Refia: I am thankful to Father for taking care of an orphan like me for all these years, but...this is something I have to do. Luneth: Wait...you're an orphan, too? Refia: "Too"? You mean— Arc: I'm one, too! Ingus: Wait a minute... I, too, have no parents...
All people come with a past, a family, friends, a heritage, and more. Every person has roots!
This past can become a large burden on the character: They need an excuse to leave their family behind, or need to constantly visit their parents and other family members in between adventures. Otherwise the hero can't believably be a social, likable good guy.
Orphaned heroes on the other hand, never have to deal with all that. They don't need an excuse to go on wild adventures or stay away for days on end, they don't have anyone waiting around for them to come home!
Conveniently, these heroes can answer the Call to Adventure because they don't have other responsibilities. This lack of older responsibilities is also exactly what allows the heroes to take on the new responsibilities that come from being hero.
Often used as character backgrounds in tabletop adventures: Such a character's background often consists of "My parents were killed by (insert Always Chaotic Evil race here), so he's out for revenge". Aside from conveniently leaving no 'annoying' ties to the past to keep the character away from the Call to Adventure, it can also result in a You Killed My Father moment should the villain race (or the Big Bad if he's responsible) appear.
Handily prevents the sadistic Game Master from exploiting 'weak links' that can get kidnapped or killed off. If the fates of the missing parents are left nebulous, it also opens the door for that infamous twist where one of them turns out to be a villain. You know the one.
Oddly enough, family outside of parents is never mentioned. Apparently no one ever has grandparents or cousins, although having an uncle (and sometimes aunt) as surrogate parents is common. Siblings (if they exist at all) seem to only show up for plot-based reasons — and not Promotion to Parent, which would give them responsibilities. One wonders how the world manages to get populated when every couple only has one child. Surrogate parents show up more regularly in the form of Raised by Natives, they tend todie a lot too.
The hero's orphaning is also a nice triggering point for the hero's journey. This part of the Hero's backstory is often covered in a Flash Back. If the orphaning happens at the very beginning of the story, instead of in the background, it's usually covered by Doomed Hometown.
If the character does have parents, but they have so little influence on his life that he behaves as if he has no family responsibilities anyway, or it just isn't talked about period, it's Parental Abandonment.
May lead to Tell Me About My Father.
Contrast with Orphan's Ordeal, where the loss of parents is the plot (or at least a subplot), rather than simply enabling the plot.
If the parents happened to be Good Parents before their death, so much so that they continue to affect the main character even after they're dead, then you've got Deceased Parents Are the Best.
Not to be confused with Self-Made Orphan.
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Anime and Manga
Combattler V: Hyoma Aoi, the captain of Combattler team, lived in an orphanage after his parents' deaths. Seeing someone killing the parents of a child -or even an animal cub- is one of his Berserk Buttons. His Love Interest, Chizuru Nanbara not only was an orphan girl but also her only grandfather died shortly after the beginning of the series.
Cutey Honey: Honey Kisaragi lost her father early on the series. His death triggered her war against the terrorist group named Panther Claw.
Daimos: Kazuya lost her parents before the start of the series. Erika's father died shortly before Kazuya's father, and THAT is what starts off the history.
Mazinger Z: Kouji and Shiro's parents died in a lab experiment gone wrong or so they were told. In reality, only their mother died. Their father would die for real at the end of Great Mazinger, though. Sayaka also lost her mother before the beginning of the series.
Great Mazinger: Both Tetsuya and Jun are orphan kids, taken in by Prof. Kabuto. And the end of the series his adoptive father would also die.
UFO Robo Grendizer: All relatives from Duke and Maria got brutally murdered before the start of the series.
Black Butler: the loss of his parents trigger Ciel Phantomhive's motives and lead to the plot.
Rosette and Joshua's parents died in a ship wreck when they were young children, and after that they spent most of their life in an orphanage—until Joshua is taken by Aion (and the orphanage is destroyed in the process), which causes Rosette to join the Order to try to find her brother again.
Azmaria's parents either abandoned her because of her powers, or were killed during the war, depending on which version you're following.
Satella's parents were killed by a demon when she was a child. Her sister was also kidnapped by the demon—leading her on a journey similar to Rosette's. However, since her parents' deaths are such a turning point for Satella in her backstory, she leans closer to Orphan's Ordeal instead.
In Slayers, Zelgadis and Gourry both have no parents (Zelgadis' great-grandfather Rezo killed his, and Gourry's were killed during a family feud), and Sylphiel, Filia, Pokota, Amelia, and Naga only have one parent each (a father, actually); in Sylphiel's case, she falls under this trope when her father is Killed Off for Real in the third Light Novel/late first season of the anime in a townwide explosion. Ironically, the main protagonist's (Lina) parents are both alive and well. And the status of the parents of Lina's later allies in the novels (Luke and Milina) is unknown.
80% of all characters in Mobile Fighter G Gundam are orphans, major and minor characters, and a few of them have only one parent. The rest are undetermined. For many of them, this plays a role in why they became Gundam Fighters.
Hayate of Magical Girl Lyrical Nanoha, which allowed her to raise a family of sentient alien programs on her own since the age of nine and, as mentioned in the supplementary comics, move to Mid-childa before she even graduated from high school. Like most orphans, she does have an "uncle" who was a friend of her father's taking care of her, although it's only financially and it turns out that he never knew her father, and believes that because she is an orphan, few will have to mourn her once she's sealed away with the Book of Darkness.
Most of the Strawhat crew in One Piece are victims of this trope, often more than once. Both Nami and Franky, for example, were orphaned at a young age, but taken in and raised by a kind foster parent...only for them to die as well. But they've still got it better than Robin, who didn't just lose her parents, but HER ENTIRE HOME ISLAND, of which she is the only survivor. Most of the others seem to have absentee parents of one form or another; the only member whose mother and father are both seen is Usopp, a victim of both this trope AND Parental Abandonment (his dad left to become a pirate, and his mom died shortly after).
For a while, it seemed that Luffy was a victim of this trope as well, his lack of parentage explained with a throwaway remark that "that kid has no parents" in the first chapter. Years later, we learned that Luffy was actually raised by his grandfather, and that his dad, at least, is alive (he's just the most wanted man in the world, which can make it tough to raise a kid).
Simon of Tengen Toppa Gurren Lagann lost his parents in an earthquake before the start of the series, so when his blood brother Kamina decides they're going to the surface, he doesn't have anything holding him back. In a twist, Gimmy and Darry are chosen to be exiled to the surface explicitly because they don't have family who will mourn their departure.
Nearly all of the members of the Gatchaman team are orphans, except for Ryu and Ken prior to his father's Heroic Sacrifice. This is the main reason Ryu is usually left tending the Phoenix while the others get all of the action; he still has a family that would miss him if anything happened to him.
Sousuke Sagara of Full Metal Panic! being rendered an orphan helps justify why he can keep risking his life with no regard for consequences. Although his mother dying for his sake and her dramatic Last Words telling him he must "live," "never give up," and "fight!" does have the other purpose of making him the Crazy Survivalist he is today, it mainly seems to serve as a plot device to allow the readers to realize he simply has no one waiting for him.
At one point in Hellsing, during the Quiet Drama Scene, while discussing Seras' progress Alucard asks Walter how they covered up her death and how her family is taking it. When Walter replies that she has none and is an orphan, Alucard sardonically replies "Of course she is". However, since Seras was already an adult by the time she died, the circumstances and consequences of her parents' deaths turns out to be a major part of her character and the series veering into Crapsack World territory and running on Black and Gray Morality, it's a justified trope.
Son Goku of Dragon Ball. Some time before the series began, he accidentally killed his adoptive grandfather after transforming into a giant were-ape. As for blood relatives, Dragon Ball Z reveals that his race was wiped out along with their home planet.
For that matter, Raditz himself is an orphan, but unlike Son Goku, their father Bardock was alive by the time their planet was obliterated, yet he took little interest in the well being of his sons. Raditz himself failed to earn respect from any of his fellow Saiyan survivors.
Vegeta himself is also an orphan who was in turn adopted by the tyrant that killed his father and ended his race.
Most, if not all Z warriors have no parents whatsoever; Yamcha is introduced as a teenage desert thief with no parents or guardians mentioned; Krillin was raised by a monastic order on where he was bullied; Tien Shin-Han and Chaotzu seem to have been raised by Crane Hermit; Yajirobe was introduced as a teenage wanderer without mentioned family.
The unnamed Namekian (the original Namekian survivor that later divided himself into Piccolo and Kami) is himself an orphan who is mentioned to be the son of an individual named Kattas. He spent a great deal of his youth waiting for his parents (or parent, for that matter) to no avail. After he becomes whole once again, he becomes disinterested in his past and even keeps a distance from the remaining survivors of his race.
In Pokémon Special, Red is the only Dex Holder to have no family even alluded to, leaving him free to travel the world where ever and whenever he wants.
Gunslinger Girl. Done plausibly as the Social Welfare Agency only selects girls for its secret killer cyborg program who don't have extended families who'll be concerned about them. As a victim of child sex trafficking, Triela's background is unknown even to the Agency. Henrietta's entire family was murdered and Angelica's parents are in prison. Petra's family are too poor to travel from Russian to see their daughter — which is just as well as her appearance has been altered completely. It's eventually revealed that they were told she had died. As Rico is one of the few cyborgs who retains memories of her previous life, the occasional visit from her estranged parents is no doubt enough to reassure them that their Ill Girl is receiving the best of care; the Agency would have no trouble getting Rico to play along.
In Berserk, all of the main cast have Parental Abandonment issues, but Griffith is the only one who has absolutely no mention of any sort of guardianship in his early life, making it quite convenient for him to up and decide that he was going to become a king someday and to get there, he needed to start a ragtag bunch of misfit mercenaries.
In Sailor Moon, both Mamoru's and Makoto's parents are dead, long before the start of the series. In the manga it's used to handwave why they live alone, but in the anime any mention is quickly swept under the rug.
Fruits Basket's Tohru Honda wouldn't have been living in a tent for the Sohma boys to discover if her mother hadn't died.
The debut issue of The Incredible Hulk makes it clear up front that Rick Jones (Bruce Banner's newly-acquired teenaged sidekick) is an orphan. Much later, we learn that Bruce is also an orphan. Bruce's mother was killed by his father when he was a child, and Bruce (accidentally?) killed his father shortly before the explosion that made him the Hulk.
Several mutant characters from Marvel's X-Books are orphans; sometimes by abandonment, sometimes by death, by murder, or by parents becoming a demon bear...
Wait, what was that last one?! Danielle Moonstar, known as the illusion-casting Mirage before House of M, lost her parents to the 'demon bear' and knew it would come for her. After the big confrontation with it, it turns out that they were the bear and she was able to free them. No, they haven't been properly killed off since... yet. This makes her one of exceedingly few X-characters to have both parents, despite having a standard-issue dead parent origin when we met her!
The Plutonian of Irredeemable is yet another convenient superhero orphan. The series actually deconstructs this Trope, examining the effect it can really have on a little boy with super-powers. The Plutonian was also abandoned by his subsequent foster parents, after he accidentally crippled their biological son. They even devoted themselves to never speak again just so he wouldn't pick up their voices by superhearing.
Tom Strong. Orphaned at around age 8, after being raised in a gravity chamber by his parents.
Tintin. Most members of his recurring supporting cast come without familial attachments.
In The Jezinkas, Johnny is an orphan and so looking for work.
Subverted in the Mass Effect fic series Uplifted. Joachim Hoch's mother is alive, but he was adopted by Gerald Langer after he ran away and hasn't seen her in years. Even after she is killed in an Allied bombing raid, Hoch's roots are still an important plot point.
Nellas was still a child when orcs killed her parents.
In Gensokyo 20 XX series, we have Maribel and Renko; apparently, the fates of both of their parents are unknown but it can be assumed they died and they don't seem to remember them, as noted in 20XXIV and 20XXV. However, the fact that both were well fed and healthy when Yukari finds them means someone had to have taken care of them and we don't even know what happens to that person, though the two did state they weren't far from a food source, having survived on scraps.
Mulan is another aversion and the titular heroine has her grandmother for added bonus. In fact her plot is kicked off by her not wanting her father to die in war.
Flynn Rider has this trope as part of his backstory in Tangled. His motivation behind being a thief is because of growing up poor.
Frozen orphans both girls within the first ten minutes, thus allowing them a strained relationship with only each other. This serves a major plot point, exacerbating the loneliness of the leads.
The two aliens of Megamind are both orphans in the extreme, given that their entire home planets have been destroyed. This allows them to experience two very different childhoods upon arriving on Earth.
Films — Live-Action
In Idiocracy, Joe is chosen for the freezing experiment partially because he is orphaned, so nobody would come ask questions if something went wrong with the experiment. It does.
James Bond is an orphan. Used as a (possible) plot point; he was chosen because he's an orphan, so family is not a factor upon training/traveling, nor will it be leverage should he be captured. The Daniel Craig films suggest that MI6 recruits orphans because they can exploit the particular brand of psychological scarring that results. It makes recruits more malleable to training and conditioning, since the bosses can frame themselves as a Parental Substitute — the Judi Dench version of M very explicitly does this with Bond.
A great many of the main characters in Star Wars are orphans. Han Solo and Anakin Skywalker are both orphans. Both Luke and Leia are orphaned - twice. Luke probably wouldn't have joined Ben Kenobi in rescuing the princess if the Imperial Stormtroopers hadn't killed his uncle and aunt. Every Jedi raised during the Clone Wars era (and a long time before that as well), save Anakin and a few others, was taken from their parents when they were still an infant and brought to the Temple.
Discussed in Moonrise Kingdom. Suzy, who's an avid reader of children's fantasy stories, says that all her favourite protagonists are orphans, and sometimes she wishes she were one too. Sam, who is himself an orphan and has lived a miserable live because of it, simply responds: "I love you, but you have no idea what you're talking about."
Operation: Dumbo Drop: Deconstructed with Linh. At first, being an orphan seems like the simple reason he gets to go on all sorts of exciting adventures with the team. Then it's revealed he he had to watch his father get shot in front of his eyes.
The Lord of the Rings: Frodo Baggins was orphaned at twelve, but was raised in his family's home by said extended family; when he turned 21 (adult-ish but not yet legally adult for hobbits) he was adopted by and went to live with his 'uncle' Bilbo (who conveniently leaves once Frodo is legally an adult). Bilbo himself is technically an orphan (his parents died of natural causes after he was fully grown), manages to avoid marriage, and thus has no family ties holding him back when he goes on his adventure.
Molly Moon from the Molly Moon books, as well as most of her friends.
Subverted in Ordinary People (the novel more than the film, though it's mentioned in both). Calvin, the father, grew up in an orphanage in Detroit. While he lives a very stable life as a successful tax lawyer with a wife and children, he's haunted by his past and admits to feelings of rootlessness when he talks to his son's psychiatrist.
In The Legendsong Saga, Glynn and Ember's parents died in a car crash a about a year ago. Despite being only 17, they live alone. They also have almost no other friends or connections, making it less complicated when they are stuck in Keltor (Ember was the only reason Glynn wanted to return to Earth; Ember doen't care about anything except her death and her music.)
Subverted in Feliks, Net & Nika with Nika. Her mum died at childbirth, her dad died when she was eleven and she's afraid of going to orphanage because she would lose everything and because Polish orphanages are terrible. While nothing holds her back, she must constantly pretend her father exists, she must work illegally (in Poland you can't work under the age of sixteen) to pay for her house and school and she has to hide all that from her classmates. The only situation when this is played straight is when characters need a safe hiding spot in alternative reality in which Nika is still an orphan.
Ragnor Blackmane, of William King's Space Wolf novels, is orphaned in the opening of the first. A major motivation for him is desire for Revenge on a fellow Space Marine who had been part of the opposing force.
You would not believe how many characters in the Star Wars Expanded Universe are orphaned. Wedge Antilles lost both his parents when he was around twelve, Tycho Celchu was a pilot for the Empire whose entire family was on Alderaan, Corran Horn lost his mother to a speeder accident and his father to a criminal. Most of these characters are adults, and the loss of their parents spurred them to join the Rebellion. While her parents aren't dead, Mara Jade was taken from them at an early age and never looked back. The Essential Guide to Characters (first edition) says that Palpatine had her parents killed. There you go; Ben's never going to meet his grandparents now…
The two assassin protagonists in Brotherhood of the Rose, by David Morrell, initially meet in an orphanage from which they're recruited by CIA chief Elliot, who presents himself as a surrogate father figure. They later discover that Elliot (and other members of his worldwide conspiracy) have done the same thing with other orphans, in order to create a team of Elite Mooks who'll obey their orders without question.
In the CHERUB books, every character as part of CHERUB is an orphan. Means they can be trained up as spies without parents wondering whats going on.
Although in the later books the rules are changed slightly so the children of staff members can become CHERUBs as well, partly because it's hard to find conveniently orphaned/abandoned children that fit CHERUB's other recruitment criteria.
A Series of Unfortunate Events has many orphans, including the three main characters and Count Olaf, whose parents may have been killed by the Baudelaire parents.
In The Belgariad, Garion's parents are killed by a servant of the enemy before the story starts.
In The Riftwar Cycle book Magician, Pug is an orphan and we never find out what happened to his parents (well, unless it's mentioned in one of the innumerable sequels).
Number Ten Ox in Bridge of Birds is an orphan, raised by an aunt and uncle.
Rincewind from the Discworld novels has no idea who his parents are/were.
His mother left before he was born.
Lampshaded/mentioned in Unseen Academicals when only people with a note from their mother are excused from playing football. Rincewind asks the Arch-Chancellor for permission to go ask his mother for such a note. "I thought you said you didn't have a mother." [beat] "Permission to go find her, Arch-Chancellor?"
In the Replica series, Nancy Candler is an orphan with no living relatives, making it easy for her to pass off an adopted genetically altered clone as her biological daughter without anyone raising eyebrows.
The title character in James and the Giant Peach was orphaned at a young age, and is being raised by his two evil aunts until they get squashed by the peach.
Doc Savage lost his father in his very first adventure, The Man of Bronze, and his mother had died at some point prior to that. Which begs the question, if you're full grown when your parents die, are you still an orphan?
In A Song of Ice and Fire, Yoren deliberately invokes this, telling Arya to claim to be an orphan, since no one will give an orphan taking the Black a second glance.
Per Word of God, virtually everyone in the web-novel Domina. "If a character's parents aren't mentioned, it's safe to assume it's because they're dead." That's what happens when you live in a Wretched Hive.
Harry Dresden, from The Dresden Files. His mother died shortly after he was born, and his father died when he was around 7. Then, later on, while living with Justin Du Morne he's orphaned again when he kills Justin.
Later on, he discovers that he does still have surviving family, in the form of his half-brother Thomas Raith and his grandfather Ebenezer McCoy.
Sisterhood Series by Fern Michaels: Okay, Nikki Quinn's parents are dead. Kathryn Lucas's parents are dead. Isabelle Flanders's parents are dead (maybe). Yoko Akia's mother is dead and her father is evil. Abner Tookus's parents are dead (maybe). There's certainly a lot of orphan characters to go around!
Subverted in The Wonderful Wizard of Oz; Dorothy is stated to be an orphan, but lives with her foster parents in Kansas. She loves them enough that despite all the beauty of Oz and the friends she made, she is determined to go back anyway.
In Bryan Miranda's The Journey to Atlantis, one of the characters is this. It is Mickello, whose dad died in the plane crash that landed Mickello on the island, and whose mother apparently has no idea what the hell happened to him.
With his parents having died a few years ago, Daniel from The Leonard Regime is able to go off and fight. It later turns out his parents died after founding the same rebellion he is fighting for.
Thomas Theisman from Honor Harrington was raised in an orphanage in the People's Republic of Haven, which quite conveniently means the government doesn't have any loved ones to hold over his head. Not so coincidentally, once he gets the chance, he puts a brutal and awesome end to the Committee of Public Safety and resurrects the old Republic, elected President and all, that had lain in ashes for two centuries. He does not, however, become President, being quite content to stick to the military side as Secretary of War and Chief of Naval Operations; that lovely duty goes to Eloise Pritchart, Theisman's fellow conspirator and firm believer in the old Republic and the Constitution.
The Heroes of Olympus: None of the major demigods have any sort of family to go back to, unless it's a sibling. The only exceptions are Percy, Piper, and Annabeth, and even the latter two don't have the best relationship with their muggle parent - Annabeth ran away from her father and stepmom while Piper's father is neglectful, although he tries his best. Percy's the only one with Good Parents to return to.
Of the four main characters in the Circle of Magic books, three are orphans. Briar grows up in a street gang, Sandry is sent to live with her uncle after her parents die, and Daja becomes an orphan at the start of the series and goes straight to the Temples. It's in a medieval-ish society, so they could have been taken on as apprentices around that age anyway, but instead form something of a magical Super Family Team. Tris Chandler, the only one who actually does have biological relatives, is an emotional orphan, if not a physical one. Her parents didn't want her because of the destructive power of her untrained magic, and by the time she comes to the Temples, she's spent years being dumped on various relatives who either didn't want to take care of her or who treated her as an unpaid servant. And the one relative whom she likes ends up trying to kill her.
In How Green This Land, How Blue This Sea, Mahir is told that only those with no living close relatives who are not in committed relationships are eligible to work in a particular research center. This was why Rey and Olivia broke up, so that he could pursue that career opportunity.
Live Action TV
Bones - Dr. Brennan's emotional interface may be glitchy, but any one she deals with who comments on her inability to sympathize gets slammed when they find out she lost her parents at a young age, conveniently explaining why she might come off disturbed but assuring everyone that she understands.
Cloud from Final Fantasy VII, due to Sephiroth killing his mother during his raid on Nibelheim. His father is never mentioned.
And Aerith (though she was raised by Elmyra for fifteen years), Tifa, Marlene (raised by Barret), Red XIII...
In Final Fantasy III, all the main characters are orphans, although three had been adopted and one was working for the king by the time the game begins.
Most of the main characters are orphans in Final Fantasy VIII as well, with the exception of Rinoa who was a Rebellious Princess. Most side characters were as well as SeeD specifically recruit from orphanages, because that is what Gardens started off as. Tyke Bomb gone into a full blown army.
Final Fantasy IV: Cecil and Kain were orphaned and taken in by King Baron, and Rydia becomes an orphan in-game. Edge orphans himself, killing his parents after they become chimaera. Polom and Porom are raised by Mysidia's elder and may or may not be orphans.
Final Fantasy V has the Idiot Hero being an orphan at the game's beginning, the rebellious princesses losing their father halfway through the game and the Sixth Ranger being a replacement for her dead grandpa, who was also her last relative. It's more done as a party of the game's theme of legacy than a plot ticket, though.
Final Fantasy VI has Terra, Edgar, and Sabin explicitly stated as orphans as part of the plot. Gau is essentially an orphan. Relm may or may not be an orphan depending on whether you save Shadow, but it's at least Disappeared Dad. The rest of the cast never mention their families.
Zidane in Final Fantasy IX. Truth be told, he's revealed never to have had parents at all.
Eiko as well, though she actually gains parents by the end of the game.
In Final Fantasy X, Tidus, Yuna, Seymour, Wakka, and Lulu are all missing both parents well... a case could be made for Tidus, but that's different. Kimahri's family disowned him, Rikku's mother is dead, and we never hear anything about Auron's parents. Only two of the main characters have siblings, and one of them is dead. Probably justified to demonstrate that Sin has touched everyone's lives.
Final Fantasy XI has Lion, Prishe, Aphmau, and Lilith. (Although the last one is trying to avert the trope through Time Travel.) Can we get Square into a 12-step program to deal with their addiction to this trope?
Ashe's father (her mother is never seen/mentioned) is killed in the opening movie. Vayne orphans himself and Larsa when he orders their father to be murdered. Basch and his sibling are orphaned during the attack on their homeland. Your party fights and kills Balthier's father during the course of the game, orphaning him as his mother was already long dead.
Lightning, Serah, and Snow in Final Fantasy XIII. Presumably Fang and Vanille as well, since they were in crystal stasis for several hundred years. Only Hope is the exception, and both his parents are seen during the course of the game, though his mother dies less than an hour in. Though this is averted with the Big Bad. It's unclear if, as a Mechanical Lifeform, it really has parents, but the game is fond of related symbolism in regards to it, and at the very least it was abandoned by the gods who created it. Unlike the heroes, it took the trauma of this situation rather badly. very badly actually. Unfortunately the heroes never discuss this.
The series as a rule enjoys making their main characters an orphan at some point in the game. Their mothers are rarely mentioned but when they are, they're dead. Their fathers will die at some point in the story for some reason. The sole exception to this so-far is Eliwood, Roy's father in The Sword of Seals who lives throughout the game but is severely bed ridden. On the other hand, both Roy's and Lilina's mothers passed away before the game starts, and Lilina loses her father Hector early on, playing this trope straight in her case. The prequel, Fire Emblem: Blazing Sword, viciously delights in killing off family. It's gotten to the point that if a character has a parent/sibling/uncle that loves them, nine out of ten times they're dead before the game is up, if not killed before it. Lyn's parents were both killed by bandits, Hector's parents and brother die of disease, Eliwood's dad is killed by Nergal, Raven's parents committed suicide when their house was attacked, Lucius's father was killed and his mother died of sickness, Serra's parents abandoned her, Erk's are absent, both Jaffar and Nino have dead parents, Lowen probably takes the cake though, having lost first his parents, then his grandparents in fairly quick succession.
The worst part of Nino's family situation: Her adopted family are all bosses late in the game. The worst part of it is, they're not bad guys at all, and some of the conversations if you force Nino to attack them are pretty heart wrenching. Worse still, their dead bodies are reanimated in the last level, which means she has to kill them TWICE.
What about the other part? When she faces off against Sonia, the woman she thought of as her mother her entire life and who she only wanted to please, the bitch is quite happy to tell Nino how she slaughtered the girl's real parents for their knowledge on dragons and Nino's real mother died shielding her. Oh, and the only reason Sonia didn't kill Nino as well is because she figured Nino might be useful later.
Pretty much every character in Genealogy of Holy War due to the entire playable cast save Fin being wiped out half way through the game leaving their orphaned children to continue the fight seventeen years later. Many other enemies are also orphaned by the player and are out for revenge.
In Tales of Vesperia, everyone in your entire party is an orphan. With most of them, all we get is either the parent left or the parent died, or both, no further explanation. We only find out how one parent died, although it's implied (very very subtly) that several of the mothers died in childbirth. In all honesty, it feels a little ridiculous at times.
Skies of Arcadia: surprisingly, not the hero, but both other core members of your party. Aika is established early on to be an orphan, and Fina... well, there's no other Silvites left but some Elders, and Ramirez.
In Baten Kaitos, Kalas has no parents, although he makes mention to being raised by his grandfather, and to having a brother. He's an Artificial Human, and his grandfather actually created him. The prequel, surprisingly, averts this: Sagi's implied to be the only biological child of the woman who runs his town's orphanage, and Milly's dad is one of the villains. Also played with: One of the boss fights culminates in YOU orphaning one of the original game's party members.
In Golden Sun, the trope is very much zig-zagged for the main cast.
Isaac's father and Jenna's parents and brother are killed off right in the intro. Then it quickly turns out that the brother survived and seems to be an enemy. Then in the second game, it turns out the trope is completely subverted: the parents and Isaac's dad also survived and were made hostages, and saving them is a big motivator to the quest. So the kids are not actually orphans... then they accidentally almost kill their own parents themselves near the end of the game. Poor Isaac's mother has to almost force her son to keep going on his quest and is a source of worry, as she falls gravely ill in his absence.
Ivan is an orphan and his adoptive father is kidnapped as you meet him, but the trope is toyed with: you're told that you can't do anything about it and you should just leave the father behind, but Ivan worries a lot, and you get an optional sidequest to free his father and ease his mind; and in the second game Ivan's mysterious parentage is a plot point.
Sheba is also an adopted orphan and joins the group because she was kidnapped, but she's an inversion of the trope: in the second game, she refuses to drop by her hometown because her worried adoptive family would force her to stay.
Piers is a straight and extreme example: he spends the first half of the game trying to go home, then when he finally does, he learns that his mother just died and he quickly gets exiled.
Mia would be a straight example, having simply no mentioned family at all... but she is the one character who is sad to leave (she says farewell to her two young apprentices) and it's more a case of "conveniently rid of her town-healer duties".
And Garet is a complete aversion: he's the only cast member who has a large, living and functional family, but they all encourage him to save the world and fatherless Isaac gets more angst; then in the epilogue cutscene of the second game Garet comes home, finds the town destroyed, and thinks for a moment that they all died.
The first four heroes of Golden Sun: Dark Dawn all have at least one parent still alive and caring for them— the previous games' heroes (whom the kids strongly resemble). However, the second set of heroes include two straight examples (Sveta, whose parents died in Morgal's revolutionary war, and Eoleo when his father dies onscreen), a subversion (Amiti, who doesn't have parents but lives with his affectionate and overprotective uncle, who tries to forbid him from heroics), and an aversion (Himi's parents aren't happy to see her going into danger, but they have to let her because she's the only one who knows what needs to be done any more).
In Metal Gear, the circumstances which led to Otacon being an orphan are a significant aspect of his woobie status.
Averted to a certain degree for some of the Origins in Dragon Age: Origins. The character does have relatives, and not all of them die in the prologue. For practical purposes, though, it still amounts to the same thing. Played straight with some of your companions (Leliana, Zevran, etc.), and in Alistair's case, it's even a plot point. Also parodied in the elven Alienage, where the number of "orphans" is directly proportional to the amount of money you're giving the beggars.
Implied to be the case with the eponymous characters of the Jak and Daxter series. They get flung forward in time in the sequel, and don't have any problem staying around. The orphan thing is explored/confirmed for Jak, but is still only an implication for Daxter, though no one is saying otherwise.
Ratchet of Ratchet & Clank believes he is the only Lombax left in the universe. Although this is proven wrong when Alister Azimuth, another Lombax, appears in Ratchet & Clank Future: A Crack In Time, Ratchet is forced to kill Azimuth at the end, leaving him alone once again.
All over the place in Persona 3; the protagonist, Akihiko, and Shinjiro are orphans, Ken is probably an orphan (dead mother, no mention of father but is being supported by a distant cousin), all three members of Strega are likely orphans (Jin mentions that they, and other artificial Persona-users were all found on the streets as children), Yukari and Mitsuru only have a mother (the latter's mother only appears in a CD drama, and her father is killed late in the game, Junpei only has a father, and only Fuuka has two living parents, and she's estranged from them. Even Koromaru, a dog, has lost his own master. If for nothing else, it makes fighting Shadows easier for them.
The parental situation of Persona 4 is far better, with the only real orphan being Naoto, and even then, she had been raised by her grandfather the entire time. Kanji's father is explicitly stated to be dead, but he still has his mother, Teddie is a Shadow, and Yu's parents travel abroad frequently. Everyone else in the party is from a completely intact family.
The tone of the game may help. Persona 3 is darker than Persona 4 and most of the time, the abandonment is ether a direct or indirect result of the Krijo group's experimentation on the Shadows, with the other two members having parents that made it personally preferable to live in the dorm.
The two earlier games do not really feature this, with the only cases of parental loss both being from Persona 2: Maya's father, a war journalist, died on the field, and Jun's father died from being thrown in a clock tower, and the Big Bad masquerades as him.
Of the seven party members in Xenoblade, only one of them has a living parent, five are stated to be orphans, and the last's parents are never mentioned. The orphan total becomes six later thanks to the parent performing a Heroic Sacrifice.
Good thing that Taiga and Mia don't have any parents in Duel Savior Destiny or else their family might be a little concerned when they get whisked off to another world and put into the special forces. In fact, nobody else seems to have any family either apart from Lily's adoptive mother.
No matter which class you elect to play in Darkstone, you are an orphan. When speaking to the guards at the gate of your hometown, one will always comment that they haven't seen you since your parents were killed.
The protagonist of Baldur's Gate is raised by Gorion the sage, and at the start of the game does not know who his/her real parents were. It turns out that both are dead, and that the PC's father was the deity of murder, Bhaal. The trope is subverted, since the latter part of the game, and the sequel, are about the consequences of Bhaal's attempts to avoid his coming death - which among other things resulted in the PC's birth and special heritage.
The main character in Find Chaos Arthur and his sister Tristan are both orphans by Arthur's doing (possible accident?).
Jordan from Skins. Apparently there's been no mention of her family at all - the supernatural agency called the Coven took her in as a child.
"Onion Kid" alias "Rex" alias "Sarda" from 8-Bit Theater was orphaned so often, that he's stopped looking for foster parents or even an orphanage who'd still take him in. This trauma is actually the cause for everything that happened in the comic to begin with, thanks to a Stable Time Loop.
Hanna of Hanna Is Not a Boy's Name never mentions his family, but it's implied that he has no immediate relatives in the city.
Jade Harley from Homestuck, who was raised by her pet dog after her grandfather died. Technically speaking, John is an orphan too: both his and Jade's biological parents are long dead. He is raised by his 'father', who is technically his half-brother. Oh, and his and Jade's biological parents are John's grandmother and Jade's grandfather. Confused yet?
And as of 2/19, all of the kids are orphans in both the traditional and technical sense. Damn.
Troll society is entirely like this, as the adults go off to conquer the universe while they leave the planet in the hands of the youth for the most part, leaving them to be Raised by Wolves. At least until events cause all of said Wolves to die, but they remained as their sprites. Until Jack Noir killed them all over again.
In the Alpha universe, Roxy and Dirk. Even more so once it's revealed that the two of them exist on Earth 400 years in the future, and their parents have been dead for centuries and left caches of food and supplies for them.
Most of the cast in Dubious Company. Sal is the only character firmly established as having living relatives.
Walter, Tiren, and Elly have fond childhood memories, but appear to no longer have ties to their families. They were visibly distraught when Sal asked if they had a home.
Grunn's orphanage is one of the settings in Dreamkeepers. The "convenient" aspect of the trope is played with in that the orphans are one big dysfunctional family, and several of them are important contributors to the plot.
In The Gamers Alliance, quite a few characters have ended up as orphans after their parents' demise.
In the Whateley Universe, Bladedancer's mother is long dead, and her father dies at the hands of a demon in her origin story. Part of her story is her quest to one day rescue her father's soul from that demon.
Tobiah, the narrator of The Graystone Saga, was orphaned some years prior to meeting Lady Gray. He doesn't talk about his parents much, since they're not important to the story and he doesn't remember them very well anyway.
In Aelan mythology from Ustal Naror islands, the oldest stone wouldn't stand death of his parents if he weren't an orphan from the beginning.
Ronaldo from the Brazil episode of The Simpsons. Conveniently as an orphan, he doesn't have parents hogging his money he gets from performing on Teleboobies, and he assists the Simpsons in paying Homer's ransom.
Sinedd of Galactik Football is able to run off and join The Shadows despite a large song and dance being made in the very same episode about the need for parental permission. His departure isn't justified with this trope for another 18 episodes. Orphan or not, Sinedd was already of age, making the parental permission unnecessary for him.
Likely a requirement to be part of the Teen Titans, because what sort of parents would let their children put their lives on the line in weekly superheroics? And sure enough, the only living parent to any of the Titans ever seen in the series is not a very nice guy.
Cyborg's father is (presumably) alive. In the comics he was the one who made him a... well, Cyborg.
We also get to meet Beast Boy's (adoptive) parents, Elasti-Girl is pretty nice, but Mento is bit of a jerk.
Robin's parents are dead as always, but this incarnation heavily implies that he even ditched his "father" Batman so he could move on. (And ended up gathering a bunch of friends around him instead, but no adults. The closest thing to a parent he has is Slade purring about what a great apprentice he could be...)
Buck and Larry 3000 of Time Squad needed Otto from the 20th century since he knows more history than they do. Since he's an orphan that was in a rather troubling situation when they found him, they adopted him despite the fact that it's forbidden by the Time Squad.
Advertisements for the Pony Express purportedly mentioned that they preferred their hires to be orphans, though original copies of these advertisements have not been discovered. Presumably a lot of dangerous occupations would prefer to have as few grieving parents as possible.