It is Wendla Bergmann's fourteenth birthday, and her mother has given her a new dress that is much longer than her old one. Wendla convinces her mother to let her wear her old dress a bit longer, and her mother seems glad that Wendla does not want to grow up too fast. Wendla both reassures and worries her mother when she teases her, saying that if she had to wear such a long dress she would wear no underclothes underneath.
In the next scene, Melchior and Moritz are playing with several of their friends. The group breaks up once Melchior decides to take a walk and invites only Moritz to go with him. On their walk Moritz complains about school, and talks about his fear that he will fail. The boys speak philosophically about topics ranging from superstition to how children should be raised, until the boys begin discussing how children inevitably start to desire each other. This leads to a frank discussion of the recent changes they have experienced. Both boys have begun feeling "the stirrings of manhood" (i.e. erections), which have usually been brought on by strange dreams. During their discussion Melchior realizes that Moritz does not know the mechanics of reproduction. He offers to explain, but Moritz suggests that he write it down instead so that Moritz can read it later - in private.
Thea, Wendla, and Martha are walking together, probably coming home from school, when Wendla suggests they go look at the flooded river. For a few moments they discuss the rumor that Melchior almost drowned in it the night before. Martha complains about how her parents insist that she wear her hair in braids. This grows into a larger discussion about the fact that Martha's parents beat her and punish her in other dreadful ways. Thea and Martha talk about how they will treat their children differently, but Wendla seems surprised that they assume that they will have children at all. The girls agree that they only want to have boy children, but Wendla insists that while she wants to have boys, she would rather be a girl, because she would rather be loved by a man. This mild argument is interrupted when Melchior and Moritz walk by.
A while later, Melchior is playing with some of his friends when he expresses the desire to know where Moritz is. He learns that Moritz was spotted sneaking into the faculty lounge, and everyone is sure that he will be caught and punished severely. However, Moritz soon appears, and they learn that not only was he not caught, but that he has discovered that he has been promoted to the next grade. Eventually either he or Ernst Robel will have to give up their place, but Moritz has earned a temporary reprieve. The other boys act as if his relief is foolish, but Melchior clearly supports Moritz, and the two friends leave together.
Melchior is wandering in the woods one day when he meets Wendla. Wendla has been gathering Woodruff so that her mother can make wine. Wendla is relieved that it is not very late, and she agrees to lie under a tree with Melchior for a bit, after which he will escort her home. He asks her about her visits with the poor, wanting to know why she goes and whether she enjoys it. She tells him that she goes because her mother sends her, but that she also gets a lot of pleasure from it. Melchior is frustrated by the idea that one can get pleasure from something that is supposed to be a sacrifice, but Wendla tries to convince him that fighting with religious authorities will only bring him pain. Wendla tells Melchior that she has been imagining what it would be like to be poor and hungry and to be beaten by her father when she doesn't bring home enough money from begging. She asks Melchior whether he would like to beat her, and when he refuses, she taunts him until he pummels her with his fists, then flees.
At the beginning of the second act, Moritz is attempting to study with Melchior. He is tired and overworked, and though he has failed one less time than Ernst, he is terribly afraid that he is going to be thrown out. He rambles a bit about the story of a headless queen that he cannot get out of his head, but is interrupted by Melchior's mother, who is bringing in the tea. She tells Moritz that his health is more important than doing well in school, and Melchior tells his mother about the school's callous response to the recent death of a student. Melchior's mother notices that Melchior is reading Faust, and counsels him to consider whether or not he is old enough to read such things. She leaves, and Moritz suggests that Mrs. Gabor was worried about the sexual part of the book. Melchior argues that not everything is about sex, but Moritz says that since he read what Melchior wrote for him, he feels like everything is about sex. He talks about how he feels that girls get more pleasure out of sex, because they merely have to surrender to it, but Melchior doesn't want to talk about the matter.
Mrs. Bergmann comes home one morning to tell Wendla that the stork has brought her sister a little boy. After hedging around the question for a few minutes, Wendla asks her mother to explain where babies really come from. Her mother tries to avoid telling her anything, but finally says that a husband and wife must love each other like they've never loved anyone in order to have a baby.
Now in the home of Hanschen Rilow, we see Hanschen slip into his bathroom carrying a picture of a nude woman: a reproduction of Vecchio's Venus. He bids goodbye to the figure, talking about how difficult it is to let her go, but how he must. He tells her of the other paintings that have gone this way, and wonders whom he will get to replace her. After a final kiss and a caress, he drops her in, and shuts the lid.
One day, Wendla searches out Melchior in a hayloft. She tries to get him to rejoin the others, but he refuses. Suddenly, Melchior starts making provocative statements to Wendla, but she tells him not to kiss her, for they don't love each other. Wendla continues to protest, but Melchior grabs and rapes her.
The next scene consists of a letter from Mrs. Gabor to Moritz. She tells him that she cannot give him money to flee to America; however, she will be happy to help him deal with his parents. She asserts that suicide will not help anything, and declares that his allusion to suicide seems a bit like blackmail. She assures him that no matter what, he will always be welcome in her house.
A few days later, Wendla comes into the garden early because she does not want her mother to see how happy she is. She wishes there were someone she could unburden herself to, someone who would be happy for her. Either later that day or a few days later (the timeline is unclear), Moritz wanders through the woods. He debates with himself whether life has any intrinsic worth. He thinks about the past, and the thing that seems to upset him most is that he will die without ever having experienced sex. He decides he will lie to whoever asks and tell them that he has experienced intercourse. He is imagining his funeral, attended by the people he cares about, when Ilse, an old friend and now an artist's model, suddenly appears out of the fog.
Ilse tells Moritz about her most recent exploits, and then describes in greater detail her recent love affair with a young man named Heinrich. She tells Moritz about how Heinrich used to make her dress up and parade in front of him, and confides that he was always threatening to kill her. Finally, she tells him how she escaped and went back to the artists who paint her. She teases Moritz, recalling when they used to play together with Melchior and Wendla. She tries to get Moritz to come inside, but he insists that he must go. As he leaves he realizes that he could have slept with Ilse, but decides that the timing was not right. He works himself into a rage thinking about Ilse, but as he calms down he decides that he will not return home from this walk.
At the beginning of the third act the teachers, headed by Rektor Sunstroke, meet to discuss the possible expulsion of a student. Sunstroke argues for the speedy expulsion of the student in order to mitigate the damage to the school, while the other teachers seem more interested in arguing amongst themselves than in making a decision. The student turns out to be Melchior. After Moritz's suicide, Rentier Stiefel discovered the treatise on copulation and turned it in to the school, where a handwriting comparison determined that the document had been written by Melchior. Sunstroke believes that the tract may have had something to do with Moritz's suicide. Melchior tries to stand up for his work, and one teacher even defends him, but the others are clearly against him, and send him away.
At Moritz's funeral, Pastor Skinnytum delivers a sermon on Moritz's sin and depravity. As Rentier Stiefel and Moritz's relatives and teachers pass by the grave, each dropping a shovelful of dirt, they continue to malign his memory, calling him depraved and corrupt. Once they depart, Hanschen bids a sad farewell to Moritz, and Ilse and Martha fill his grave with flowers. Ilse tells Martha how she heard about Moritz's suicide and took the gun so that no one else would find it.
At home, Mr. and Mrs. Gabor discuss what to do with Melchior now that he has been expelled from school. Mr. Gabor argues that they must send him to a reformatory if they want to save him from himself, but Mrs. Gabor insists that he has done nothing wrong and declares that she will stand up for him if no one else will. After fighting for several minutes, Mr. Gabor tells Mrs. Gabor that just that morning a woman brought him a letter, purportedly written by Melchior, which revealed that he had taken advantage of a young woman. Mr. Gabor believes that Melchior did not write the letter, but he also believes that it describes true events. Horrorstruck, Mrs. Gabor agrees that Melchior must go to a reformatory, especially once Mr. Gabor admits that he has already confirmed the story.
In the reformatory, Melchior tries not to become involved with the other boys, who masturbate competitively, gamble, and seem utterly corrupt. He is planning his escape, but he fears that he will fail, and that he will die of loneliness. He thinks confusedly about Wendla and Moritz, and wonders whether Wendla hates him. Just after he leaves the room, Dr. Procrustes walks by with a locksmith, revealing that they are going to put bars on the window that Melchior was going to use to escape.
Mrs. Bergmann has called Dr. Fizzpowder to examine Wendla, who has been feeling very ill. He assures her that she will be fine, and gives her some pills to take. Ina comforts her sister, and then departs. Wendla is convinced that she is dying, and finally forces her mother to confess that Wendla is pregnant. As her mother berates her, it becomes clear that Wendla does not understand how she could be pregnant, but she finally tells her mother about what happened in the hayloft. Mother Schmidt arrives at the door, and Mrs. Bergmann shows her in.
In this interlude, Hanschen and Ernst sit at the edge of a vineyard, eating grapes. They have just masturbated, and begin again during the course of the scene. They discuss how they want to be when they are adults, and Hanschen convinces Ernst that he should not fall for adult lies - he does not want to grow up to be a provincial, ordinary man, but rather one who manages to get a lot of pleasure out of life. Eventually, the boys kiss, and Ernst is relieved and happy, for he was worried that such a thing would not happen. They decide that virtue is overrated, and express their certainty that they will look back on these events happily in the future.
Late one night in November, Melchior climbs into the graveyard. He has escaped from the reformatory. He finds Wendla's grave, and berates himself for having destroyed her. Suddenly Moritz appears, carrying his head under his arm. He tries to convince Melchior to take his hand and join the dead, insisting that their existence is far superior to that of the living. When he promises Melchior that he could forget his wrongdoings if he were dead, it almost seems like he will succeed. Suddenly, a man in a mask appears and intercedes. Melchior wants to know who he is, but although the masked man will not tell him, he forces Moritz to reveal that he is making empty boasts. Moritz wants Melchior to join him because he is lonely and envious. Melchior decides to trust the masked man, and says goodbye to Moritz. Telling Moritz that he will never forget him, he allows the masked man to lead him away. Moritz, regretful but perhaps at peace, returns to his grave.