On the night of June 1, six-year-old Brant Elliott hides under his bed after his father wakes him in a frenzy, hands him a phone to dial 9-1-1, and orders him to stay upstairs. His father's final words are "Cover your ears." Brant hears a gunshot. Unable to wait until morning, he goes downstairs and discovers his mother, Caroline, strangled with his father's work tie and his father dead from a self-inflicted gunshot wound. Emergency responders find Brant clinging to his mother's body. He blames himself because he had wished for a baby sister and believes the wish cost him his parents.
Caroline had written the Bailey family, her neighbors, into her will as Brant's guardians. Brant's Aunt Kelly, Caroline's sister, brings him to the Bailey home, where he joins his best friend, Theo Bailey, and Theo's parents, Samantha and Andrew. There he meets eleven-week-old June Bailey, born on June 1, the same date his parents died. Brant initially resists liking June, fearing she represents his traded wish. But when she cries at night, he brings her his own stuffed elephant. She clutches it and calms, and they name the toy "Aggie." When June grips his pinkie through the crib slats, Brant feels a sense of belonging for the first time since losing everything.
As the children grow, Brant refuses to see the Baileys as his family, insisting he is Caroline and Lucas Elliott's child. At eight, he nicknames June "Junebug." Samantha begins singing him "Over the Rainbow," a lullaby Caroline once sang him, and Brant eventually adapts the song for June. At June's first dance recital, the four-year-old freezes with stage fright. Brant tells her she just needs to be brave the first time, and the other times come easy. She performs beautifully and never stops dancing.
On Halloween night, a classmate retells the story of Brant's parents' murder in front of six-year-old June. Brant flees the family tree house in distress, and the other children follow, leaving June alone. She tries to climb down, falls, and breaks her arm. Brant blames Theo, shoves him, then immediately regrets his violence and vows never to react that way again.
At twelve, Brant saves Christmas Eve by cooking a feast during a blizzard. He and Andrew stay up all night carving June a wooden sword from the old tree house lumber. The family gives Brant a photo ornament of him as a child with his mother.
At eighteen, Brant rescues twelve-year-old June after neighborhood bully Wyatt Nippersink and his older friends pressure her onto a frozen pond. The ice cracks and June plunges into the frigid water. Brant dives in and pulls her out. Both are hospitalized.
As June enters her teenage years, Brant struggles with feelings he cannot accept. He begins an on-again, off-again relationship with Wendy Nippersink, Wyatt's sister, that lasts nearly eight years. When Wendy tells him the way he and June interact looks romantic, Brant is furious. That night he has a sexually explicit dream about June and, horrified, drives to Wendy's apartment to sleep with her. After seventeen-year-old June crawls into his bed for comfort and they fall asleep entwined, Brant wakes horrified by his own arousal and breaks up with Wendy for good.
At sixteen, June attends a party at Wyatt's house, where he manipulates her into his bedroom and makes crude advances she stops before they go far. Brant storms to Wyatt's house, and they fight violently before Brant lets go, refusing to become his father. He returns home and reconciles emotionally with June, calling her "Junebug" for the first time in weeks.
On June's eighteenth birthday, she drives Brant to his mother's grave for the first time. He breaks down, shouting at Caroline for breaking her promise to protect him. June reveals that Caroline kept her promise by writing the Baileys into her will, ensuring Brant would have a loving home. That night, Brant fully acknowledges to himself that he is in love with June.
At June's senior prom, her friends dare her to kiss Brant, and the kiss escalates into a passionate encounter. Theo, now a police officer on patrol with his partner Kip, witnesses the kiss and beats Brant. A radio call summons them to a car accident, where a vehicle careens into the wreckage. Theo shoves Kip to safety and is crushed between two cars. In his dying moments, Theo forgives Brant and asks that a message be delivered: Tell Brant it is okay, and to take care of "Peach," their childhood nickname for June. Brant, who drove through the accident scene after fleeing prom, witnesses Theo's death and returns to tell June, who collapses and has her first asthma attack.
In the aftermath, June clings to Brant, terrified of losing him. When she claims the prom kiss was just a dare, Brant snaps, declaring he is not her brother. He moves out of the Bailey home a month later, believing his presence prevents June from healing.
At nineteen, June moves into Brant's apartment. After Andrew's birthday dinner, where June dances for the first time since Theo's death, a tickle fight escalates into a sexual encounter. Brant discovers June is a virgin; she has been saving herself for him. They begin a secret relationship. His boss, Pauly Marino, offers him a chef position in Seattle, but Brant declines.
Andrew and Kip arrive one morning and find Brant and June in bed together. Andrew books June a one-way flight to New York. Guided by a dream of Theo, who tells her that pursuing her career and loving Brant are not mutually exclusive, June decides to leave. She and Brant share an agonizing goodbye. June covers Brant's ears, echoing his father's last words, and whispers everything she cannot bear for him to hear: that she wants to marry him, have children, and build a life together. When he asks what she said, she lies.
During their years apart, both heal independently. June thrives in New York, performing in Broadway's
The Lion King. Brant reconnects with Aunt Kelly, who reveals that "Brant" means "sword." June tracks down Bubbles, Brant's childhood elephant that was lost the night of his parents' deaths, which Kelly had cleaned and stored for twenty years, and ships the toy to Brant with a poem.
Two years after the fallout, Andrew visits Brant. He says he is done being angry and done losing his family, embraces Brant, calls him "Son," and tells him to go to New York. Brant accepts Pauly's chef position at his Manhattan restaurant and surprises June backstage at her show. They reunite and begin building a life together.
Brant proposes beneath a rainbow in Central Park, and June reveals she is pregnant. They marry on Pauly's horse farm. A seat of honor holds Aggie, Bubbles, Theo's framed photograph, and his police badge. A bluebird is released into the sky.
In the epilogue, thirty-six-year-old Brant lives with June and their two children: Theodore Andrew, named after Theo and Andrew, and Caroline, named after Brant's mother. He continues Samantha's tradition of recording family moments on index cards. On June's thirtieth birthday, the family shares pizza on the bedroom floor. Brant realizes he no longer fears his last moments, because every last will be with them.