan, he explains to him why he has been absent for so many years and wasn't around to save Refan's mother from death. He had in fact been kidnapped and imprisoned by demons and was thus unable to help his family when they needed him the most. Although he claims that he managed to flee from demons, the truth ends up being much more horrific: he was actually tortured and brainwashed to become a servant of the dark god Mardük and was ordered to return to the world of mortals to make sure his sons would fulfill an ancient prophecy which would result in Mardük's resurrection and a full-scale demon invasion. He eventually breaks free from the god's taint but at that point it's too late because his actions end up causing the Cataclysm as well as turning his son into a bitter person. He does his best trying to set things straight and regain his sons' trust.
Homer's mother Mona on The Simpsons. As it turns out, she was quite surprised when she found out that Homer believed her to be dead. The misunderstanding came up because (1) Grandpa Simpson was unwilling to reveal to young Homer that his mother was a criminal (she rolled her eyes at this reason), and (2) Homer's mistreatment of his mail carrier prevented any of her care packages from reaching him until he specifically asked about them. It's what happens when you don't tip them.
Also, we're led to believe Nelson's father abandoned him. Turns out his peanut allergy caused circus dwellers to kidnap him and use him as an attraction. Thanks to Simpsons' negative continuity, he is never referred to again.
On Futurama, Leela grew up thinking she was a one-eyed alien, when in reality she was an unusually normal-looking human mutant. Realizing she could pass for "normal," her parents left her at an Orphanarium when she was a baby with a note in an alien language, allowing her to live on the surface rather than as a second-class citizen in the sewers. When they reunite years later and this is revealed it's quite the Tear Jerker, as well as the fact that they never truly abandoned her, since the ending montage showed that they cared for and watched over her from the shadows.
Avatar The Last Airbender has a mild version of this; Hakoda hasn't been gone all that long, and explained his reasons to his kids first, but Katara at least still felt abandoned. She even says that she knew and understood Hakoda did what he had to do, but she couldn't help feeling like crap for not having him there when she needed him the most. They make up at the end of the episode, though.
Also, the reason why Princess Ursa is Zuko and Azula's Missing Mom? She killed her father-in-law to protect young Zuko. Or so we think. It is probably what happened, but ones who reveal this information are Azula and Ozai, who are... not the most trustworthy of people.
Supposedly Ursa was meant to come back sometime during the series finale, but the Avatar team didn't want to have to waste a perfectly good plot by squeezing her in. This is probably the biggest unresolved plot thread.
In We Are the Strange, Rain had his Robot servant take his son to be raised in the Forest because The Big Bad had discovered his giant robot plans and had sent minions to kill him and his family. Unfortunately, the robot died on the way so the son had to grow up in total isolation.
In Scooby-Doo! Mystery Incorporated we learn that Fred's father, Mayor Fred Jones Sr., actually stole him from his birth parents, Brad Chiles and Judy Reeves of the original Mystery Incorporated as part of a way to get hold of the rest of the Planespheric Disc pieces. In the second season, when Brad and Judy finally show up, they say that Jones had also threatened bodily harm onto Fred if they ever came back. Though they came back for a different reason...