When the story begins, Lily Bloom is sitting on the roof of a building in Boston, gazing out at the city and the stars and reflecting on death. She recently returned from her father’s funeral. She’s thinking about how much she resents her father for assaulting her mother when a man joins her on the roof and begins aggressively kicking a patio chair. The man, Ryle Kincaid, is a neurosurgeon, and the two begin to flirt and share increasingly personal “naked truths.” Ryle admits that he lost a kid patient after the boy’s sibling inadvertently shot him. Lily tells Ryle that she delivered the eulogy at her violent father’s funeral and couldn’t think of anything decent to say, so she stood there for two minutes in deliberate quiet. Lily also informs Ryle that she lost her virginity to a homeless boy named Atlas. Ryle tells Lily that he wants to sleep with her, but he only has one-night stands and does not want to marry or have children. Though Lily is attracted in Ryle, she cannot envision having sex without developing a relationship.
Six months later, Lily uses her inheritance to purchase a storefront that she plans to transform into a flower business. A woman called Allysa volunteers to work with Lily, and the two quickly become friends. Lily and Allysa are cleaning up the shop when she slips and injures her ankle. Allysa asks her husband Marshall and her brother for assistance. When Allysa’s brother comes, Lily recognizes Ryle. They pretend not to know one other for Allysa’s sake, but Ryle admits to Lily that he still wants to sleep with her. They believe they should avoid each other since their desires diverge. Lily reads her adolescent journals, which she wrote as letters to Ellen DeGeneres, as she heals from her sprained ankle for a week. They relate the narrative about Atlas and Lily.
As a teenager, Lily discovers a boy living in an abandoned house behind hers. She feels for Atlas and starts leaving him food, lending him her father’s clothes, and allowing him to shower at her place. When Lily’s father harms her and her mother, Atlas becomes her confidant and protector, and the two grow closer and fall in love. They watch Ellen and Finding Nemo together and advise each other to “just keep swimming” when things get rough, repeating a line from the film. Atlas discovers that a family relative in Boston can house him, and despite Lily’s reservations, Atlas relocates to pursue more stability. She’s distraught, but he returns on her sixteenth birthday. He offers her a magnet that reads, “Everything is better in Boston.” They are making love for the first time. Atlas vows to come for Lily when he believes his life is suitable for her. Then Lily’s father comes in on them. He violently beats Atlas with a baseball bat. An ambulance transports Atlas away. This is the last time Lily sees Atlas, and she has always wondered why Atlas never returned for her.
Back in the present, Ryle follows Lily, and after attempting to get her to have sex with him, he acknowledges he has emotions for her. Lily urges that they avoid sex and instead attempt dating since she does not trust him to be in a relationship with her. They rapidly fall for one other. After a few dates, Ryle invites himself to supper with Lily and her mother. At supper, Lily notices Atlas working at the restaurant. She’s astonished. During a brief talk, Atlas informs Lily that he has a girlfriend but wishes they had met a year ago. Lily does not inform Ryle about her encounter with Atlas and avoids returning to the restaurant. When Ryle and Lily are hanging out one night, Ryle burns himself on a casserole dish that he attempts to remove from the oven without a glove. When Lily laughs, Ryle pushes her, and she smacks her head. She is bleeding, terrified and sad, and she is instantly concerned that she has become her mother. He promptly apologizes, and she finally forgives him, promising that if anything violent happens again, she would leave him.
They celebrate Allysa and Marshall’s pregnancy with supper at the same restaurant where Atlas works. Atlas approaches the table, and the waiter introduces him as the chef. Atlas observes Lily and Ryle’s injuries and suspects Ryle is to blame. When they’re alone, Atlas instructs Lily to leave Ryle. When she refuses, he compares her to her mother. Ryle sees them together and discovers that the chef is Atlas, the boy from Lily’s past. When it comes to blows, Atlas tosses Ryle out of his eatery. Lily tells Ryle that there is nothing going on between her and Atlas. They enjoy a time of tranquility and plan to marry in Las Vegas. Ryle’s envy, however, continues to stew. When Ryle realizes Atlas has given Lily his phone number, he becomes enraged and knocks her down the stairs. She sustained serious injuries. When Allysa learns what occurred, she pushes that Ryle inform Lily about his background. He admits that, like the young kid he lost the night they met, his brother died from a gunshot wound when Ryle accidently shot him. He identifies this as the source of his fury. Lily forgave him, and they strive to reconcile.
Allysa and Marshall have a kid and name her Ryle. The night Rylee is born, Lily returns home to find Ryle in a peculiar mood. He has her read a newspaper item in which Atlas references a woman who is precious to him and explains that the name of his restaurant (Bib’s) means “better in Boston.” Ryle holds the magnet in his palm and has read through all of Lily’s adolescent writings. He attempts to rape Lily and headbutts her so hard that she passes out. She phones Atlas to come get her, and he brings her to the hospital, where she learns she is pregnant. She takes her time deciding what she wants out of life, puzzled by her feelings for Atlas as well as her mixed sentiments of fury, love, and hurt for Ryle. She gradually brings Ryle back into her life in a platonic way, telling him about the baby, but she’s not sure what she wants from him.
When the child is born, Lily and Ryle name her Emerson, after Ryle’s brother. Lily says she wants a divorce because she never wants her kid to go through what she and her mother went. Ryle agrees, but is upset about it. They share custody of Emerson. One day, Lily runs into Atlas. He claims his life is good enough for Lily for now, and if she ever wants to fall in love again, he’ll be there for her. She says she is ready, and they hug. He tells her she can stop swimming.
after a tumultuous relationship marked by love and violence, Lily decides to divorce Ryle to protect their daughter, Emerson, from experiencing the same cycle of abuse she endured. She reconnects with Atlas, who reassures her that his life is now stable and ready for a future together. Embracing the possibility of new love, Lily and Atlas share a heartfelt moment, symbolizing hope and healing.