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Elite Beat Agents gives us one of the biggest Tear Jerker takes on this trope with its "A Christmas Gift" mission. The girl loses her father in an accident and the mission is to help her accept her loss. The usual EBA way of using song and dance is toned down in wackiness to reflect the somberness of the scene and successful completion allows the father's spirit to return and deliver the Christmas present he promised.
In Kingdom Hearts, Sora's mother gets two lines near the beginning of the first installment, Kairi mysteriously appeared and was apparently adopted by the mayor of the Destiny Islands (she is the only one whose close relative we actually see, her grandmother is shown telling her suspiciously plot relevant fables in a flashback), and Riku's parents are briefly mentioned, as the world crumbles around him. This is the only time anyone's parents are mentioned and it makes the proceedings very awkward if one is inclined to stop and think about it. Also, Roxas from the second game gets along amazingly well despite never having had parents. Since Roxas is Sora's Nobody, his parents would seem to be Sora's, who he's never met, due to Sora's parents being worlds away and not mentioned even once in the second game.
This makes the first game sorta headscratchy, as Sora spends the whole game trying to find Riku and Kairi, yet doesn't even mention his family ONCE (though then again, the very beginning of the game has them planning to go off on a raft, so I guess he didn't think much of his family to begin with).
This sort of thing hits Birth by Sleep even harder. None of the PCs mention any relatives - Master Eraqus is the only father figure Terra has, and Ven was adopted by Eraqus, Terra and Aqua after losing his memory. After Xehanort murders Eraqus and tries to do the same to Aqua and Ven, Terra demands "Was my teacher - no, my father not enough for you?!", suggesting he really doesn't have any other parental figures.
Ienzo / Zexion became the ward of Ansem and his other apprentices after losing his parents. What happened to them isn't explained, but it's a rare case of this actually being addressed in a KH game.
Colette: spends the first third of the game under the belief that her loving father and grandmother are merely a foster family and that her true father is an angel — and said angel is something of an uncaring prick towards her. Subverted once we learn that the angel was lying (or as he claims, the characters just misinterpreted him using "daughter" as a priest would) — and her foster family is really her family..
Raine and Genis: Father died, mother abandoned them at a dimensional gate to escape persecution, leaving them to fend for themselves in another world. Mother later went insane with grief over having to do this and, upon meeting her children again twelve years later, fails to even acknowledge them, instead treating a ragdoll as her still-infant daughter and believing she's pregnant with his now preteen son.
Sheena: Abandoned by parents, taken in by ninja. Was used by said ninja as a bargaining chip for a political alliance. She later screwed up a summoning ritual that ended up killing over a quarter of the clan and sending her adoptive father into a permanent vegetative state, causing the survivors to ostracize her.
Presea: Mother died when she was young, father became sick. At the age of twelve, Presea underwent Magitek surgery to do his job, which brainwashed her and caused her to ignore his subsequent death, leaving his decaying body lying in the bed he died in for sixteen years until the party frees her.
Zelos: Mother forced to marry his father to extend the mana bloodline, causing her to hate her child. Father ignored them both and took a half-elven mistress, who decided to make the child of their union the chosen of mana by killing Zelos. During her attempt on Zelos' life she killed his mother in front of his eyes — his mother's last words to him was "I wish you had never been born."
Ironically, the only one who angsts about his problems is Regal, who doesn't have any parent related issues. Granted, he's a full grown man, but he does angst quite a bit over his one and only problem.
Subverted with Emil: Both parents were killed during the Palmacosta Blood Purge. However we later learn that they weren't even his parents, nor is he the real Emil Castagnier.
Marta: Mother killed when the giant tree went berserk and destroyed Palmacosta, Father went Brainwashed and Crazy and started the Vanguard.
From Tales of Phantasia, there are Cress' parents who are murdered by Mars searching for his family pendant. Chester's parents were already dead by the time the game rolls around. Mint's mother dies trapped in a jail where both Cress and Mint were locked. Claus is old enough to get married, so it's very likely they would die of old age (they are simply never mentioned). Suzu's parents where brainwashed to assassinate Cress in Euclid. Arche is the only one to have both living parents, but mom was forced to move to Hidden Elf Village together with all other elves.
In the Baldur's Gate series, your character is raised by a foster father, and never knew who his or her mother was (the series, in fact, gives two conflicting descriptions of who she was; both might be true). As for your blood father, well, better you didn't know: the freaking god of murder.
While we're on the subject, we also have your half-brother Sarevok and your half-sister, Imoen. And there are companions such as Valygar Corthala, who killed his own parentswhen they turned into ghouls. And Viconia deVir, whose mother was killed by her brother for trying to kill her. And Aerie, who was kidnapped from her home by slavers and raised by a gnomish carny. And Anomen Delryn, whose mother is dead and whose father is abusive and drunk. And Nalia de'Arnise, whose mother is long dead and whose father is killed by trolls during the course of the game. And Lord Keldorn Firecam doesn't spend enough time at home with his kids. And Cernd doesn't even know that he has a kid.
Similarly, in Neverwinter Nights 2, the closest thing you have to living relatives are your foster father and his brother. You never learn anything about your real parents.
There's also Gannayev in the expansion pack, Mask of the Betrayer. When asked about his history (Well, after you get him to stop dicking around and spinning one out of whole cloth), he says that he never knew his father and that his mother cast him out in the wilderness. You eventually do get to meet his mother, a Nighthag that's gone utterly insane. After enraging the Coven for refusing to kill her lover, they decided to punish her by tracking him down, killing him, and forcing his charred remains down the mother's throat in front of their son. It's probably a good thing that Gann doesn't really remember that part.
Also Neeshka, who says she doesn't really remember/know her parents and was taken in by Priests.
All of the Final Fantasy games are like this. You could probably count the number of characters in the whole series that actually have a named parent on one hand, and forget finding a character with both a named mother and father.
All heroes in all versions (so far) of Final Fantasy I are amnesiac and, thus do not remember their parents. True, this doesn't necessarily imply that they are dead... but the overall effect is the same, and given the series' track record...
Final Fantasy II: Maria and Leon's birth parents, who are also Firion and Guy's adoptive parents, get slaughtered by Imperial troops right at the start of the game. As for Guy and Firion—Guy was abandoned by his actual parents at birth and raised by wild animals (specifically a beast named Mauza) until Maria and Leon's family took him in. They also took in Firion, who had been orphaned in the city of Salamand. Moreover, Josef and Ricard are fathers, and they both die during the course of the game, leaving Ricard's son without a father and Josef's daughter without either parent.
Final Fantasy III: The four main characters all turn out to have been orphaned by the same event — Cid's airship was torn apart by the cataclysm that froze most of the world in time, and only the four children and Cid himself survived the event, with their birth parents all perishing. They aren't the only ones either, since Prince Alus had already lost his mother some time before the events of the game, and then his father, King Gorn, tries to kill him as he sleeps and eventually has to commit suicide to prevent himself from carrying out the deed. At least Gorn was being controlled by Garuda, making his actions that bit less horrific.
Final Fantasy IV: Parental Abandonment plays a big role in Theodor's transformation into Golbez and Cecil's adoption by the King of Baron. On the same day, Kluya died at the hands of angry humans and his wife Cecilia died giving birth to Cecil. In addition, Rydia's mother is inadvertently killed by Cecil's hands near the start of the game. She later finds a new family of sorts in the Land of Summoned Monsters. Kain's mother is never mentioned, and it's All There in the Manual that his father died when Kain was a child. Edge's parents are turned into monsters by Dr. Lugae, and commit suicide upon realising what they have become. Edward's parents are both killed in the assault on Damcyan and are never seen by the player. Rosa's father is dead, but remarkably, her mother is still alive.
Also inverted, since Anna dies before her father, Tellah, albeit not by very long.
Final Fantasy V: Bartz lost both of his parents to natural causes before the events of the game, while Lenna lost her mother in similar circumstances, and then her father is killed by Exdeath partway into the game. Faris initially has no knowledge of who her birth parents are, having apparently been orphaned in a shipwreck and raised by pirates. It later turns out that she's actually Lenna's older sister, a fact which is confirmed just in time for her to watch their father die. Poor old Krile has it the worst however, as not only did she lose both of her parents prior to the game's events, but her last surviving relative Galuf, her grandfather, dies battling Exdeath in the game's Tear Jerker moment, leaving her completely alone in the world. Well, apart from the other player characters, anyway
Final Fantasy VI: Relm's mother died and her father ran away and became a Ninja mercenary with a pet dog who's Made of Iron, although Relm was raised by her grandfather - Relm's true parentage is never explicitly stated. Gau's mother died in childbirth, causing his father to go insane and abandon him on the Veldt. Terra loses her parents both at the same time—her mother Madeline/Madonna is killed when The Empire raids the Esper world, and her father Maduin, being an Esper, is taken by the Empire's scientists as a laboratory subject who dies over the course of the game. Edgar and Sabin lose their mother in their very early childhood, and their father dies in their teens, strongly implied to have been killed by The Empire. Locke's mother is never mentioned and his father is dead by the start of the game.
Final Fantasy VII: Tifa's mom died when she was 6 years old, leading her to throw herself off a mountain, Cloud's mom and Tifa's dad were killed by Sephiroth, Cloud's dad is never mentioned. Aeris is not only an orphan, but the last of her race. Barrett is raising a little girl, Marlene, the orphaned daughter of a former friend of his. Red XIII's father was turned to stone by monsters. The two optional characters (Yuffie is understandable). Vincent's dad was killed in a materia experiment performed by the woman he loves. Yuffie hates her father (who was a disgraced warrior after Wutai lost a war with Shinra) and left to find a way to restore honor to her village (somehow this involves thievery).
Sephiroth was told that his mother, Jenova, died during childbirth. In truth, he was taken away from his biological mother shortly after he was born. She then tried to commit suicide, but failed, and then sealed herself away in a crystal to atone for her misdeeds. His real father, Hojo, neglected to ever mention that he was his father.
The Turk member Cissnei from Crisis Core was raised by Shinra after being found in an orphanage, her parents' death never explained.
In Dirge of Cerberus Shalua and Shelke Rui's parents are dead years before the Compilation takes place.
Weiss and Nero's mother gets sucked into darkness when she gives birth to Nero.
Denzel from Advent Children had his parents killed when the Sector 7 Plate collapsed.
Zack is an inversion: he abandoned his parents in order to join SOLDIER, without their knowledge. They still have no clue as to what happened to their son (as we assume that Cloud and company never bothered to fill them in).
In Final Fantasy VIII, almost all of the main cast are orphans, which becomes something of a plot point.
Their surrogate mother-figure, Edea, abandoned them when they were still very young because she became possessed by an evil sorceress from the future. Their surrogate father figure, Cid, had all of them trained to be elite mercenaries, and allowed (if not actually arranged) for their memories of Edea to be wiped, in order to later send them to assassinate her.
Although Quistis, Zell, Selphie, and Irvine were all adopted, only Zell still appears to have a loving relationship with his adopted mother; Selphie and Irvine's adopted parents are never mentioned, and Quistis' adoption "didn't work out," causing her to be sent to Garden by the age of ten. Seifer was never adopted at all.
Rinoa's mother died in a car accident when she was a little girl, and she and her father are estranged over political conflicts.
And Squall takes the prize for Parental Abandonment issues: on top of the abovementioned abandonment by his surrogate mother and father, he also got abandoned by his other surrogate mother/big-sister figure at the age of about four, and between one and the other is left with crippling emotional issues that he struggles with throughout the game. On top of that, he eventually learns that his mother died in childbirth and his father is the president of a prosperous nation and had no idea he ever had a son.
Even when they do meet, Squall's father only awkwardly hints that they have some things to talk about, and Squall doesn't indicate openly whether he's aware of the connection or not.
Final Fantasy IX: Zidane not only has no parents, but is phenotypically unique on Gaia (and in that game's verse, that's really saying something) and doesn't know anything about his origins. Garnet's an orphan who's been raised by Queen Brahne, who also dies part-way into the game. Vivi also is unique and unaware of his origins. Eiko is an orphan who lives alone in the ruins of her hometown... I think what we can take away from this is that Final Fantasy loves this trope.
Tidus' father went missing when he didn't return from swimming practice in the sea, and his mother died when he was eight and it left him to Auron to be taken care of.
Yuna's father is a legendary hero because he sacrificed himself to defeat Sin ten years ago. Her mother's own demise was the inspiration for her father's act of heroism.
Wakka's parents were killed by fiends when he was a child and so were Lulu's.
Rikku's mother was killed when malfuctioning machina went on a rampage.
Seymour gradually turned bad because when he was a child, his mother died to become an Aeon. And then he later killed his own father.
And Final Fantasy XII. Vaan and Penelo are both orphans (Vaan's parents died in a plague, Penelo's parents and Vaan's Promotion to Parent brother died in war with Archadia). Ashe's parents (and presumably the rest of the royal family) were wiped out two years ago. And Balthier keeps dropping vague references to unresolved issues with his own dad which are perfectly understandable, since his old man Cid is now a mad scientist who'll stop at nothing to unlock the secrets of immortality and ultimate power. Interestingly, while it's All There in the Manual that Basch believes his mother to be dead (his father is never mentioned), there's no confirmation one way or the other.
In Final Fantasy XIII Lightning's and Serah's parents died some years ago, causing Lightning to deny her emotions to care for her younger sister.
Snow is an orphan, everyone in NORA is..
Sazh is a single father and cares for his son Dajh alone.
Hope's mother Nora (who is tough) dies in a failed attempt to help the purge victims escape from PSICOM. He's also very distant from his father and only visits him to tell him what happened after heavy convincing by the other party members. However, his father is devestated by the news of Nora's death and there are several pictures of her in his home, so it's unclear if they actually lived seperated.
The final boss Orphan should be one because of his name.
That's actually a fair point to make, considering Orphan's genocidal plot is only formed because the fal'Cie wish to call back the Maker, the creator deity which allegedly abandoned the world and all his creations millions of years ago.
Final Fantasy Tactics Advance goes back and forth with the trope. Marche's parents are never seen, but are mentioned to always being busy taking care of his sick brother, Doned. Ritz's father is never mentioned and her mother only gets a single mention over how sad she looked every time she dyed Ritz's hair. Mewt is a special case regarding his parents; his mother passed away when he was young, causing his father, Cid, to be "crying in the gutters" (or an alocholic in the Japanese version). Most of the plot revolves around Mewt using the powers of a magical book to make his own life better again by making his father a powerful judge master and reviving his mother back to life to become queen of Ivalice. Turns out that Mewt's mother isn't real and is a powerful magical being who is preying on Mewt's emotions.
Final Fantasy Tactics A2 doesn't use dead parents as the main plot point, but it's still there. Luso's parents aren't mentioned at all except for one scene where it's revealed that both of his parents died while he was young, leaving him in the care of his aunt. Adelle's parents also died while she was young because her entire village came down with a plague and she was the sole survivor.
In La Pucelle Tactics, Prier's and Cullotte's parents were killed in a wagon accident years before the game begins. Homard became a Sky Pirate to defeat the demon who injured his father and attacked his kingdom, Marl Kingdom, making him the grandson of Cornet from Rhapsody
In Disgaea: Hour of Darkness, Flonne's parents are never mentioned. Etna is an orphan, and the closest thing she had to a father figure, the Overlord and Laharl's dad, died two years ago. Laharl's mother died before the game began when she sacrificed herself to cure him of an incurable disease and his father, the Overlord, died choking on a black pretzel which is just a rumor and actually died after sealing away Baal. Both his parents, however, do return to watch over him...though his mother is a Prinny and his father is The DandyGoldfish Poop Gang. Jennifer was orphaned, and her adopted father is The Dragon.
In Phantom Brave, both of Marona's parents die in the opening cutscene. Ash's parents are never mentioned. Walnut was adopted and then later left his adoptive parents so that he wouldn't burden them and his sister, Castille.
In Makai Kingdom, we see Alex's family during the credits, but they're never mentioned nor do they appear in the game. Pram took her Netherworld from her father at the age of two (Making this a case of the child abandoning the parent) and depending on how you interpret King Drake's accusation of her taking his Netherworld, he may be her father. Other than that, none of the Overlords have visible parents.
In Disgaea 2 , Adell reveals to Rozalin early on that he was adopted, and likely abandoned by his blood-parents. It turns out that Adell's parents are the masked man and woman serving under Overlord Zenon against their will. Triggers a rather tragic case of Self-Made Orphan. Rozalin shamefully admits that she never met her father in person and really the "father" was an old foe with a grudge who got off on the idea of the God of all Overlords being subservient to him, who was actually Rozalin in her past life. It's also implied that he killed her mother in his attack on the Snow Tribe that also claimed the lives of Yukimaru and Fubuki's parents. Tink's parents are never mentioned at all, but presumably aren't there as he seems to live with Rozalin instead.
In the manga version of Disgaea 2, we are treated to a flashback of Rozalin's mother... and her fate alongside the rest of the clan. Rozalin's mother is actually seen in the official art book. Also in the manga Adell's parents sacrifice their lives so that he can reach Zenon before he escapes with Rozalin. Finally, Zenon is killed by Rozalin, but despite being a fake, Rozalin still sees him as her father.
According to the Updated Re-release's Axel Mode, it's very common for a demons to abandon their children. Axel himself and the rest of his siblings are all revealed to be orphans and their mother actually adopted them.
Danette's parents in Soul Nomad & the World Eaters were killed by Thurists. Gig has no parents, being a god, and Revya has no parents. In his/her past life, his/her mother died 200 years and his/her father, Lord Median, is currently a zombie.Tricia, Levin, and Euphoria were also orphaned at a young age. Trish was eventually adopted for the purpose of being raped at the age of 17 (Whether or not this happens depends on which path you chose) and Levin and Euphoria were being used by the World Eater Raksha so that he could put his Evil Plan into action as his body couldn't move.
In Disgaea 3, Mao's mother is never mentioned, and lives under the custody of his butler rather than his father because, as we find out later, said father is actually dead. Mao repressed the memory out of guilt over indirectly causing his death.. Sapphire's parents died when she was little, and she's rather infamous in the human world for not mourning either of their deaths. Almaz's parents aren't mentioned but, considering that he went on an almost suicidal mission to defeat the Netherworld's Overlord for the sake of a crush, we can probably assume they weren't around to stop him. Raspberyl's parents are brought up during a flashback with Mao, but they are never seen.
In Sapphire's case, I think it's only her mother who is dead.
In Disgaea 4, Fuka's mother died long ago and her father is always at work, though it turns out that her father was creating a little sister for her.
It's easier to list which Nintendo characters actually have parents or explain the lack of them.
Samus Aran had parents that were murdered by Space Pirates when she was very young, and she was adopted by the Chozo. And it's strongly implied that the Chozo are now all extinct. This would make Samus an orphan twice over!
Star Fox: Fox's father is mentioned in the intro, assumed to be killed by Andross. His mother is only mentioned in the comics, though. Other than that, direct relatives are scare in the Star Fox setting, though. Slippy has a father that isn't canonically mentioned until Assault, Peppy eventually becomes a father (the wife is only mentioned in one ending in Command), but that's about it.
In Fire Emblem Tellius, aside from Ike, Mist, and Soren being parentless (well, Soren had both parents alive for some time, but unknowingly participated in the killing of his actual father, who had disowned him at birth)...
Elincia had both her parents killed in the events starting Path of Radiance.
Boyd, Rolf, and Oscar's story is a little complex. Boyd and Oscar had the same parents, but their mother died. Their father remarried and produced Rolf by the new wife, but then the father died, and wife number two fled. In one of this series' many instances of Guide Dang It, you have to have one of the three brothers visit one specific house in Chapter III-1 to learn this.
Micaiah's parentage is unknown through most of Radiant Dawn, though she's understood to be an orphan of sorts. Her true heritage, making her the true Apostle of Begnion, means she was forced to flee her family when the assassination was carried out against her grandmother, though presumably either her mother or father or both remained alive long enough to conceive Sanaki, her sister, and it was never explained why the Apostleship skipped a generation like that.
There's actually implications that she was not aware of her heritage as Apostle of Begnion. Micaiah is not the kind of person who would order the death of her own sister, even under threat of the Blood Pact. Due to Miacaih's age being unkown, there is a window of error for the events and how they unfold. There is actually more reason to theorize that she lost her memory, as that would explain her ignorance of her heritage as well as help accomodate Micaiah's aging.
Sothe, Laura, Aran, and Edward are explicitly stated to be orphans.
The Heron Royals' mother is stated to have died in the Serenes Massacre, and their father was severely debilitated to the point where even Reyson, the one royal who remained with their father after the incident, was raised by Tibarn and/or Naesala.
Jill is an inversion. She abandoned her father, a Daein General, to fight for the other side when she figured out that what he was doing was wrong. Doubly inverted in that Shiharam knew what he was doing was wrong, but had to fight for the good of the people of the Daein fiefdom that he ruled. Indeed, if Jill is made to fight her father, she'll turn into an Enemy unit.
Fire Emblem Awakening Chrom and Lissa's father was a warmongering tyrant, which they're still cleaning up after when the events of the game roll around. The Avatar as well as the most of the second generation suffer from this as well. In the case of the children, their parents died in the war against Grima. This is brought up by most of the children during their support conversations with their parents. The Avatar's parents are revealed to be Validar and an unnamed woman who tried to save him/her from their father.
The Legend of Zelda: Many fans have expressed curiosity as to where Link's parents are during any of his adventures. This is perhaps most glaring in the original game in the series; since Zelda II The Adventure Of Link is stated to be taking place a couple years after the original game, and the game's manual clearly remarks that Link is now sixteen years old, one has to wonder how young he was the first time around.
Considering how in Wind Waker Link's grandmother reacted to his quest to save Aryll (becoming ill with grief and anxiety), it's not too hard to imagine why he's an orphan in a lot of these games. It avoids the Fridge Horror element of asking what kind of parent would allow their young son to go off and experience all of that.
The original Grandia has a few. Justin lives with his mother (his father, who gave Justin his McGuffin, is mentioned as having passed away), Sue is an orphan who lives with her aunt and uncle, the parents of Feena and her sister Leen are never mentioned, and Rapp's parents were petrified when the original Cafu village turned to stone. The rest of the cast is of adult age (and a few several times older than that, the oldest being a few centuries old), though it's also worth mentioning that Colonel Mullen's mother, a humanoid that General Baal married in order to learn ancient secrets about the ancient world, is also dead.
Devil May Cry. Dante and Vergil's father, the uber-Devil Sparda who awoke to justice, has been missing since their early childhood and both are bitter about it. It's never explicitly stated what happened, but it is suggested that he was either killed or captured by the demons. Their mother Eva was killed some time later in a demonic attack on their house. Lady's mother was killed by her father as part of a sacrifice, and later pays him back in turn.
Nero was not only abandoned in Fortuna at an early age by his biological parents (who are dead now, kthx), his adoptive parents end up dying from a demonic attack in his early childhood. No protagonist is safe from this trope.
Even better, Capcom has revealed that his father is Vergil, who we all know what happened to. Considering the 3rd game's events, Nero was no doubt abandoned by his father.
From the makers of Ace Attorney we then get Ghost Trick which goes all out in taking away poor Camila's parents in the cruelest ways imaginable. However, thanks to the timeline-altering efforts of the two most loyal pets ever, she ends up living happily ever after with both of them alive. Fans of Ace Attorney collectively cried tears of joy upon witnessing this unexpected outcome.
Halo's SPARTAN-II's are taken away from their parents at a young age to be raised by the military. The military made sure that the subject's parents won't search for them by creating a flash clone. While flash cloning works perfectly for stuff like replacement organs, cloning a human is problematic since the accelerated growth results in the clone succumbing to metabolic cascade faliure after a few months.
The Redfields' parents died in an accident when Claire was fourteen and Chris was twenty (source: a bonus material book that was supplied with Resident Evil 2 when it first was released)
Leon's parents were both victims of criminal activity (Leon's father was a criminal himself, actually). He was raised for most of his adolescence by one of his uncles, and he was the one who inspired Leon to become a police officer. (Source: Word of God)
It's implied that Jill Valentine's mother is dead and something is up with her dad, who's missing at least. In S.D Perry's novel adaptations, her father was a con artist.
Jake Muller is the illegitimate son of an Eastern European woman who died of illness when he was in his early teens, and the series' now former Big Bad, Albert Wesker. Wesker had a one-off affair with the woman, and she left for her home country not long after she got pregnant.
Sherry Birkin's parents die on-screen in Resident Evil 2; her mother Annette falls into a pit underground, while her father William turns into a murderous multi-eyed blob monster courtesy of the G-Virus that Leon and Claire are forced to put down.
The Ashford twins impose this upon themselves by torturing their father Alexander and turning him into the monster Nosferatu, which Claire kills during the game.
Barry Burton is the only protagonist who has a family -a wife and two daughters. While all of them are alive and well, it is possible for him to be killed off during the first game and its remake, putting this in effect for his daughters.
In Persona 3, every member of SEES has parents who are either distant or dead. That makes it a lot easier to go live in a dorm full of teenagers and a creepy old guy, and a lot easier to go out at midnight on a near daily basis.
Jade's parents in Beyond Good & Evil disappeared mysteriously when she was an infant; she was raised by her father's best friend. A Final Speech by an Almost Dead Guy near the end of the game implies that they were killed trying to protect her... And the Big Bad himself implies that she never had any, due to her nature as a MacGuffin Girl.
The Normandy from Mass Effect is often nicknamed the "SSV Daddy Issues." There is a very good reason for this.
Two of the three possible origins of Commander Shepard involve parental abandonment: in one (Colonist), both of Shepard's parents were killed when slavers raided the colony they lived in, and in the other (Earthborn), Shepard grew up on the streets of Earth and never knew his or her parents at all. Averted with the Spacer origin — both of Shepard's parents are alive and well, and a sidequest in the first game even involves having to call up your mom.
Liara never knew her "father" and her mother was brainwashed into joining the Big Bad of Mass Effect 1. The "Lair of the Shadow Broker" DLC for the second game reveals Liara's dad's identity (Matriarch Aethyta, the bartender at Eternity on Illium). In the third game, you can encourage Liara to talk to her.
Wrex never mentions his mother, but does explain that his father betrayed and tried to murder him, causing Wrex to kill him.
Ashley's father is also dead, but it's never said how. That her mother is still alive and she actually had a decent relationship with her dad means she's still one of the luckier ones on this list.
Tali's mom died several years before the beginning of the story, and her father (an Admiral of the Migrant Fleet), while not having abandoned Tali, was emotionally distant for most of her life. Then, in the second game, Shepard and Tali find her father's corpse on the science ship he was working on, killed by the geth he was brutally experimenting on in order to "give his daughter the homeworld."
Garrus's mother is never mentioned in the game, but his father is. The "Lair of the Shadow Broker" dossier reveals that she's dying of an incurable disease, which, coupled with Garrus's numerous failings, puts him at odds with his sister. In the third game, Garrus only mentions his father and sister when talking about his family, implying that his mother died in the year between the second and third games. Averted in the third game, mainly due to the fact that Garrus decided to talk with his father about preperations for the Reapers, and he listens.
Miranda never had a mother—she was created using her father's DNA, his Y chromosone altered with traits from a number of women. However, she wasn't created so he could love someone, rather, to preserve his legacy. She left her father at the age of 16 and hasn't spoken to him since. In the third game, she kills him.
Jacob's father was the Executive Officer of an freighter which disappeared in 2176, almost nine years before the events of the second game. During the course of Jacob's loyalty mission, Shepard and Jacob discover that the freighter crashed on an uncharted planet with plant life that causes neural degradation in humans. As the crew succumbed to the effects of the toxic food, Jacob's dad set himself up as the cult-like leader of the crash's survivors, killing off anybody who questioned his rule and making a harem out of the female survivors. Of the three options the player has of dealing with him, two lead to his death.
Jack never knew her parents, having been raised in a laboratory and experimented upon to create the ultimate biotic. Her "Lair of the Shadow Broker" dossier reveals that when Jack (then named Jennifer) was a baby, her mother sent her in for a routine checkup. The doctor, noting that the infant had great biotic potential, convinced the woman that her daughter had died from a seizure and sent Jack off to Pragia to be studied.
Grunt's "father," Warlord Okeer, created him to be the "perfect" krogan using DNA from himself and several prominent krogan. Okeer is killed before Grunt ever leaves his growth pod. Even then, he cared nothing for Okeer, as Okeer was considered a joke by other krogan.
Thane, on the other hand, is an inversion of this trope. He abandoned his son, Kolyat, after his wife was killed by slavers that were trying to get to him. Shepard can reunite father and son during the course of the game.
The fact that both of Kaidan's parents are alive and well, and he dealt with his father issues long before the events of the game, makes him a distinct anomaly in the squad. As if to correct this, his dad goes MIA during the third game and is presumed dead.
Captain Bailey gives the opinion that many of the Citadel's social problems relate to this trope. When you ask him to help a man take responsibility for his son's welfare, he jumps at the opportunity. He implies that a lot of it is guilt over not being there for his own son.
James Vega lost his mother as a teenager, after which his father fell into drugs. Their relationship died when James's father tried to blackmail James into being a drug courier.
Averted with Mordin. While he doesn't have any children to speak of, he does keep in contact with his nephew, even stating that he is inspiration to survive the upcoming suicide mission.
Aethyta faced what may be one of the funniest examples ever. Her father was a veteran of the Rachni Wars, while both of her parents fought on opposite sides of the Krogan Rebellions. Aethyta's mother figured things out pretty quickly, but stayed quiet while Aethyta's father boasted. He was pushing a thousand and she was a matriarch when he finally found out. They called up Aethyta - who was about a hundred years old and working as a stripper - to tell her that they were going to have it out and she should keep loving whichever one survived. In Aethyta's words: "Turned out to be damned easy, since neither one did. Family, huh? What a kick in the quad."
Dragon Age: Origins - Most of the possible Wardens have bad stuff happen to their families - in fact, the only origin where they're both present puts them through Death by Origin Story almost immediately. Zevran is the son of a brothel worker who suffered Death by Childbirth. Alistair couldn't be acknowledged by his parents due to him being a Royal Bastard, and his substitute father figure sent him to a monastery after marrying. Leliana's mother had her out of wedlock and died young. Morrigan never knew her father and her mother is...a whole other kettle of fish. Circle Mages get this both ways - not only are they allowed little to no contact with their families, but any children they have in the Circle are taken from them almost at once. In Wynne's case, she never knew her real parents at all - her earliest memory is of hiding in a hayloft to keep warm. The farmer's family took her in until her powers manifested. The Qunari simply practice No Blood Ties.
Dragon Age II - Hawke's apostate father is already dead when the game starts. Their mother, Leandra, is murdered late in the game's second act. Anders, being a Circle Mage, hasn't seen his parents since he was taken from them as a child. Isabela never knew her father, and her mother sold her into a loveless marriage. Both of Aveline's parents are dead. Merill left the clan she was born in to train as another clan's Keeper, and hasn't seen her parents in years. Sebastian is introduced seeking revenge for the murder of his entire family. Get the idea?
In the Sonic the Hedgehog games, it's easier to list who is over 18 or has parents or guardians. You'd think the social workers would come poking around to see why there is an 8 year old is doing living on his own in the middle of a factory, with a 15 year old best friend that's constantly running away and cart him off to a care home, but apparently not.
Blaze the Cat is a 14 year old princess who guards the Sol Emeralds, her world's equivalent to the Chaos Emerald. In Sonic Rush, she tells Sonic that she had always been alone, but in the sequel, Sonic Rush Adventure, it's stated that she has a living family, although they are unseen.
Otacon's mother died while he was still young, his father committed suicide (for which Otacon blames himself) and his stepmother seduced him into having sex with her. Throw in his notorious bad luck with women and we have the god of woobiedom on our hands.
And where to begin with Solid Snake...
Compared to Otacon Snake got off easy His father disowned him but his mother loved him and probably only gave him up because of Zero. His mother even told him everything right before he inadvertantly killed her. His father even came around and saved his son's life knowing that it woud cost him his.Snake's real problem is his brothers.
Averted in Skies of Arcadia: Not only are both of Vyse's parents alive, he's on good terms with them, and they encourage him to go out adventuring.
Played straight with his friend Aika however, who lost both her parents before the game began. However, save one cutscene, she never really angsts over it.
Star Force also takes it one step further with Sonia Strumm, as her mom died 3 months before the main story and Pat Sprigs, who like Roll Caskett, Vent and Aile has both parents missing.
In most Pokémon games, the player character usually has a mom and a mom only; whatever happened to dear old Dad is never explained. Averted quite noticeably in Pokémon Ruby and Sapphire/Emerald, though — not only is Dad still around, but he's a Gym Leader, and yes, you do have to wail on Pappy for a badge. He does not go easy on his own son/daughter. Not. In. The. Least.
The original games also have your rival, Blue — who is supposed to be Professor Oak's grandson, but appears to live with his sister. Where did the Professor's son/daughter go?
The player character's father is mentioned in Platinum, but only so that Mum can say that you're just like him. What happened to him is, as ever, not explained.
I believe the mom also makes a comment like that in either Red/Blue/Yellow or Gold/Silver Crystal.
Your rival's father also appears as the Battle Tower Tycoon. He also brings up that fact that he and the player's father started their adventure in a similar manner to the player and their rival.
A special event in the recent remakes of Gold and Silver actually shows you the very moment Silver's father, Giovanni, abandoned him.
Professor Birch of Ruby/Sapphire/Emerald is the father of one of your rivals (the player character you didn't choose, not Wally).
That's right, and your rival also has a mother. Wally also has both parents who love and support him, and an aunt, uncle and cousin who love and support him. Lucky guy.
The obscure platformer Scaler has the main character, a human boy transformed into a lizard, who has decided to go by Scaler. He lives with his mom; his dad, a scientist, disappeared in the backstory; it's implied that he was sucked into the "reptile world" that Scaler now finds himself in. Naturally, he finds his father. It's Leon, his Older Sidekick.
Lampshaded in EarthBound. Ness's parents are alive and present throughout the adventure, apparently pleased that their son is engaging in a potentially lethal quest to save the world. However, his father is never seen for the entirety of the game, only talking to Ness through phone conversations to save the game.
It's the same situation for Ninten in Earthbound Zero game. Although there was a (ultimately abandoned) Sequel Hook that seemed to imply his father would be more involved.
Mother 3. Don't get us started on Mother 3. In the same night Lucas loses both his mother and his twin. He still has his father, but Flint's reserved, and everyday is out either at his wife's grave or still searching for his son.
Dustil Onasi in Knights of the Old Republic thinks his father Carth abandoned him. Carth at least had something of an excuse, since he believed his son had been killed during the Sith bombardment of Telos.
Overlord II: Not only is the Overlad's father stuck in The Abyss, his mother Rose soon after giving birth to him leaves him in a village where he's hated for being a Creepy Child who shoots lightning out of his hands to assist The Empire in what she thought would be the restoration of order to the lands by assisting Florian's conquest of the lands.
Ace Combat 04: Shattered Skies, where the narrator's parents die after a downed plane crashes into the cape where the family home is. In Joint Assault Sulejmani'sFreudian Excuse is that he was sold off by his parents to be a Child Soldier.
Subverted in Lunar: The Silver Star, one of the rare RPGs to do so. The main character, Alex, not only has both parents intact, they manage to survive to the end, despite being abducted halfway through the game.
The sequel, Lunar: Eternal Blue plays this trope straight, however. Hiro is raised by his grandfather, with no mention of any parents.
In the Jak and Daxter series, there are only five fathers and mothers are only mentioned in passing.
In Secret of Mana the Boy was left to be raised by the Potos Village elder and never knew his parents. Near the end of the game he finds out that his dad is a sword and his mom is a tree.
In the original Tomb Raider series, Lara Croft's aristocrat parents disowned her after she chose to take up a life of adventuring.
In the Crystal Dynamicsreboot, Richard Croft disappeared in Cambodia (later revealed to have been killed by Natla), while Amelia Croft got pulled into the Underworld and turned into a zombie.
In Dungeon Fighter Online, both the Fighter and the Slayer have lost their parents. The Fighter lost her parents to monsters, but the manner in which the Slayer lost his parents was muchmoresinister.
The surprisingly dark twist of the otherwise child-friendly Scenario A in obscure DS RPG Deep Labyrinth is that the main character - a young boy - must come to terms with the fact that his parents' marriage is failing and they both harbor feelings of resentment towards each other and him.
Touhou proudly features hundreds of characters, most of which live in what are functionally adoptive families of Ragtag Band of Misfits. You can count on one hand how many characters even have parents ever mentioned to have existed in the entire course of the series. Since many characters are youkai, such as a wild animal or inanimate object such as an umbrella given sentience through age and magic power, many of these characters perfectly understandably never remember their parents. Still, the only family ties any characters who appear ever have are direct blood siblings.
Marisa Kirisame explicitly has an estranged father. Her mother is implied to exist.
Youmu Konpaku was apparently abandoned when Youki Konpaku went on a "journey for enlightenment" completely out of the blue, and dumped all his duties on his young student (actual relationship between the two is unknown). While she was left under the care of an adult, Yuyuko is not an ideal parental figure.
Sakuya's backstory is a canon area of doubt and uncertainty, but it's extremely unlikely that her parents are anywhere near her, as she's a lone human working for a group of youkai. Not even likely to have any parental figures, as she's the most mature person in the mansion.
Despite coming from the Outside World, AKA modern Japan, Wind Priestess Sanae Kochiya's parents are utterly unmentioned and unaccounted for, with her goddesses (one of them being her distant ancestor) often acting as substitute parents for her in Fanon.
Reimu's parents are never mentioned. It's generally assumed that they died somehow, as we should really has seen them by know, given her main character status.
Rune Factory 3 nearly takes this Up to Eleven. No one has two parents, and most of the cast has none whatsoever, and there is absolutely no explanation. The missing relatives are as follows: Raven, Gaius, Pia, Kuruna, Oromis, Zaid, Daria, Shara, Monica, and Marion have no parents. Sakuya and Karina have no father. Sofia, Evelyn, Colette, and Rusk have no mother. To the best of my knowledge, the only character who actually acknowledges the fact that she has no living family is Raven. The hero's father gets one line of dialogue in a flashback, and the hero calls for his mother in the same flashback, but otherwise they never appear.
Blaise (Colette and Rusk's father) does occasionally mention his "dear wife's cooking", so she may have existed at some point.
The Hero IV has a loving adopted family until his/her parents are killed off at the beginning of his/her chapter.
Maya and Meena's father is killed. No mother is mentioned.
The Hero V doesn't know his mother. His father takes him on a quest to find her. Then Pankraz is killed, telling The Hero to search for her mother before she dies, thus the major objective of the game after the Time Skip.
Bianca's mother dies from illness between the Time Skip. In the original game her father will also pass away if chosen over Nera. This thankfully dosen't happen in the remakes.
Parry and Madchen have this issue because their parents, The Hero and his wife, are cursed into stones for years.
The Hero VI has only his sister. Except not really, it turns out that both your parents are quite alive and after you find them, are quite helpful and play a role in the plot. Making this the biggest aversion of this trope in the whole series.
The Hero VIII doesn't seem to have any parents. His relatives are dragons.
In the Spore cutscence for when for when your creature family migrates to a new nest, one of the adults will stay behind to watch over the eggs. Your creature then hatches and you have to find the new nest.
Eroge Snow Sakura, Yuuji Tachibana has jerkass parents who force him to move from Tokyo to Hokkaido to live with an uncle and a tsundere female cousin while they have a nice, long holiday in Hawaii.
Depending on the version, either Yonah and Nier have lost both their parents (Replicant), or Yonah has lost her mother and her father Nier spends a very good deal of time searching for a cure for her condition (Gestalt).
Jakob and Gideon loose their mother, the Masked King lost his father, and both Fyra and Kainé were abandoned by their parents.
Advanced Variable Geo: Satomi's parents died in a car accident. The whereabouts of most other characters' are never elaborated upon, although in Erina's case, her desperate longing to bring her grandmother to Japan might be a good indicator that her parents are gone as well.
Riki, the protagonist of Little Busters!, has been an orphan since he was only a child. This is relevant to the plot in three ways: firstly, he became such great friends with the Little Busters in the first place when Kyousuke was able to drag him out of his depression, secondly, because the only family he's shown to have is a guardian he clearly doesn't hold any real fondness for meaning he's even more dependent on Kyousuke and the other Little Busters than he otherwise would be, and thirdly, because Refrain shows that it was witnessing his parents' death that made Riki closed off from and scared of the world, unable to go out there himself on his own.
In a contrast from the partners of the previous games, your partner in Pokémon Mystery Dungeon: Gates to Infinity actually brings up their past and mentions that they've been alone from the moment they were born. It's their concern that the hero might not be the same (When asked about this, they simply respond with Visible Silence) that helps them accept that they have to return to their world in the ending, and also initially makes them reluctant to try bringing them back in the post-credits segment.
In both the NES and Wii versions of A Boy and His Blob, the boy's parents are never seen, even when he's at home. This is specially disturbing in the Wii version, since the extra material states that the boy is supposed to be around six years old.
The Firstborn from Clive Barker's Jericho. Oh, and the parent just happens to be God. Who booted the Firstborn out of reality itself. The Firstborn is understandably pissed at humanity for being favored over him.
Emeralda is an Artificial Human created from a nanobot colony, and her "parents" were killed just before she was supposed to be "born," leaving her in suspended animation for 4000 years. However, her parents have reincarnated as Fei and Elly, so she actually becomes one of the few video game characters with an intact family at the end of the game.
Shion and Jin's parents died when Shion was a little girl. What happened to them is a major plot point.
Junior never knew his mother and his father is a Mad Scientist villain whom Junior ran away from after a certain incident.
MOMO is an Artificial Human, but the man she thinks of as her "father" is dead, and the woman she thinks of as her "mother" does everything she can to avoid seeing MOMO.
KOS-MOS may or may not be an aversion, depending on who you think of as her parents. Shion is clearly the closest thing she has to a mother. If you think of her "father" as Kevin, the scientist who originally designed her and built her Black Box components, then she counts. If you think of her "father" as Allen, who was the main male scientist working on the current version and who helped build her replacement Black Box components after the first ones were damaged, then she actually has both "parents" still alive and with her.
Only ONE of the main characters (Melia) has a parent that actually appears in game. Her father is Sorean Antiqua, King of the High Entia. Her mother is not seen and is only mentioned in passing, but this is likely justified as she was the second (Homs) consort and likely died long before the beginning of the game.
Shulk's parents are mentioned; they, along with many other members of their expedition were killed when the Monado absorbed their life forces to awaken Zanza's soul.
Dunban is Fiora's older brother and acts much like a father to her (Riki even lampshades this) but their parents are only ever mentioned in passing.
Sharla, Reyn, and Riki's are not mentioned at all, though Riki may be justified since his back story revolves around HIS OWN wife and children.