As she works on her memoir in the present day, successful middle-aged cartoonist Alison Bechdel recalls two time periods in her life. The first is her childhood, around age 10 (Small Alison), when she struggles against her father Bruce's obsessive demands and begins to identify her inchoate sexuality. The second is her first year in college (Medium Alison), when she begins her first relationship and comes out of the closet as a lesbian.
Alison remembers herself, as a child, demanding that her father play "airplane" with her, while Bruce sorts through a box of junk and valuables he has salvaged from a barn ("It All Comes Back"). Bruce tells the family that a visitor from the local historical society is coming to see their ornate Victorian home that he has restored, and his wife Helen prepares the house to Bruce's demanding aesthetic standard ("Welcome to Our House on Maple Avenue"). In a phone call with her father and a journal entry, Medium Alison expresses her anxiety about starting college ("Not Too Bad"). At the Bechdel Funeral Home, Small Alison and her brothers John and Christian hide in caskets while Bruce talks to Pete, a mourning young man. The children perform an imaginary advertisement for the funeral home ("Come to the Fun Home"). Medium Alison hesitates outside the door of the college's Gay Union, and is flummoxed when she meets Joan, a confident young lesbian. Bruce invites into the house Roy, a young man whom he has hired to do yard work. Bruce begins to seduce Roy in the library while Helen is playing the piano upstairs, trying her best to ignore it ("Helen's Etude").
Medium Alison writes a letter to her parents but does not mention Joan or the Gay Union. Bruce orders Small Alison to put on a dress, but she would rather wear a jean jacket. Bruce tells her that she would be the only girl without a dress and that the other children would laugh at her; she leaves on the dress ("Party Dress"). Medium Alison proudly tells Joan that she has written a letter to her parents telling them that she is a lesbian, but begins to second-guess herself (beginning to wonder if she's asexual) until Joan kisses her. That night, she is excited and joyful at having had sex with Joan ("Changing My Major").
Alison considers the connection between her coming out and her father's death. Small Alison has a homework assignment to draw a map of places her family has lived, but Bruce aggressively takes over, drawing it the way he thinks it should look. Alison realizes that despite having traveled and lived in Europe, her father's place of birth, life, work and death can all be placed in a small circle in Beech Creek, Pennsylvania ("Maps"). Bruce offers a ride and a beer to an underage boy, and it is later implied that they had sexual intercourse. Medium Alison writes to her parents, asking for a response to her coming-out letter. Small Alison watches The Partridge Family, but Bruce switches it off. Small Alison talks to him, and finds out that he is going to see a psychiatrist because he is "bad" and not good like her. Alison expresses annoyance that he lied to her; the actual reason he was going was because he was arrested for what he did to the underage boy. Helen tells Small Alison that the psychiatrist will help her father, and attempts to reassure her. Bruce starts a vicious argument with Helen and breaks several of her possessions along with some library books. Small Alison fantasizes about her family as the happy family singing together on television ("Raincoat of Love").
Alison remembers a time when Bruce took her and her brothers to New York City and stayed in a borrowed Greenwich Village apartment. After a long day, Small Alison, Christian and John settle into sleeping bags. Small Alison wakes up and catches Bruce sneaking out. Bruce sings a lullaby ("Pony Girl"). He reassures his daughter that he's just going out for a paper, but he leaves to go cruising. Medium Alison is angered by a noncommittal letter from Bruce, responding to her coming out. At a luncheonette with her father, Small Alison notices a butch delivery woman and feels an inexplicable kinship with her ("Ring of Keys").
Medium Alison calls home to demand a fuller response from her parents and is astonished when her mother tells her that her father has had sexual relationships with men and boys. Alison explores the tensions her family was under at this time and watches a heated argument between her parents. Medium Alison returns home for vacation with Joan in tow. Helen confesses to Medium Alison her devastation at spending her life in an unfulfilling marriage with Bruce ("Days and Days"). Medium Alison, Joan and Bruce have an unexpectedly pleasant evening around the piano. Bruce asks Alison if she'd like to go for a drive, and (adult) Alison realizes that Medium Alison is gone; she joins her father in the car, breaking the boundaries of time. On the drive, she and Bruce struggle to express themselves to each other ("Telephone Wire").
Bruce, manically engaged in a new restoration project, tries and fails to find a way to hold his life together. He steps in front of a truck and is killed ("Edges of the World"). Alison, newly reconciled to her past, remembers and draws a moment of perfect balance: playing "airplane" with her father, while reminiscing about the past with the other Alisons ("Flying Away").