Clay Jensen finds a box filled with audio cassette tapes anonymously dropped on his front doorstep. He plays the first one in his dad's boombox and realizes it is his recently deceased classmate Hannah Baker who is talking, before accidentally dropping it when scared by his mom. On his friend Tony's Walkman, which he stole, Clay listens to the first tape, in which Hannah relates the experiences that triggered her. She starts by sharing the story of her first kiss, with Justin Foley, who spread a salacious rumor that began her downward spiral. Clay is revealed, through numerous short flashbacks, to have been in love with Hannah and to have worked with her as cinema attendants.

On the tape, Hannah reminisces about her friendship with two other new students: Jessica, who moves frequently because her father is in the Air Force, and Alex, whom they met at a coffee shop. Jessica and Alex eventually become an item and stop hanging out with Hannah. When Alex breaks up with Jessica, Jessica blames Hannah. In the present, Hannah's mother, Olivia, finds a note in her daughter's textbook that leads her to believe Hannah was being bullied. Bryce Walker's circle of peers meets with knowledge about Clay listening to Hannah's recordings.

Hannah's relationships are threatened by a 'best/worst list' made by Alex Standall, who has put a "target" on Hannah. In the present, Hannah's mother, Olivia Baker, seeks out the school principal about her suspicion of bullying and makes a disturbing discovery. In the midst of his investigation, Clay turns to Alex for answers, who warns him against trusting Tony, whom Clay later finds in a hostile occurrence. As Justin tries to recuperate from his recent slump, Bryce strong-arms Clay and Alex into a drink-off in an alleyway.

Hannah hears someone outside her window, and confesses to her friend, Courtney, that she has a stalker. Courtney offers to help her catch the creeper in the act. While waiting for the stalker to arrive, they play an alcohol-fueled game of truth or dare which leads to the two of them making out on Hannah's bed. The stalker, school photographer Tyler Down, takes a photo of the girls and sends it around to the school. This effectively ends Courtney and Hannah's friendship. In the present day, Clay takes a naked picture of Tyler and sends it around the school as payback, instead of throwing a rock through his window as suggested by Hannah on the tapes.

Courtney, afraid of her classmates finding out about her sexuality, spreads the rumour that the girls in the leaked photos are Hannah and Laura, an openly lesbian classmate. Courtney also adds to the rumor about Hannah and Justin, furthering Hannah's poor reputation. Meanwhile, in the present, Clay takes Courtney to visit Hannah's grave. She leaves quickly, not ready to face the loss of her classmate and her involvement. Tony arrives with Clay's bike and gives him a tape with the song he and Hannah danced to at the Winter Formal. Later the boys force Clay into the car with them and scare him into silence about the tapes by driving over the speed limit. They are pulled over by the police but get away with it as the officer is revealed to be Alex's father.

Hannah's date on Valentine's Day with Marcus doesn't go as planned due to the rumors that she's 'easy'. In the present, Alex gets into a fight with Montgomery and they both have to appear before the student council.

After Hannah refuses to go out with Zach, he sabotages her emotionally during a class project. Out of revenge, Clay damages Zach's car, but in the present, things turn out to be different than they appeared. Clay is having both audial and visual hallucinations of Hannah during the day as well, including seeing her dead body on the floor of the basketball court during a game and hearing her tape playing over the school's intercom system.

Hannah is touched by poetry recited by fellow student Ryan Shaver and pours her heart out after encouragement from his side. Ryan betrays her by publishing the poem against her will in his school magazine. In the present day, Tony confides to Clay about the night of Hannah's death.

While hiding in Jessica's room during a summer party, Hannah witnesses Bryce Walker raping an unconscious and intoxicated Jessica, with Justin's consent. In the present, Clay talks to Justin who claims it's better Jessica doesn't know the truth. Marcus warns Clay the worst is yet to come.

After the party, Hannah gets a ride from Sheri. They get into a small accident and hit a 'Stop' sign, but Sheri refuses to call the cops. While Hannah is on her way to find a phone, a tragic accident occurs at that same crossing, causing the death of Jeff Atkins, a friend of Clay's. When Hannah tries to tell Clay about the 'Stop' sign he pushes her away thinking it's one of her drama moments again. In the present, Jessica's behavior becomes more erratic.

Clay finally listens to his tape and is overcome with guilt because he could not do enough to prevent her suicide. In present day, Justin finds out Jessica is at Bryce's. He confronts her there and admits that Bryce raped her on the night of the party. Olivia Baker finds a list with the names of all the people on the tapes, although she doesn't know what the list means.

After accidentally losing her parent's deposits which were supposed to go to the bank, a depressed Hannah stumbles upon a party thrown by Bryce. The night ends in tragedy when she ends up alone with him and he rapes her. In the present, Clay goes to Bryce's house on the pretext of buying weed from him and confronts Bryce about the rape, taping his confession. Everyone on the list Olivia found is subpoenaed for the lawsuit between the Bakers and the school. The episode ends with an ambulance treating an unknown teenager with a gunshot wound to the head.

Clay gives Tony the confession tape to copy. Hannah, with only one tape left, decides to give life one more chance and look for help. She visits Mr. Porter, the school guidance counselor, and tells him about her rape, without admitting who was the responsible. Mr. Porter implies that she has no chances of being taken seriously and insists that she continue with her life as if it never happened. Hannah records the conversation, which will become the side A of tape 7, gets her things in order, goes home, and commits suicide by cutting her wrists and bleeding out in the bathtub. She is later found by her mother. In the present, Clay confronts Mr. Porter about the incident and gives him the tapes, with the side B of tape 7 being Bryce's rape confession. Meanwhile, Tony, who at first wished to honor Hannah's wishes, decides to give her parents audio files of the tapes after her parents realized he was keeping secrets from them. All those named as complicit in Hannah's death confess their faults except Alex, who tries to commit suicide by shooting himself in the head. He is in critical condition and it is not revealed if he survives. Justin leaves his home and town out of guilt for not telling Jessica the truth, but not before telling Bryce about the tapes. Before leaving his home for his meeting about the lawsuit, Tyler hides various guns and ammunition in his room. At school, Clay reaches out to Skye, a classmate whom he previously noticed with scars on her wrists. Later, he, Skye, Tony and his boyfriend drive down the road.