Clay Jensen, a quiet, shy high school student, returns home from school one day to find a package from an anonymous person sitting on his doorstep. He discovers that it is a shoe box containing seven cassette tapes recorded by the late Hannah Baker, his classmate and crush who recently committed suicide by drug overdose. The tapes were initially mailed to one classmate with instructions to pass them from one student to another, starting from the one involved in the first story to the last. On the tapes, Hannah explains to twelve people how they played a role in her death, by giving thirteen reasons explaining why she took her life. Hannah has given a second set of tapes to one of their classmates and warns the people on the tapes that if they do not pass on the tapes, the second set will be leaked to the entire student body.
The first to receive the list is Justin. He was a year older than Hannah, and her first crush in her new town. Justin was Hannah's first kiss. She describes having a recurring dream of her sliding down a slide in the park and into their kiss. After dreaming about kissing him, she finally kisses him, but Justin turns it into a rumor that it was a sexual encounter and she earns a low reputation. They break up after one month.
Justin later appears as reason ten of why Hannah killed herself- at the party where Hannah and Clay bonded and kissed, he allows his friend (presumably Bryce Walker, reason 12) to rape Jessica. Hannah feels guilty for the rape and is disgusted at the fact that she did not find the voice to stop Bryce.
The second is Alex. Alex wrote a list of people of who was hot or not in the freshman class at her school. He published the list and it was discovered that Hannah earned the title of the best ass, ahead of Jessica (who was in the "not" column). It is later revealed that Alex put them together for revenge against Jessica for breaking up with him.
The third is Jessica. As she, Hannah, and Alex were new their freshman year, the three of them would always meet at Monet's to chat. After Hannah beat her on Alex's list, she slapped her and scarred her over her eyebrow by digging her nails into Hannah's forehead. People started gossiping about her once again. The scar becomes a physical manifestation of the internal scars Hannah feels inside.
The fourth is Tyler, a renowned photographer for the yearbook. He took photos of her when she was in her room, so she invites Courtney over to stop him. After the two girls mime having a dirty conversation complete with a back rub, they snap open the curtains to see the figure of Tyler running away. Tyler takes away the safety of Hannah's home, leaving her to feel trapped.
The fifth is Courtney. Courtney was known as the sweetest girl in school but she started a rumor about Hannah after they stopped the peeping tom. Courtney then uses Hannah to get a ride to a party. She never had any interest in being Hannah's friend.
The sixth is Marcus, the boy who threw rocks at Tyler's window. Marcus took part in the school's Valentine's Day program where you complete a quiz to find your perfect matchand got Hannah, who he asks on a date to Rosie's, the local burger place. Marcus tries to take advantage of her and she pushes him away. He calls her a tease loudly and leaves, angry. This is where Hannah realizes she has no control over her life anymore and becomes depressed, seriously considering ending her own life.
The seventh is Zach. Zach came up to Hannah when Marcus leaves in an attempt to comfort her (though she later realizes he only came because his friends dared him to). He sits next to her for a little while, and she ignores him. Soon he stands up and leaves. Then in Hannah's favorite class, Peer Communications, each student has a pouch at the back of the room where other people in the class can write down compliments to their classmates and slip them into that person's bag anonymously. To spite Hannah, Zach takes out all the little slips she is given. Eventually Hannah catches him though he just runs off as if nothing has happened. She confronts him in the hallways in tears. In Peer Communications, Hannah leaves an anonymous note for the teacher that she is considering suicide. The class discusses it, not knowing who had written it. The responses are all tinged with annoyance until one student says that since the person who wrote the note didn't leave their name, they couldn't take it seriously.
Eight is Ryan, the editor of the Lost N Found column in the school newspaper. After taking a poetry class with Hannah, he steals a poem of hers that he puts in his column, called "Soul Alone". English classes around the school examine it, but some people figure out Hannah wrote it and mock her for it, reading scathing parodies to her before class, making Hannah to feel that even her thoughts aren't safe.
While he is listening to the tapes Tony tells Clay that his story is next and offers to drive him around while he listens to the tape.
Hannah explains that Clay was probably the nicest person she had met. She never heard anybody saying anything bad about him. So one night at a party they finally talk after years of knowing each other, but casually. Hannah says that on that night she and Clay connected. They end up talking for hours, then eventually going up to a bedroom where they kiss. They stay in the room for a while though Hannah is scared that Clay will betray her just like Justin. She starts shouting at Clay to leave her and at first Clay tries to protest, though eventually he just leaves and Hannah breaks down crying.
Clay is shocked and asks Tony how he got the tapes. He learns that Hannah asked Tony for some tapes and a tape recorder. Soon he is mailed the set of tapes on the same day that Hannah dies. There is no note left there though Tony realizes that he's the person given the second set of tapes and makes sure the tapes are passed on.
Clay thanks him for driving him around and then Tony leaves to go home while Clay continues to listen to the tapes. He comes upon number ten, which is again Justin, this time for allowing Bryce to rape Jessica. Hannah was hiding in a closet and witnessed it but was only a bystander and did nothing to save Jessica.
Number eleven is Jenny, a cheerleader. She offers Hannah a ride home after the disastrous party, only to crash into a stop sign. When Hannah tries to call the police, Jenny, not wanting to get in trouble, kicks her out of the car. There is a car accident later caused by the missing stop sign which kills a senior at their high-school.
Hannah is depressed, upset, and seriously considering the ways to kill herself when number twelve comes along. Though Hannah didn't go to Courtney's latest party, she was house-sitting at a house near Courtney's and ends up at the after party, where Courtney and Bryce are in Courtney's hot tub in their underwear. Hannah strips to hers and joins them, and Bryce pushes himself on to Hannah, who gives in. Courtney turns a blind eye.
The last reason is Mr. Porter, her English teacher and counselor. Hannah records this conversation, where she turns to him for help and expresses her thoughts of suicide. He tells her that if she doesn't want to press charges against Bryce, she should simply move on. Hannah leaves his office at this and he does nothing to get her back in there, even though he knows she plans to kill herself. The last sentence Hannah says on her tapes is seemingly "I´m sorry", but as Clay reflects on the fact that he just heard Hannah's last words, the tape clicks over and Hannah says, with warmth, "Thank you".
Clay goes to school the next day unable to stop thinking about Hannah and runs into Skye, his middle school crush who is showing the signs of suicide. Brushing past a classmate and a class he knows he should be in, Clay turns to her and says "Skye".