Noah Sweetwine and his twin sister, Jude, are thirteen years old. Noah, a burgeoning artist, has trouble socializing and often retreats to the “invisible museum” inside his mind—a space where he imagines portraits of himself and others in order to process what’s happening around him. Noah and Jude are extremely close, a comfort in the face of the many arguments that arise between their whimsical art-professor mother, Dianna, and practical research-scientist father, Benjamin. Noah and Jude can practically read each other’s minds, and have a hard time playing rock-paper-scissors because they always pick the same symbols. Noah and Jude’s relationship is tested, though, when Dianna decides that she wants to start preparing the twins for admission to the prestigious local art school, CSA—and Jude’s jealousy of Noah’s talent causes her to sabotage his application.
Three years later, Jude, now sixteen, is a student at CSA—but Noah is not, and has in fact fallen in with Jude’s old popular friends. Noah doesn’t make art anymore, while Jude has grown eccentric through her obsession with the deceased Grandma Sweetwine’s “bible” of superstition, lore, and aphorisms. The withdrawn Jude has shorn off her long blonde hair and dresses in baggy clothes—she carries onions in her pocket and adorns herself with strange talismans meant to ward off bad luck, evil spirits, and boys. Since Dianna’s death, Jude has sworn off men—and has cobbled together a halfhearted artistic practice, though she is convinced that Dianna’s ghost destroys every clay sculpture she makes. On the brink of expulsion, Jude has an idea—she decides to make an indestructible stone sculpture as a way of communicating with Dianna. Though there’s no carver in residence at CSA, there is someone in town who could help—the “rock star” of the sculpture world, Guillermo Garcia. Jude looks Garcia up on the internet and is impressed by his enormous carvings. She hunts him down at his studio, stopping at a church along the way. In the church, she meets an attractive older teen—an English guy who flirts with Jude and takes her picture. When Jude arrives at Garcia’s, she encounters him in a drunken state—and the English guy from church shepherds him into his studio and begs Jude to leave. As Jude heads home, she heads to the beach where she nervously watches Noah cliff-dive into the sea, his dangerous new hobby.
Back in the “past,” Noah begins spying on summer figure drawing classes at CSA. He briefly befriends one of the models there—an English teenager—and witnesses the model as he is caught for his drinking on the job and is let go from his post. Meanwhile, Noah slowly befriends a new boy in the neighborhood, Brian—an amateur astronomer who attends boarding school on the East Coast and is the all-star pitcher for his school’s baseball team. As Brian begins drawing attention of girls, Noah worries that his feelings for Brian will never be returned—and that Brian will soon abandon him for cooler friends. Noah, attempting to avoid both Brian and the tense environment at home, begins hanging out more at CSA. When Brian tracks him down there one day and apologizes for being distant, Noah senses that Brian does indeed have feelings for him, and the two rekindle their friendship. For the rest of the summer Noah frequently blows off Jude to hang out with Brian and his cool friends. Brian and Noah hold hands one evening during a movie, but nothing more happens. At the end of the summer, during a going-away party in Brian’s honor, some kids start up a game of seven minutes in heaven. Noah urges Brian to leave the party with him, but Brian insists on staying. Noah is paired up with Heather and sent into the closet, but as he begins kissing her, he imagines Brian and gets into the game. When he emerges from the closet, Brian is furious—and proceeds into the closet with Jude. Noah leaves the party, and on the lawn runs into the English model, who urges him to seek real lessons from a sculptor who lives inland—Guillermo Garcia. Noah stumbles home, where he rips up all of his drawings of Brian.
In the future, Jude returns to Garcia’s studio to beg him to be her teacher. After a contentious first meeting, Jude tearfully explains how desperately she needs to make a certain sculpture out of stone—and Guillermo reluctantly tells her to come back the next day with a portfolio. The next day, Guillermo, Jude, and the English guy—whose name is Oscar—all sit down together, and Oscar disrobes so that he can model for Jude. Guillermo explains that to carve or sculpt, one must first learn to draw by feeling rather than seeing. After the lesson, Jude and Oscar have a flirtatious conversation, but Jude becomes suspicious when a girl named Sophia arrives to take Oscar out to dinner. While exploring Guillermo’s studio, Jude comes across a series of notebooks which contain passionate love letters. The letters spook and excite Jude, and she pockets them. As Jude begins her next carving lesson, she realizes that the sculpture she needs to make is not of her mother, but of herself and Noah. After the lesson, Jude goes to the room where Oscar sleeps and begins going through his things. She is elated to find a series of photographs Oscar took of her scattered on his desk, with various love notes attached, but is startled when she hears him coming upstairs, accompanied by a woman named Brooke. Jude hides in the closet while the two begin kissing, and overhears Oscar telling Brooke that the photos are of “nobody.” Jude bursts from the closet and flees the studio.
Back in the past, in the wake of his heartbreak, Noah decides to follow the English guy’s advice and seek out Guillermo Garcia. He arrives at the man’s studio and peeks through the yard to find him leading students in carving, sculpture, and figure drawing—Guillermo is happy and carefree, and his studio is a veritable utopia of art and learning. As Noah leaves the yard, he sees his mother’s car parked on the street—though she is hunched over, clearly trying to avoid being seen, he approaches her, and she tells him to get inside. On the drive home, Dianna makes excuses for why she was parked on a street so far from home. Over time, Dianna takes up smoking and spends hours on the porch talking on her phone; when she’s present in the house, she’s lost in thought and easily distracted. Eventually, Benjamin and Dianna inform Noah and Jude that they are embarking upon a trial separation. Benjamin leaves for a hotel with nothing but a drawing Noah made him for his birthday in tow, and that evening, Jude and Noah reconcile as Jude informs Noah that nothing happened between her and Brian, and she’s in fact interested in Zephyr instead. Over winter break, Brian comes over one morning to say hello, and he and Noah soon run off together into the woods. Brian kisses Noah passionately, but warns him that no one can ever know that Brian is gay—because of his athletic career, he is afraid of facing ridicule and discrimination. A week later, when Noah and Brian are masturbating together in Noah’s room, Dianna walks in on them. Brian panics and leaves through the window, telling Noah that things between them are over. When Dianna attempts to talk to Noah about what happened, he refuses to answer her questions about his feelings or his sexuality. The next morning, Noah overhears a phone call between Dianna and someone he assumes is his father. Afraid that Dianna is going to tell Benjamin the truth about Noah, Noah follows Dianna to a local landmark—where she meets up with Guillermo Garcia, and kisses him passionately. Realizing the two are having an affair, Noah dashes home and draws a portrait of Dianna and Guillermo, leaving it for his mother to find. He runs into Brian—and a girl named Courtney—and sees that they are kissing. Noah screams out, “Brian Connelly is gay!” but instantly regrets his words and rushes home, where Dianna confronts Noah. She tells him that she wants to leave Benjamin and marry the sculptor—Noah is devastated.
The morning after her run-in with Oscar and Brooke, Jude goes into the studio, where she works on her “NoahandJude” sculpture. Jude asks Guillermo to show her how to use a powerful diamond-blade saw, and, with it, she cleaves the NoahandJude sculpture in half—“killing” them in Guillermo’s view, but “saving” them in her own. On the way home, Jude receives a text that Noah is drunk at a bonfire and about to attempt a perilous jump. Jude rushes to the beach and, with the help of Zephyr, tracks Noah to a high bluff overlooking the sea. She attempts to stop her brother from leaping off the cliff, but he squirms from her grasp and she is knocked out. When she awakes, she sees that Oscar has tackled Noah and stopped him from jumping. Noah is angry, as he wanted to jump badly—when he cliff-dives, he believes Dianna’s ghost helps him to avoid injury, and it is the only time she “forgives” him. Oscar helps Jude and Noah home, and Oscar at last kisses Jude. Jude is nervous to embark on a relationship with Oscar, but over the course of their conversation in which they venture the idea that they might be soulmates, she becomes convinced that Oscar is the one. As Oscar looks at various photographs around Jude’s room, though, he spots one of the whole Sweetwine family—and flees out the window, muttering under his breath, “Guillermo doesn’t know.”
Back in the past, Dianna leaves in the rain to tell Benjamin she’s ending things. As she pulls out of the driveway, Noah screams after her, telling her that he hates her. Soon, Benjamin arrives home with a policeman in tow and informs Noah that Dianna has been killed in a car accident. Noah tells Benjamin that she was on the way over to his hotel—to tell him that she loved him and wanted him to come home. The day after Dianna’s funeral, Noah goes to Day Street, where he runs into Guillermo Garcia. He runs to the sculptor and the two weep together for several moments before Noah is overcome with anger. He tells Garcia that Dianna didn’t love him and was never going to marry him.
The next morning, when Jude arrives at Day Street with a series of new sketches of her mother for Guillermo to peruse, the sculptor realizes for the first time who Jude really is. Noah and Oscar burst into the studio, and Noah begins explaining to Jude just who Guillermo is. He reveals the truth—Dianna was planning on leaving Benjamin and marrying Guillermo. Jude allows herself to collapse into Noah’s arms, at last letting down her guard and surrendering to the pain of their loss. On the walk home, Noah and Jude reconcile, coming clean about all the secrets they’ve kept from one another for years, and Noah brings Jude to an abandoned construction site to show her an expansive mural he’s been working on in secret for years. Jude and Noah return home, where they tell their father the truth about Dianna and Guillermo’s love—he is relieved rather than angry. The atmosphere in the house is truly happy for the first time in years, and the three of them even discuss moving to a houseboat as part of a new adventure together. Oscar shows up to talk to Jude—he tells her that she’s too young for him, and that they should wait to begin dating until she’s older. Jude begs him not to pass up a chance at destiny and true love, and after some convincing, Oscar agrees that they shouldn’t waste a chance at happiness. The next day, Jude and Noah go to Guillermo’s studio so that Jude can work on her sculpture and Noah can begin drawing lessons. As they all work together in harmony, Jude reflects on the role of destiny in people’s lives, and considers that Dianna’s affair actually strengthened their family rather than weakening it. Two weeks later, Brian returns to town, and he and Noah rekindle their relationship at last. Benjamin and Jude come back from a swim in the ocean, and as a ladybug lands on Jude’s hand, she makes a wish.