In the early hours of her first school day, Mary (Mckenna Grace) is far from enthusiastic about leaving the comfort of her home. She wishes that Frank (Chris Evans) could continue homeschooling her, but he insists that she must gain new experiences through social interaction. As he sees Mary off, he is approached by Roberta (Octavia Spencer), his landlady and a close friend, who expresses her deep concern. She urges him to fetch Mary before it’s too late, fearing that her extraordinary talents will attract unwanted attention and potential separation from him. Frank reassures her that Mary requires friendships and social skills, but Roberta remains unconvinced.
At school, Mary quickly finds herself disinterested as Bonnie (Jenny Slate), her teacher, drones on about basic arithmetic. Unable to endure the mundane lesson, Mary speaks up about the lack of challenge. When Bonnie attempts to discipline her by presenting a series of increasingly complex math problems, Mary's brilliance shines through, as she answers them all effortlessly. Following recess, the Principal observes Bonnie's class and upon introduction, Mary boldly questions if she’s "the boss." She then demands that the Principal contact Frank immediately to have her removed from the class. When Frank arrives to pick her up, Bonnie tries to speak with him, suggesting that Mary could be a gifted child. Frank dismisses the notion, attributing her success to simple algorithms he's taught her.
Bonnie delves deeper and uncovers Mary’s background, learning that her mother, Diane, was a mathematical prodigy working on a Millennium Prize problem before her tragic death. This revelation prompts Bonnie to confront Frank at his usual bar, where he reveals a heart-wrenching family history—Diane had shown up unexpectedly with baby Mary, seeking help before ultimately taking her own life shortly after. Frank has cared for Mary ever since.
One day, Mary witnesses bullying on the school bus and bravely intervenes, delivering a decisive blow to the older bully. This incident leads to a meeting with the Principal, who proposes a gifted school opportunity for Mary. However, Frank declines, believing that a normal childhood is paramount. Subsequently, the Principal reaches out to Evelyn (Lindsay Duncan), Frank’s estranged mother and Mary’s grandmother, who arrives at Frank's doorstep with an air of entitlement, eager to take Mary away.
Evelyn’s arrival stirs tension, as she criticizes Frank's lifestyle and expresses her controlling nature. When Frank refuses to allow her to take Mary to Boston, Evelyn resorts to legal action. Their court battles uncover deep-rooted resentment; Evelyn laments Diane's perceived weakness and harbors bitterness towards Frank for abandoning his academic career. Although Frank doesn't confront her directly, he insists that her motives threaten Mary’s happiness. Through the turmoil, Roberta steadfastly supports Frank, while Frank's lawyer negotiations seem promising. Yet, as the situation intensifies, Evelyn proposes to place Mary in foster care near Frank, forcing him to grapple with his insecurities and guilt.
Frustrated and infuriated by the situation, Mary refuses to see Frank after he leaves her with the foster family, despite her heartfelt pleas. Dejected yet determined, Frank learns from Bonnie that the foster family has put Mary’s cherished one-eyed cat up for adoption. He rushes to save the cat and, surmising Evelyn's allergic reaction, confronts her at the foster home. Upon arrival, Mary tries to flee, so Frank tracks her down, seeking forgiveness. In a touching reunion, Mary embraces him and is overjoyed to learn her cat is safe back at Frank’s house.
Returning to the guest house, Roberta takes Mary to the car while Frank confronts Evelyn about a vital discovery—the completed proof for the Millennium Prize problem that Diane had been working on. Evelyn, skeptical, questions Frank's claims, but he reveals that Diane had instructed him to wait until after her mother's death to publish the findings. He offers Evelyn a choice: publish the proof and leave Mary alone, or he would refrain from sharing it until after her own death. Faced with this heartbreaking ultimatum, Evelyn reluctantly agrees.
In the end, Mary finds balance, attending university classes in the mornings and elementary school in the afternoons, while Frank and Bonnie share a warm glance, signifying hope and connection amidst the challenges they’ve faced.
