When Henry was born, he was given away as a baby by Emma Swan, who felt that she could not be his mother and give him the life he needs. Henry was put into adoption, and was nearly adopted by John and Michael Darling, until he was adopted by the mayor of Storybrooke, Regina Mills, who raised Henry as her own son.
Ten years later, Henry runs away to Boston, where he manages to find the apartment of his biological mother Emma. Emma takes him back to his home in Storybrooke, Maine with the intentions of not seeing her son again. However, when she becomes concerned about his well-being when his adoptive mother Regina begins showing ill-tempered traits towards Emma, she decides to stay for a while. Henry knows about the Enchanted Forest and the Dark Curse due to a mysterious storybook in his possession, and tries to get Emma to believe as well. When Regina bakes a poisoned apple turnover - with a Sleeping Curse embedded in it - and gives it to Emma, Henry eats it instead and falls under the curse. He is rushed to the hospital, but is eventually declared dead. Distraught and heartbroken, Emma and Regina rush to his side, and Emma kisses Henry on the forehead which both wakes Henry up and breaks the Dark Curse. With everyone's memories back, Regina tells Henry that despite what people will tell him, she does love him, before fleeing to her house where she laments losing Henry.
When the first Dark Curse is broken, Rumplestiltskin cashes in on the favour that Emma owes him, stating that the favour will be Emma helping Rumplestiltskin locate his son, who apparently is in Manhattan. Henry comes along as well, and all three of them go to Manhattan, where they discover that Rumplestiltskin's son Baelfire is also Henry's father, who went under the alias Neal Cassidy while dating Emma. This shocking revelation prompts Rumplestiltskin recalls a prophecy that a seer once told him, that a young boy would lead him to Bae, but that young boy will be his undoing. Suspecting his newfound grandson Henry, Rumplestiltskin contemplates killing him. However, when Henry is kidnapped by Tamara and Greg and taken through a portal to Neverland, Rumplestiltskin goes with Emma, Regina, Snow, David and Hook on his ship and follows them to Neverland.
In Neverland, it is revealed that Tamara and Greg have been inadvertently working for the Lost Boys. Realizing they had been tricked, Tamara and Greg refuse to hand over Henry, until Peter Pan's shadow arrives and kills Greg, while the Lost Boys shoot Tamara with arrows. Henry manages to run away, before running into a teenage boy who claims to be a fugitive running from the Lost Boys. However, when the fugitive boy takes Henry back to the Lost Boys, it is revealed that the "fugitive" is actually the leader of the Lost Boys, Peter Pan. Pan tells Henry that magic is dying in Neverland, and shows him a sickly girl named Wendy, claiming that her illness is apart of the aftermath of Neverland losing magic, stating that only the "heart of the truest believer" can save it, with the truest believer being Henry. Henry eventually willingly gives his heart to Pan, apparently killing Henry. It is revealed that the real reason Pan wanted Henry's heart was to become immortal forever. However, Regina manages to take Henry's heart out of Pan's body and return it to Henry. Pan swaps bodies with Henry, before Pan's body - inhabited by Henry - is sucked into Pandora's Box by Rumplestiltskin, who is revealed to be Peter Pan's son. Pan, in Henry's body, plans to re-enact the Dark Curse to make Storybrooke "the new Neverland".
He manages to cast the Dark Curse, before Rumplestiltskin uses the Black Fairy's wand to switch their bodies back. However, since Pan's body is outside Pandora's Box, he manages to defeat Rumplestiltskin. It isn't until Rumplestiltskin realizes that the boy who would be his undoing is Pan, when he then uses the Dark One's dagger to stab himself and Pan at the same time, exploding into light which incinerates Pan. With the second Dark Curse billowing through town, Regina allows Emma and Henry to escape Storybrooke with new memories. One year later, Henry - who doesn't have his memories - returns to Storybrooke with Emma, whose memories had been restored by Hook. Storybrooke had been restored due to a mysterious third Dark Curse, but it isn't until Henry's memories are restored through his old storybook and Regina kisses him on the forehead, which breaks the third Dark Curse. Snow and David also have a new son whom they name Neal, who is Henry's uncle.
After Regina distances herself from everyone, Henry becomes upset and goes to Regina's house, where they hug. Henry decides to help Regina discover the author of the storybook, and call their mission "Operation Mongoose". Since Rumplestiltskin has found his happy ending, he presumes that Rumplestiltskin must have made the author change his fate, and decides to go undercover and work at his pawnshop, although he ends up just doing chores. When Geppetto gives Regina some of Pinocchio's belongings, Henry goes through it. He finds a piece of paper with a drawing of a door, with a mentioning of the mysterious Author. Pinocchio says The Author is trapped in the book. Henry finds the key in the Sorcerer's mansion, and they manage to free the Author, who flees the scene. Cruella De Vil uses Pongo to lure Henry into an alleyway, where she abducts him and holds him at ransom, demanding that Emma and Regina kill the Author. Henry's mothers search for him, and Emma finds Cruella holding Henry at gunpoint. Fearing for her son's life, Emma uses her magic to blast Cruella off the cliff, killing her. Henry manages to stop the Author from permanently changing reality, and becomes the next Author himself. However, Henry decides nobody should have that power, breaking the pen.
When Emma absorbs the Darkness from Rumplestiltskin and becomes the new Dark One, Henry and the other heroes manage to get to the Enchanted Forest via cyclone, where they find Emma. They are all then greeted by King Arthur, who invites them to Camelot. However, six weeks later, they return to Storybrooke with no memories of their time in Camelot. Henry meets Violet, and develops a crush on her. When the Darkness is taken from both Emma and Hook, who also became the Dark One, the process causes Hook's death. Henry is among those who venture with Emma into the Underworld to retrieve Hook. However, their quest is all for nought and they leave the Underworld, having failed to resurrect him. Zeus resurrects Hook due to his part in Hades' defeat. Henry and Violet briefly try to destroy magic, although they are later convinced to abandon their plans.
When Emma starts receiving visions of her own demise, Henry starts blaming himself for bringing her to Storybrooke to become the Savior in the first place. He shares his guilt with Jasmine, who feels guilty for making Aladdin become the Savior of Agrabah, and later apologizes to Emma, who dissuades Henry from blaming himself. Henry starts becoming weary of Hook, until they are both briefly kidnapped by Hook's brother Liam. When Henry starts to fear Violet has lost interest in him, she is quick to quell his doubts. After Gideon, the hooded figure destined to kill Emma, arrives in Storybrooke, Henry's Author powers start taking over him, as they can sense the upcoming final chapter of the story – the final battle. Henry is later asked by Killian to be the best man at his and Emma's upcoming wedding, and Henry is put in charge of the wedding rings. At Emma and Killian's wedding, however, they are all consumed by Fiona's curse. Under the curse, Henry is Fiona's adopted son, although he remembers everything. The curse is broken when Henry gives Emma true love's kiss.
- Peter Pan (deceased great-grandfather)
- Fiona (deceased great-grandmother/cursed adoptive mother)
- Cora Mills (deceased step great-great-grandmother/adoptive grandmother)
- Henry Mills Sr. (deceased step great-great-grandfather/adoptive grandfather)
- Xavier (step great-great-great-grandfather/adoptive great-grandfather)
- the Miller (step great-great-great-grandfather/adoptive great-grandfather)
- Regina Mills (step great-grandmother/adoptive mother)
- Emma Swan (mother)
- Cinderella Mills (wife)
- Lucy Mills (daughter)
- Baelfire (deceased father)
- Killian Jones (stepfather)
- Rumplestiltskin (paternal grandfather)
- Belle (step grandmother)
- Colette (deceased step great-grandmother)
- Maurice (step great-grandfather)
- Drizella Tremaine (stepsister-in-law)
- Milah (deceased paternal grandmother)
- David Nolan (maternal grandfather)
- Snow White (maternal grandmother)
- Eva White (deceased great-grandmother)
- Leopold White (deceased great-grandfather)
- Ruth Nolan (deceased great-grandmother)
- Robert Nolan (deceased great-grandfather)
- James (deceased great-uncle)
- Neal Nolan (uncle)
- Robyn (step great-cousin/adoptive cousin)
- Gideon (uncle)
- Zelena Mills (step great-aunt/adoptive aunt)
- Henry is named after Regina's father, Henry.
- Like his mother and grandmother, Henry enjoys cinnamon in his hot cocoa.
- His middle name, Daniel, is named after Daniel Colter, Regina's first love, who was killed by Cora.
- Henry's birthday is on August 15th, which means that he is a Leo.
- This is shown when Regina types in "815" as her password - she allegedly uses Henry's birthday for all her passwords.
- S1, E01: "Pilot"
- S1, E02: "The Thing You Love Most"
- S1, E03: "Snow Falls"
- S1, E04: "The Price of Gold"
- S1, E05: "That Still Small Voice"
- S1, E06: "The Shepherd"
- S1, E07: "The Heart is a Lonely Hunter"
- S1, E08: "Desperate Souls"
- S1, E09: "True North"
- S1, E10: "7:15 A.M."
- S1, E11: "Fruit of the Poisonous Tree"
- S1, E12: "Skin Deep"
- S1, E13: "What Happened to Frederick"
- S1, E15: "Red-Handed"
- S1, E16: "Heart of Darkness"
- S1, E17: "Hat Trick"
- S1, E18: "The Stable Boy"
- S1, E19: "The Return"
- S1, E20: "The Stranger"
- S1, E21: "An Apple Red as Blood"
- S1, E22: "A Land Without Magic"
- S2, E01: "Broken"
- S2, E02: "We Are Both"
- S2, E03: "Lady of the Lake"
- S2, E04: "The Crocodile"
- S2, E05: "The Doctor"
- S2, E07: "Child of the Moon"
- S2, E08: "Into the Deep"
- S2, E09: "Queen of Hearts"
- S2, E10: "The Cricket Game"
- S2, E11: "The Outsider"
- S2, E12: "In the Name of the Brother"
- S2. E13: "Tiny"
- S2, E14: "Manhattan"
- S2, E15: "The Queen is Dead"
- S2, E16: "The Miller's Daughter"
- S2, E17: "Welcome to Storybrooke"
- S2, E18: "Selfless, Brave and True"
- S2, E19: "Lacey"
- S2, E20: "The Evil Queen"
- S2, E21: "Second Star to the Right..."
- S2, E22: "...And Straight On 'Til Morning"
- S3, E01: "The Heart of the Truest Believer"
- S3, E03: "Quite a Common Fairy"
- S3, E04: "Nasty Habits"
- S3, E05: "Good Form"
- S3, E07: "Dark Hollow"
- S3, E08: "Think Lovely Thoughts"
- S3, E09: "Save Henry"
- S3, E10: "The New Neverland"
- S3, E11: "Going Home"
- S3, E12: "New York City Serenade"
- S3, E13: "Witch Hunt"
- S3, E14: "The Tower"
- S3, E15: "Quiet Minds"
- S3, E16: "It's Not Easy Being Green"
- S3, E17: "The Jolly Roger"
- S3, E19: "A Curious Thing"
- S3, E20: "Kansas"
- S3, E21: "Snow Drifts"
- S3, E22: "There's No Place Like Home"
- S4, E01: "A Tale of Two Sisters"
- S4, E02: "White Out"
- S4, E03: "Rocky Road"
- S4, E04: "The Apprentice"
- S4, E05: "Breaking Glass" (photograph)
- S4, E06: "Family Business"
- S4, E07: "The Snow Queen"
- S4, E08: "Smash the Mirror"
- S4, E09: "Fall"
- S4, E10: "Shattered Sight"
- S4, E11: "Heroes and Villains"
- S4, E12: "Darkness On The Edge Of Town"
- S4, E13: "Unforgiven"
- S4, E14: "Enter The Dragon"
- S4, E15: "Poor Unfortunate Soul"
- S4, E16: "Best Laid Plans"
- S4, E17: "Heart Of Gold"
- S4, E18: "Sympathy For The De Vil"
- S4, E19: "Lily"
- S4, E20: "Mother"
- S4, E21: "Operation Mongoose, Part One"
- S4, E22: "Operation Mongoose, Part Two"
- S5, E01: "The Dark Swan"
- S5, E02: "The Price"
- S5, E03: "Siege Perilous" (flashback)
- S5, E04: "The Broken Kingdom" (flashback)
- S5, E05: "Dreamcatcher"
- S5, E06: "The Bear and the Bow"
- S5, E08: "Birth" (flashback)
- S5, E10: "Broken Heart"
- S5, E11: "Swan Song"
- S5, E12: "Souls of the Departed"
- S5, E13: "Labor of Love"
- S5, E14: "Devil's Due"
- S5, E15: "The Brothers Jones"
- S5, E16: "Our Decay"
- S5, E17: "Her Handsome Hero"
- S5, E18: "Ruby Slippers"
- S5, E19: "Sisters"
- S5, E20: "Firebird"
- S5, E21: "Last Rites"
- S5, E22: "Only You"
- S5, E23: "An Untold Story"
- S6, E01: "The Savior"
- S6, E02: "A Bitter Draught"
- S6, E03: "The Other Shoe"
- S6, E04: "Strange Case"
- S6, E05: "Street Rats"
- S6, E06: "Dark Waters"
- S6, E07: "Heartless"
- S6, E08: "I'll Be Your Mirror"
- S6, E09: "Changelings"
- S6, E10: "Wish You Were Here"
- S6, E11: "Tougher Than The Rest"
- S6, E12: "Murder Most Foul"
- S6, E14: "Page Twenty-Three"
- S6, E15: "A Wondrous Place"
- S6, E16: "Mother's Little Helper"
- S6, E17: "Awake"
- S6, E18: "Where Bluebirds Fly"
- S6, E19: "The Black Fairy"
- S6, E20: "The Song in Your Heart"
- S6, E21: "The Final Battle, Part One"
- S6, E22: "The Final Battle, Part Two"
- Bk 1: "Reawakened"