In crossovers between Fate/stay night and Fate/Grand Order, it's common to make the protagonist of the game the child of Shiro Emiya and Rin Tohsaka, since both versions of Grand Order's protagonists are designed to be Gender Flip versions of the Stay Night characters.
Speaking of the Fate Series, due to Shirou's orphaned status, it has become quite the Fandom-Specific Plot for crossovers to start with Shirou finding members of his lost family.
In Marvel Comics crossovers, it is common for a character to be a descendant of Wolverine, whose slow aging, Walking the Earth biography and amnesia allow him to easily have children, including ones he is unaware of.
Additionally, in Marvel/Harry Potter crossovers, it's very common for Harry Potter to be a cousin/nephew/miscellaneous relative of Jean Grey, owing her being a Significant Green-Eyed Redhead just like Lily Potter, meaning notable bright green eyes.
It's extremely common in Marvel and DC Fusion Fics to make Deathstroke and Deadpool into brothers, not just because they share the same last name, but because Deadpool started out as a deliberateExpy of Deathstroke before evolving into the fourth-wall breaking nutjob we know today.
In crossovers between X-COM and Mass Effect, it is common to make Chryssalids descendants of Rachni. Less commonly, Mutons are related to Krogan.
In The Elder Scrolls series fanfics and roleplays, the Player Character of one game is commonly the descendant or relative of characters from previous games. A particularly popular example is having the Dragonborn of Skyrim be the descendant of Martin Septim and a female Champion of Cyrodiil from Oblivion. (This would make the Dragonborn the rightful heir of the Empire.)
Certain communities on DeviantArt have a habit of creating entire crossover family trees, usually on the basis of "I like these two characters, so they should be related to each other". For just one example, this picture adds on to Glimmer's family by making Ryan Akagi her brother, the Captain of the Guard her uncle, and Cassandra and Marcy Wu her cousins.
In the Miraculous Ladybug fandom, "Marinette turns out to be the daughter of a crossover character" is practically a genre of its own — partly due to Hollywood Genetics (she has blue eyes when no one else in her family does), partly so the author can use it as an excuse to get her out of Paris for whatever reason. Bruce Wayne is arguably the most popular choice, though plenty of other characters have been used as Marinette's "actual" biological mom/dad/parents.
Generally, any instance where characters in two different fandoms are played by the same actor (or the two actors are related in Real Life) opens up the possibility for this to happen.
Specific Examples
Adopted Displaced: In Three More Things!, Bai Tza is mentioned to have three Siren daughters — D'gi, A'ri, and S'na — who were exiled after she herself was sealed. They are Adagio Dazzle, Aria Blaze and Sonata Dusk.
In the Akko Kagari UniverseChariot du Nord's siblings are Izetta and the Master (who's named Orion in this story). On account of Chariot being Akko's mother this also makes them her aunt and uncle respectively.
Starting with her unnamed father: her paternal grandfather is Sakura Haruno who was taught how to transform into a functional hermaphrodite by her own mother Tsuande Senju and Sakura's father just so happens to be Minato Namikaze. Kaede's patrenal grandmother is Karin Uzumaki, who herself is a product of incest through Kushina and Naruto Uzumaki due to time-travel hijinks as is Kushina who is the child of Tsunade and Nawaki. If your wondering about Sarada, Sakura's daughter with Sasuke, she's also here and in fact Sakura and Karin had their sexual encounter almost immediately after Sakura gave birth.
Kaede's mother is revealed to be Yaku from the hentai, La Blue Girl which also makes her part of the Miroku clan and all that entails. Apparently, some incident happened that caused the Naruto universe to go through a Universal Metaphysical Annihilation and a few of the survivors escaped into the MMC world that is this fic. Kaede's father and mother fell in love but not a few years after her birth, their romance soured and eventually divorced.
And the cherry on this cake is that when Sarada escaped into the new world, she met a man whom she married and had a child with. That child being Reika Kitami of Bible Black infamy.
In the Andromeda/Star Wars Legends crossover All That Glitters, the leader of the Empire expeditionary force learns that Magog seem to be based on genetic material from his own galaxy. At the end, he is defeated, runs away and starts working on creating them, but doesn't succeed until he gets access to the last donor species, Yuuzhan Vong.
Sakaki from Azumanga Daioh and Nonna from Girls und Panzer are cousins, an idea likely derived from their similar appearances as tall girls with long, dark hair.
Implied with Kagura and Minamo "Nyamo" Kurosawa. The former's full name in this fic is Kagura Kurosawa, which means that she might be related to Nyamo.
Avengers: Infinite Wars: Asajj Ventress' father was another manifestation of Ego, making her Peter Quill's half-sister.
Murakumo Units are clones of a young girl by the name of Saya, the younger sister of Ragna and Jin Kisaragi. Penny Polendina is one of these clones. Making her the cloned sister of Ragna and Jin, and as well as a "sister" to her fellow clone Noel.
It's revealed in the final chapter of Volume 3 that Ragna is Salem's son. The first chapter of Volume 4 further reveals that he's the reincarnation of Ozma and Salem's firstborn son, meaning that he's also related to Ozpin/Ozma as well. Jin's dream in Chapter 75 reveals that the same applies to him and Saya, with them being Ozma and Salem's youngest son and only daughter.
Blood Sisters features Bella Swan and Bo Dennis as sisters who have been separated basically all their lives, which also makes Trick Bella's grandfather.
Madame Mim turns out to have been the Masters' adoptive mother.
"Charmed Wizard" reveals that Harry Potter is actually the son of Cole Turner and Phoebe Haliwell (Charmed (1998)); when the Seer "stole" the baby from Phoebe's womb, the subsequent vanquish expelled the child's spirit and he survived by placing himself in Lily Potter's womb instead, so while Lily gave birth to Harry he is still Cole and Phoebe's son.
Child of the Storm has a lot of this, to the point where it was the first work of any kind with a Tangled Family Tree page of its very own. Some of the basics:
The central premise of the story is that James Potter was an incarnation of the Mighty Thor. Additionally, Lily's mother's maiden name was Grey, which makes Jean Grey Harry's second cousin.
Agent Coulson is revealed to be "Molly's accountant squib cousin", tying him to their family tree and making him one of the Weasleys' extended relatives, and related in one distant fashion or another to all the other Pureblood families as a result, including - very distantly - Harry.
Emma Frost's family is descended from a squib of the Malfoy family. This also means that the Malfoys are related to the Summers family, as Emma hooked up with Alexander Summers senior, eventually resulting in their grandchildren, Scott, the late Alex Junior, and via cloning, Gambit.
The Phoenix is one of the Endless, specifically Destruction, making it siblings with Death, Destiny, Dream, Despair, Desire and Delirium.
Hermione Granger, not that she is aware of it until near the end of the second book, is adopted and biologically the daughter of Wanda Maximoff and John Constantine, also making her the granddaughter of Magneto, and niece of Lorna Dane and Pietro (with Lorna, at least, being about her age. The awkwardness is lampshaded). Additionally, given that Wanda is Harry's godmother, that ties another connection between them. Since this was a secret from her and she only discovered the truth when it literally blew up in her face, she is very much not happy about most of this.
Diana is the daughter of Marvel's Hercules and Hippolyta (which additionally means that that was a consensual and happy encounter, unlike the one in DC canon), and adopted as a Ward of the Crown by Odin and Frigga to protect her from Hera.
All pantheons are descended from Gaia's children with the various Allfathers; for instance, the DC Zeus and Marvel Odin are cousins through their mothers. In addition to making Diana and Harry third cousins, this means that they're relatives with, among other people, Jesus. Probably. It's worth noting that no one is entirely sure what 'the White God' of the Abrahamic faiths actually is, but the general guess is that he's one of the Elder Gods and thus a sibling of Gaia.
Donar Vadderung from The Dresden Files, the current holder of the mantle of Santa Claus, is not Odin as he was in the books, but is in fact Vidar, Odin's oldest bastard child, and about the same age as his stepmother Frigga. This makes him Thor's half-brother, and Harry's uncle.
Conquest ends with the revelation that the Star Wars humanity is a time-displaced FederationLost Colony (a heavily damaged Enterprise made an emergency landing on prehistoric Coruscant).
Relativity, a print anthology fanzine, was published from 1992 to 2001 over ten issues. According to its entry at the Fanlore wiki, the idea was based on a character in one television show resembling another character in a completely different show. They decided such occurrences were due to the characters being cousins. The result was The Cousins Universe, and many crossover fics used the convenience of a visit by a cousin to a particular show's world.
Dad's Old Shirt is a Calvin and Hobbes fanfic that ties into Peanuts, with the former taking place about a generation after the latter. Calvin is biologically Lucy's son but was Happily Adopted as an infant by Patty and Mark (AKA, Marcie).
"Daddy" and its sequel "Crazy runs in the Family" (set in a slight AU of Buffy the Vampire Slayer) reveals that Faith is the daughter and second child of Rocky Balboa, who ran away from home after an argument with her parents when her Slayer abilities kicked in. When the rest of the gang learn the identity of Faith's father, Xander is so shocked that he asks if Faith's sure she's a Slayer, given her father's legendary ability to take and deliver damage.
"Dark Clouds May Hang", a Buffy the Vampire Slayer/Charmed (1998) crossover, makes Xander Harris the son of Cole Turner and Phoebe Halliwelll; in the future where Wyatt turned evil, the Halliwells sent Xander back in time for his own protection while binding his magic, until Chris decides to look him up after his own conception in the past so they can start making arrangements for Cole's resurrection.
"Detective Annabeth Chase of the 99th Precinct" focuses on Annabeth Chase joining the 99th precinct as their new detective. As she spends more time with the group, it is revealed that two of the 99 staff have ties to the gods; Holt's husband Kevin is a great-grandson of Apollo, and Gina's daughter Iggy is a child of Hermes (which even shocks Gina when she learns her child's father was a literal god).
Shanks is Izuku's uncle by virtue of being Hisashi's younger brother.
Garp and Dragon are respectively Izuku's grandfather and uncle on his mother's side
Tatsumaki and Fubuki are Izuku's cousins and Inko's nieces as daughters of Inko's older brother Dragon.
The Dark Knights are siblings to All for One, though they don't hold him in high regard.
Tsuru is Midnight's mother.
Rudbornn Chelute appears as an associate of Merciless and one of the new recruits to the League of Villains, with fellow Shinigami Gang member Nnoitra Gilga joining the League.
Airi from Zombie Makeout Club shows up as Parten's cousin and a new recruit to the League of Villains.
Thanoseid from the Amalgam Universe is the father of the Dark Knights and All for One.
Celestia and Luna are the daughters of the Princess Ponies via their magic wands. Additionally, Megan, Danny, and Molly were their honorary aunts and uncle.
Twilight, Firefly and G1 Applejack are the ancestors of Twilight Sparkle, Rainbow Dash, and FiM Applejack, respectively.
Spike is the grandson of King Spykoran, who's the grownup version of G1 Spike.
An Extraordinary Journey: Characters speculate that the resemblance between SGC Major Lauren Satterfield and the Number Eight Cylon models is because the Eights were based on a distant relative of Satterfield's, and it is eventually revealed that Willow Rosenberg and Dawn Summers are formerly-Ascended Ancients who were actually sisters in their original lives; Athena/Willow chose to take human form again as an experiment, and Hera/Dawn bonded herself to the Key to help trap it and prevent Glory using it to destroy the universe.
The spin-offs also feature other characters learning they're related; The Faith Chronicles is based on the twist that Faith is actually the daughter of Samantha Carter (she was stolen by the Council at her birth and Sam was led to believe that her baby was stillborn), and Tara Sheppard makes Tara the half-sister of John Sheppard (his father had an affair with her mother when Laura worked as Patrick's secretary for a time).
Eva, the human wife of the Demon Sparda and mother to Dante and Vergil, is the older sister of Layla Heartfilia. This also makes Lucy cousins with Dante and Vergil.
The Devil Hand Arc reveals that Mirajane, Elfman and Lisanna are distant relatives of Angel/Sorano and Yukino, all of them being descendants of a mortal priestess that Sparda was forced to sacrifice in order to seal Temen-ni-gru.
Fairytales is a series of vignettes set over 1,000 years, and puts all the Disney Princesses (up until Tiana, the most recent when it was written) into one extended family.
"Faith Wayne" is based on the premise that Faith (Buffy the Vampire Slayer) is the daughter of Bruce Wayne (Batman), after he spent a few days with her mother in Boston shortly before he officially became Batman.
Fantasia Times: Yui Komori from Diabolik Lovers and Tsukune Aono from Rosario + Vampire are siblings. They were born as Evangeline and Adam Alakami, but after the murder of their birth parents, the two were split up and sent to be raised by different families.
"God is My Judge" reveals that Oz (Buffy the Vampire Slayer) is a nephew of Sara, the ex-wife of Jack O’Neill (Stargate SG-1), the two remaining close even after Jack and Sara divorced. As a more distant link, Jack’s mother was a Watcher who left the Council because she disagreed with Quentin Travers’ more extreme views.
"A Grimm Possibility": Kim's mother Anne is Nick Burkhardt's cousin, making Anne — and thus Kim — a Grimm herself, serving the dual purpose of giving Kim supernatural abilities and justifying the family's interaction with Nick.
Harry Potter and the Boiling Isles: Lilith Clawthorne is Harry's biological mother, having accidentally impregnated herself while demonstrating a Mystical Pregnancy spell to James. And since he looked physically human, she gave him up for James and Lily to raise in the Human Realm out of a belief that he'd have a more normal life there.
Honey and Magic: When Vernon Dursley meets Matilda and Jennifer Honey at King's Cross, he confirms that Miss Trunchbull is his cousin, prompting Miss Honey to observe that she shares his relief that they're not related to him.
Honey and Vinegar: Integra is Trevor's grandmother, while Alexander is a more distant cousin to the both of them. As a result, they both have the last name Belmont rather than their canon last names of Hellsing and Anderson, respectively
Ice Fury: It's mentioned that Rapunzel is Elsa and Anna's cousin.
In an Instant: Suitcase Sam, a suitcase salesman in Beach City, is revealed to be Barney Barton, Hawkeye's brother. He was an excellent archer and a former criminal, but reformed and moved to Beach City.
A major element of the story is various fictional vampires as siblings and part of a private investigation agency. The siblings consist of Lily as the eldest, followed by Alucard, Seras, D, Draculaura, and Sibella.
A human version of Prowl appears in chapter 4 as Tom Dupain's younger brother, making him Marinette's uncle as well.
The Super Smash Bros. fan blog Incorrect Smash Bros Quotes has had multiple examples of this over its run. The most notable are the children of the Palutena Party (a polyamorous relationship between Palutena, Ganondorf, Bayonetta, and Dracula); Palutena and Dracula sired Sothis (making them Seiros/Rhea's grandparents, as well as making Alucard Sothis' half-brother), while Ganondorf has three kids from three different relationships (he had Captain Falcon with Palutena, Joker with Bayonetta, and Hapi with an unknown woman) on top of adopting Chara.
Shizuru of My-HiME and Shizuma of Strawberry Panic! are cousins. This is given special attention in a later chapter, when Natsuki meets Shizuma for the first time, and Shizuma decides to test Natsuki's faithfulness to her cousin.
Iron and Magic: Tony Stark is revealed to be Harry Potter's biological father; James Potter was rendered sterile on a past mission, and he and Lily selected Tony to be a sperm donor as he looked enough like James that most people wouldn't question it.
James I: James Henry Trotter is revealed to be the Squib older brother of James Potter (his parents' deaths were the result of a memory charm intended to give him a chance at a normal life without missing magic). After graduating Hogwarts, James and Lily track down James 'Trotter' and re-establish a relationship with him, leading to James Henry becoming the Potters' secret keeper and thus saving them from Voldemort.
Lydia Twilight (nicknamed "Twilight Sparkle") is the adopted sister of Jonathan Joestar, as George Joestar is a friend of her father and took her in after her father's death. She would later marry Robert Speedwagon, with Shining Armor and Iro "Rainbow Dash" Dashell as their descendants.
Caesar Zeppeli and Jackie "Applejack" Applaine are the parents of Gyro Zeppeli and Hol Horse (with Hol Horse being their third and youngest child), while Rarita "Rarity" Zeppeli is Caesar and Applejack's granddaughter through her father, Gyro and Hol Horse's unnamed brother.
Himari "Fluttershy" Utsukushicho marries Jotaro Kujo and is the mother of Jolyne Kujo and Josefumi Kujo.
Noriaki Kakyoin is the descendant of Izuru Kamakura, the founder of Hope's Peak Academy, through his mother, whose maiden name was Kamakura. This becomes a plot point as Kakyoin exploits his family ties to take control of Hope's Peak Academy from the Steering Committee and become Jojolion'sBig Good.
Wamuu became the father of Rei Ayanami when he met and fell in love with the then-widowed Dr. Naoko Akagi, making Rei a Gigan-Human hybrid instead of one of Yui Ikari's clones.
Downplayed example with Funny Valentine being Narciso Anasui's uncle, as while they are part of the same franchise, Stone Ocean and Steel Ball Run are part of different continuities.
Another downplayed example with Koichi Hirose from Diamond is Unbreakable and Yasuho Hirose from Jojolion, who in the story are cousins. Played straight with Koichi and Yukako's daughter Tsukuyomi, the human version of Princess Luna.
Part 4 Josuke Higashikata is a cousin of both Joshu Higashikata and Shinji Ikari here due to Josuke and Shinji's respective mothers being sisters, while Joshu's father, Norisuke, is their older brother. This means that Yui's husband, Gendo, is Josuke and Joshu's uncle-in-law, while Josuke's wife, Diane "Pinkie Pie" Hanasakura, is their cousin-in-law.
The J-WITCH Series: Season 2 reveals that in this universe, Nerissa is Drago's mother, implying a relationship with Shendu. And Word of God confirms that Nerissa is still Caleb's mother as well as per canon, making him and Drago half-brothers.
Kings and Khans: Tantor is Hathi's son — notably, despite the former being an African elephant and the latter being an Indian elephant, and thus from different species.
Lantern Prime: Primus and Unicron are the Avatars of Hope and Rage, respectively, and as such are family to the other embodiments of emotion from the Green Lantern mythos.
Rebecca 'Newt' Jordan is revealed to be the last living descendant of the Sarah Connor who exists after Terminator Genisys, prompting "Pops" to defend her as though she was his own 'child'.
At the same time, Corporal Dwayne Hicks is revealed to be a descendant of the Kyle Reese who existed in the new timeline, as an Actor Allusion to the fact that Michael Biehn portrayed both characters.
Life as Lily Evans-Potter: Mystique is revealed to have adopted the identity of Lily Evans when she accidentally caused the real Lily's death when Lily was a child; her relationship with James and the decision to fake her death were inspired by Destiny's advice, but, when she meets Harry for the first time after he's allied with the X-Men, she reveals her identity and affirms that she genuinely loved James.
Mad Bond, a crossover between James Bond and Mad Men, reveals that Joan Holloway is Miss Moneypenny's cousin. This is why Joan covers for Moneypenny while she's on vacation.
Tony Stark is Ned Stark's cousin, making him first cousin once removed to the Stark children.
Bruce Banner becomes Bruce Tarth, Brienne's cousin.
Natasha Romanoff becomes Natasha Martell, Oberyn's oldest and only legitimized daughter.
Mystique is the long-lost daughter of Duncan Targaryen, making her Daenerys' first cousin once removed and Jon's first cousin twice removed. Also, Magneto is a Blackfyre, making him a more distant cousin to all three.
Hellboy and Raven of the Teen Titans are half-siblings, with Trigon as their mutual father (although there is such a significant age gap that Raven is raised as Hellboy's daughter rather than his sister, as requested by Raven's mother).
The main premise of the story is that Izuku is Loki's son.
Denki is Thor's son, and by extension, Loki's nephew.
Shinso is descendant of Kevin Thompson/Purple Man/Killgrave.
Morningstar Family Values: Sabrina is Lucifer's daughter conceived during a ritualistic orgy with her parents, neither aware of their connection (and in Lucifer's case, Sabrina's very existence) until her teens.
Mutant Storm starts with Harry finding out Jean Grey is his mother's twin sister and going to live with her and Cyclops.
When Crowley visits Storybrooke, he reveals that his mother Rowena is also Cora's mother, as she fled to this world after teaching Cora her magic, which makes Crowley Cora's half-brother and Regina's uncle.
Tamara is revealed to be the daughter of Dean's old foe, Gordon Walker.
On the Run establishes that Brian O'Connor is a cousin of Chloe Sullivan, justifying his role in her going into witness protection.
"Outgoth the Goth" sees Jade West (Victorious) learn that new school rival Wednesday Addams (The Addams Family) is actually her cousin; Jade's mother is Morticia's sister, but the two had a falling-out years ago as they were both interested in Gomez but Morticia caused a near-fatal accident that left Jade's mother in a coma until after the wedding.
The Parliament of Heroes: The Collector and the Archivists are the children of Mother Night in this series, making them cousins/family to the Endless. In fact, Morpheus (aka Dream of the Endless) is implied to have played a role in The Collector's imprisonment at the hands of The Titan.
Pine Trees And Honeybees: in this Gravity Falls / The Secret World / The Park, it's revealed that the town of Gravity Falls actually used to exist in the alternate reality prior to being destroyed in a catastrophic fire during the early 1900s; as result, it's heavily implied that Lorraine Maillard was actually descended from the Corduroy family, for when Dipper encounters a vision of Lorraine's teenage self, he can't help noticing that she bears an uncanny resemblance to Wendy. In the later chapters, it's also revealed that ruthless theme park tycoon Nathaniel Winter is actually the alternate-universe version of Auldman Northwest, father of Preston and grandfather of Pacifica... and as bad luck would have it, a servant of Bill Cipher.
The Pirate's Soldier: A major revelation is that Heero Yuy is of Juraian descent, with Katsuhito Masaki/Yosho being his maternal grandfather. This connects him by blood to the rest of the Juraian Royal Family, including naturally Ayeka and Sasami.
“Posterity”- part of a trilogy where the Doctor meets the Time Lord who will become his father before the Doctor's birth- reveals that the Doctor's biological mother is Buffy Summers, selected as the Father wanted a strong example of humanity.
"Physics of the Spin" opens with Rory Gilmore (Gilmore Girls) learning that her biological father is Rodney McKay (Stargate Atlantis) rather than Christopher Hayden, as Lorelei was involved with McKay for a week or so when she and Christopher were on a break and McKay was in Hartford on an exchange trip.
RogersVerse: Rick Castle's mother Martha Rodgers is the secret daughter of Steve Rogers and Peggy Carter, who took her father's surname as her stage name (with a slight spelling difference). When Steve awakes from the ice and goes to Martha's play, Martha reaches out to him, since Steve went under the ice before he even knew of Martha's existence.
RWBY Zero: Arturia Pendragon is Jaune Arc's mother, having married his father following the Fourth Grail War. This also makes him Mordred's half-brother, which comes into play when he summons her during the next Grail War.
Spellbound: After the Grangers are killed in a car accident, Hermione (Harry Potter) discovers that Tony Stark (Marvel Cinematic Universe) is her biological father; Obadiah Stane paid her mother to keep her existence secret from Tony, Tony speculating that Obadiah's intention was to bring Hermione in to be a figurehead of the company if he had genuinely died in the original ambush.
The Swarm of War: It's strongly implied that the Tyranids are the descendants of another Zerg group which got sucked into Warhammer 40,000 universe in the same incident, but into another time and place.
In the Stargate SG-1/Farscape crossover Syndication, not only are John Crichton and Cameron Mitchell cousins, but it turns out that Aeryn Sun and Vala Mal Doran are half-sisters, as Talyn's death was faked and he stumbled on a wormhole that led him into Goa'uld space.
Titania Falls: Erza Scarlet is the mother of Dipper and Mabel Pines.
In Transposition F, it's implied that not only are the humans of Earth from Dragon Ball and Remnant are the same species, but due to the wording of Dende's wish to send Frieza and the heroes away, namely wishing they would be sent to where the humans came from, Remnant is the birthplace of all humans.
In the Once Upon a Time/Descendants crossover Villains and Happy Endings, Regina is actually the daughter of Cora and Rumpelstiltskin, which leaves Gold horrified when he learns that he put his own daughter through such a brutal training regime.
What's in a Name and its sequels operate on the idea that Buster Bunny is Bugs Bunny's biological son. The two keep it secret because Buster doesn't want to be accused of trading on Bugs' name, and doesn't want friends (Plucky) bugging him for favors. Later in the series it's revealed another Toonster has a famous classical relation, namely Shirley the Loon being Daffy Duck's daughter.
What Insertion?: Azusa Shiratori and Shiho Miyano are revealed to be cousins, something which is a bit of a bombshell in-universe. On an occasion when Azusa accidentally broke up a Black Organization operation just by being herself, this results in Sherry becoming both respected and feared by the B.O.'s lower-ranked members.
Winter's Child has Harry Potter instead living with his maternal great-grandfather James "Bucky" Barnes; Bucky unknowingly impregnated a girl before he shipped out, and once Dumbledore determined that Harry had another relative he was able to track down Bucky and free him from Hydra's control.
A Witching Happiness: Mildred's family tree reveals that her father is Alec Trevelyan (GoldenEye, although in a new continuity that makes reference to Spectre), with Mildred and Alec being shocked to learn about the other's lives but quickly settling into a father-daughter dynamic.