Two weeks after his classmate Hannah Baker commits suicide, Clay Jensen, the "nice" boy who had loved her from afar, finds "a shoebox-sized package" on his porch. The box contains seven audiotapes, with each side numbered separately from one to thirteen. The tapes, created by Hannah, are to be passed on, in order, to a list of individuals whose names all appear on the recordings. Hannah promises that the tapes will explain why she took her life, and she warns that each of those who receive a tape contributed in some way to her death.

Hannah names Justin Foley, her "freshman crush," first on the tapes. She concedes that he, like most of the people named, had no idea about the significance of his actions, but in the end, everything added up to "betrayal...one of the worst feelings." Hannah had long dreamed of receiving her first kiss on a playground rocket ship, and Justin made her innocent dream come true. Sadly, he then bragged to his friends about what had happened, embellishing the details, and starting rumors having little resemblance to the truth.

Alex Standall and Jessica Davis are the next students implicated on the tapes. Hannah, Jessica, and Alex had enjoyed hanging out at a coffeehouse during their freshman year, and Alex and Jessica had began a romantic relationship that quickly went sour. In a mean-spirited joke aimed at hurting Jessica, Alex created a "Who's Hot/Who's Not" list and distributed it among the students at school. Alex put Hannah at the top of the list entitled "Best Ass in the Freshman Class," with Jessica opposite her under "Worst Ass." Hannah knew it was a joke, but the repercussions for her were severe. Jessica, humiliated, struck Hannah, leaving a scar on her forehead, and, by naming Hannah "Best Ass," Alex had unintentionally affected the way people looked at her, giving some "the go-ahead to treat (her) like (she was) nothing but that specific body part." Hannah was subsequently groped by an arrogant upperclassman at a local convenience store.

Tyler Down hastened the destruction of Hannah's world when he stripped her of privacy and security by surreptitiously photographing her from beneath her bedroom window.  When Hannah realized that she was being watched, she confided in Courtney Crimsen, a popular classmate with a reputation for being a good friend, only to discover that the girl was not what she seemed to be. Courtney went to Hannah's house and initiated a salacious scene with her to distract Tyler before exposing him as a Peeping Tom. Hannah had hoped that after this escapade, Courtney and she might become friends, but instead, Courtney ignored her until she finally invited Hannah to go to a party because she needed a ride. Courtney ditched Hannah as soon as they arrived, and later sent a boy over to approach Hannah after telling him provocative lies based on Hannah's false reputation as an easy sexual conquest.

Subsequent experiences intensified Hannah's isolation and contributed to her downward spiral. The cheerleaders at school ran a Valentine's Day fundraiser in which students were to complete a survey expressing their preferences in a mate, then pay to discover whom a computer matched them with. Hannah was paired with "goof-off" Marcus Cooley, who facetiously asked her out on a date. Calling his bluff, Hannah accepted, but while Hannah went to Rosie's, their agreed-upon meeting place, at the designated time, Marcus arrived late, with an "endgame" in mind. Marcus maneuvered Hannah into a secluded booth and, encouraged by the false rumors that she could not escape, tried to make "a move on her"; when Hannah fought back, he loudly called her "a tease" and left. As Hannah sat alone, crushed, Zach Dempsey, a classmate who had been sitting with a group at another table, came over to see if Hannah was all right; when Hannah did not respond, he returned to his friends. Immediately afterward, Hannah, eavesdropping, learned that Zach had come to her table on a dare, trying to get a date. The next day, Hannah gave up on ever being able to establish a mutually caring relationship with anyone, and began to entertain the idea of killing herself.

Desperate for support, Hannah submitted "suicide" as a topic for discussion in her favorite class, Peer Communications, only to find that her classmates responded to the subject with an attitude of thinly veiled annoyance. Someone even conjectured that the person who submitted the topic was only looking for attention because she did not give her name. In Peer Communications, each student had a bag in which they received notes of encouragement from their classmates. Hannah's bag remained empty, even when she impulsively cut off her hair. Zach, apparently angry about his unsuccessful attempt to get a date with Hannah, had been stealing her notes in a petty gesture of revenge, depriving her of the small tokens of support she so desperately craved.

The next person named on the tape is Ryan Shaver, the editor of the school's Lost-N-Found Gazette. Ryan and Hannah shared a common interest in poetry, and Hannah had shown Ryan a very personal poem she had written. A few weeks later, Hannah's poem was published in the Gazette. It then made it into the English curriculum, and Hannah was forced to sit among her classmates while they dissected her poem. Word got around that Hannah was the author, and when she refused to confirm this, students began to write parodies of her work. Hannah, who had already had her image irrevocably tarnished and her home violated, now had to endure hearing her own deepest thoughts held up to ridicule.

Clay Jensen, who has been listening with revulsion to Hannah's story, finally comes to the place where his name is mentioned. Clay had long had a crush on Hannah, but although they were classmates and had worked together at the local theater, they had never gotten to know each other, because Clay was afraid of her reputation. Unbeknownst to Clay, Hannah had wanted to get to know him too because everything she had ever heard about him was good. Hannah assures Clay on the tape that he does not belong on her list like the others do; she only included him to tell her story more completely.

The tapes go on to recount one fateful weekend when Clay, who did not often attend parties, decided to go to one. When Hannah discovered that he would be there, she made sure she was in attendance as well. The two had an opportunity to really talk, and for once, Hannah felt that she had truly connected with someone and was not alone. Hannah and Clay went to a bedroom and kissed, just kissed, but memories of her first kiss with Justin and his subsequent betrayal came rushing back to Hannah, and she pushed Clay away, screaming at him to leave. When he had gone, Hannah remained in the room, huddled in the dark on the floor. A short time later, Justin came in carrying a very drunken Jessica, and, realizing that she was virtually passed out, he tucked her in bed and exited the room. Justin could then be heard telling Bryce Walker, the most notoriously unscrupulous boy in school, that Jessica was insensible, but as Bryce was insistent, Justin relented. Bryce came in and, unaware of Hannah's presence, raped Jessica. Hannah knew that both she and Justin had had a chance to save the girl, but neither did anything.

Hannah was offered a ride home from the party by Jenny Kurtz, a cheerleader who perceived her distress. On the way home, Jenny inexplicably drove over a curb and hit a stop sign. Hannah tried to persuade Jenny to notify the police that the stop sign had been destroyed, but Jenny, determined not to have to take responsibility, ordered Hannah out of the car and drove away. An accident later occurred at the location because of the missing sign, and a student from the high school was killed. Hannah was once again wracked with guilt, knowing that she might have prevented the accident if she had only reported the incident that caused the stop sign to be absent, but again, she had done nothing.

Fully understanding that, no matter how others treated her, she alone was responsible for determining the course of her own life, Hannah made the decision to commit suicide. On her last weekend alive, there was a party at Courtney's house. Hannah did not attend, but afterward, she walked by the house to get some air and was called over by Bryce Walker, who was relaxing in the hot tub. Beyond caring, Hannah finally allowed herself to complete the destruction of her personhood and succumb to the reputation that was set for her by others, submitting to the sexual advances of the boy she had witnessed raping Jessica.

Hannah made one last attempt at life, consulting her guidance counselor, Mr. Porter, the final person on her list. Mr. Porter was kind, but though Hannah tried to make it clear that she was at the end of her endurance, he could not offer her any viable solutions and did not stop her when she walked out of his office. Hannah killed herself soon afterward, overdosing on pills. Despite the tragedy of her death and the devastation of those who received the tapes, the book ends with an element of hope. Clay Jensen, who will forever regret that he did not do more to try and reach Hannah when he had the chance, understands the destruction that can result from doing nothing. There is a girl he knows, Skye Miller, who "insist(s) on being an outcast." Remembering how Hannah's isolation ultimately led to her death, Clay takes the initiative and reaches out to Skye.