Wendla Bergmann, an adolescent in late-nineteenth century Germany, laments that her mother gave her “no way to handle things” and has not taught her the lessons she needs to learn (“Mama Who Bore Me”). She tells her mother that it is time she learned where babies come from, considering that she is about to be an aunt for the second time. Her mother cannot bring herself to explain the facts about conception clearly to Wendla despite knowing her daughter is reaching puberty. Instead, she simply tells Wendla that to conceive a child a woman must love her husband with all of her heart. The other young girls in town appear to be similarly innocent and are upset about the lack of knowledge presented to them ("Mama Who Bore Me" (Reprise)).
At school, some teenage boys are studying Virgil in Latin class. When Moritz Stiefel, a very nervous and intense young man, sleepily misquotes a line, the teacher chastises him harshly. Moritz’s classmate, the rebellious and highly intelligent Melchior Gabor, tries to defend him, but the teacher will have none of it, and hits Melchior with a stick. Melchior reflects on the shallow narrow-mindedness of school and society and expresses his intent to change things ("All That’s Known").
Moritz describes a dream that has been keeping him up at night, and Melchior realizes that Moritz has been having erotic dreams which Moritz believes are signs of insanity. To comfort the panicked Moritz, Melchior, who has learned sexual information from books, tells Moritz that all of the boys at their age get the dreams. The burned-out boys tell about their own frustrating thoughts and desires. ("The Bitch of Living"). Moritz, who is not comfortable talking about the subject with Melchior, requests that he give him the information in the form of an essay, complete with illustrations.
Some girls are gathered together after school and tease each other as they fantasize about marrying the boys in the town. At the top of the list is the radical, intelligent, and good-looking Melchior ("My Junk"). Meanwhile, Hanschen masturbates as he looks at an erotic postcard, and the piano student Georg indulges in some lively fantasies about his well-endowed female piano teacher. Moritz has eagerly digested the essay that Melchior prepared for him, but complains that his new knowledge has only made his dreams even more vivid and torturous. Melchior tries to calm and comfort his friend, but Moritz runs off in frustration. All of the boys and girls express their desires for physical intimacy ("Touch Me").
Searching for flowers for her mother, Wendla stumbles upon Melchior. The two share a moment while sitting together in front of a tree (they were childhood friends, but grew apart as they got older). Each of them considers what it would be like to give in to their physical desires, but they do not do so ("The Word of Your Body"). Meanwhile, at school, Moritz sneaks a look at his test results and is thrilled to learn that he has passed his midterm examinations, but the teacher and schoolmaster cannot pass everyone, so they decide to fail Moritz anyway, deeming his passing grade is not up to the school's lofty standards.
Martha, one of the teenage girls, accidentally admits to her friends that her father abuses her physically (including sexual abuse) and that her mother is either oblivious or uncaring. The other girls are horrified to hear this, but Martha makes them promise not to tell anyone, lest she end up like Ilse, a friend from childhood who now wanders homeless and aimless because her parents kicked her out of the house ("The Dark I Know Well"). Later, Wendla finds Melchior again at his spot in the woods and tells him about Martha's abuse. Melchior is appalled to hear this, but Wendla convinces him to hit her with a switch, so that she can try to understand her friend’s pain. At first Melchior is determined to do nothing of the sort, but reluctantly complies. He gets carried away in the beating, taking his own frustrations out on Wendla and throws her to the ground. He then runs off, disgusted with himself, as she weeps curled up on the ground. Alone, Wendla finds that Melchior has left his journal on the ground. She picks it up and takes it with her.
Moritz is told he has failed his final examination, and his father reacts with disdain and contempt when Moritz tells him that he will not progress in school; rather than attempting to understand his son's pain, Moritz's father is only concerned with how the others in town will react when they see 'the man with the son who failed'. Moritz writes to Melchior’s mother, his only adult friend, for money to flee to America; she tenderly but firmly denies his request and promises to write his parents to discourage them from being too hard on him ("And Then There Were None"). Devastated by the refusal and feeling he has few choices left, Moritz begins to contemplate suicide.
In a stuffy hayloft during a storm, Melchior cries out in his frustration at being caught between childhood and adulthood (“The Mirror-Blue Night”). Wendla finds him once again, telling him she wants to return his journal, and each apologizes for what happened the last time they met. Before long, they begin to kiss; Wendla resists his advances at first. Although she doesn't really understand what's going on between them, Wendla is reluctant, sensing that what they are doing is something very powerful, and very unlike anything that she has known before. As Melchior becomes more insistent, he overpowers her objections with a combination of affection and sheer force, although they continue, and they begin to have sex in the hayloft ("I Believe"). At the very moment Melchior commits the act, Wendla cries out against it, and the darkness falls. (Note: This scene was slightly softened from the show's Off-Broadway run, when the act as a rape without Wendla's consent was more straightforward. Later, as staged by the Broadway show, Wendla still objects to Melchior, but gives in without understanding what he is actually trying to do, leaving the question of consent still ambiguous on many levels.)
Wendla and Melchior are finishing their moment of confused intimacy in the hayloft; they reflect on and discuss what has just happened (“The Guilty Ones”).
Moritz, having been thrown out of his home, wanders the town at dusk, carrying a pistol ("Don't Do Sadness") when he comes across Ilse, an old childhood friend. Ilse, who is secretly in love with Moritz, tells him she has found refuge at an artists' colony; and they reminisce in some childhood memories and "remarkable times" ("Blue Wind"). She invites him to come home with her and join her in sharing some more childhood memories and maybe something more. But Moritz refuses, Ilse does everything she can to change his mind ("Don't Do Sadness/ Blue Wind"). After coming close to kissing and admitting their mutual feelings, Moritz refuses and Ilse leaves, distraught and upset. Realizing his true feelings for her, he changes his mind and calls after her, but it is too late; she is gone. Believing that he has nowhere to turn, Moritz shoots himself.
At Moritz's funeral, each of the children including Ilse, drops a flower into his grave, as Melchior laments the passing of his friend while touching on the factors that led to his death, including Moritz's treatment by his parents ("Left Behind"). Back at school, the schoolmaster and teacher feel the need to call attention away from Moritz, whose death was a direct result of their actions. They search through Moritz's belongings and find the essay on sex which Melchior wrote for him. They lay the blame of Moritz's death on Melchior, and although Melchior knows that he is not to blame, he knows there is nothing he can do to fight them, and he is expelled ("Totally Fucked"). Elsewhere that night, Hanschen meets up with his shy and delicate classmate Ernst. Hanschen shares his pragmatic outlook on life with his classmate before seducing him ("The Word of Your Body (Reprise)").
Wendla has become ill, and her mother takes her to visit a doctor. He gives her some medication and assures them both that Wendla is suffering from anemia and will be fine, but he takes Wendla's mother aside and tells her that Wendla is pregnant. When her mother confronts her with this information, Wendla is completely shocked, not understanding how this could have happened. She realizes that her mother lied to her about how babies are made. Although she berates her mother for leaving her ignorant, her mother rejects the guilt and insists Wendla tell her who the father is. Wendla reluctantly surrenders a passionate note Melchior sent her after they consummated their relationship. She reflects somberly on her current condition and the circumstances that led her to this difficult position, but ends with optimism about her future child ("Whispering"). Meanwhile, Melchior's parents argue about their son's fate; his mother does not believe that the essay he wrote for Moritz is sufficient reason to send him away to reform school. When Melchior's father tells his wife about Wendla's pregnancy, she finally agrees that they must send Melchior away, which they do without telling him that Wendla is pregnant.
During this time, Melchior and Wendla only keep contact through the use of letters, with Ilse delivering them back and forth. At the reform school, Melchior gets into a fight with some boys who grab a letter he has just received from Wendla and use it in a masturbation game. As one of the boys reads from the letter, Melchior finally learns about Wendla and their child, and he escapes from the institution to find her. He does not know that Wendla's mother has already taken her to an underground practitioner to have an abortion. When Melchior reaches town, he sends a message to Ilse to have her get Wendla to meet him at the cemetery at midnight. But she can take no action as Melchior "hasn't heard" about Wendla. There, he stumbles across Moritz's grave and swears to himself that he and Wendla will raise their child in a compassionate and open environment. When Wendla is late to the meeting, Melchior begins to feel a little uneasy. Looking around, Melchior sees a grave he hadn't noticed before. He reads the name on the stone – Wendla's – and realizes that Wendla died from the botched abortion. Overwhelmed by shock and grief, he takes out a razor with the intention of killing himself. Moritz's and Wendla's spirits rise from their graves to offer him their strength. They persuade him to journey on, and he resolves to live and to carry their memories with him forever ("Those You've Known").
Led by Ilse, everyone assembles onstage to sing "The Song of Purple Summer."