Five students are held in detention by Mr. Avery, a stickler for social media and cell phones, who caught all five with phones in their bags during class despite his zero-tolerance policy. All of the students claim that the phones were planted in their bags, and even produce their real cell phones to prove their innocence, but Avery ignores their claims and leaves them all to work on their essays about how social media is ruining American teens. The students in detention are Bronwyn Rojas, the class brain; Addy Prentiss, the most popular girl in school; Cooper Clay, a jock; Nate Macauley, a druggie “criminal”; and Simon Kelleher, who runs the school’s reviled but ubiquitous gossip app, About That. After Simon can’t find his water bottle, he pours himself a cup of water from the sinks at the back of the lab; a car crash in the parking lot brings all the students over to the window, and when they turn back around, Simon has taken a drink from his glass and fallen to the floor, suffering a potent allergic reaction. As the students and Mr. Avery scramble to find Simon’s epi-pen—he’s allergic to peanuts—they find that not just Simon’s bag but the nurse’s office, too, has been emptied of all epi-pens. Simon chokes and writhes until he’s taken away by paramedics.
A few days later, as the student body grapples with Simon’s death, Cooper, Addy, Nate, and Bronwyn are all called into the main office. A policeman reveals that Simon’s autopsy shows he ingested a large amount of peanut oil shortly before his death. The officer asks the four students if any of them ever ran into any trouble with Simon or his app, but they all deny ever having been featured on it. All four students worry separately about the secrets they possess: Cooper is indifferent to his girlfriend, Keely, and spends all his time texting a mystery person; Addy struggles with her controlling boyfriend Jake and her vain mother; Nate spends all his time taking care of his alcoholic father.
All four students are called down to the police station and are separately informed that Simon had queued up an About That post shortly before his death that detailed secrets about each of them. The rumors reveal that Bronwyn stole tests from a teacher’s Google Drive; Nate is dealing drugs; Cooper is using steroids to enhance his baseball performance; and Addy cheated on her boyfriend with a student named TJ. All four students are now suspects in Simon’s murder—and their secrets are less than safe. Bronwyn is forced to come clean to her parents; Nate texts all of his suppliers and tells them he’s not dealing anymore; Addy confesses to Jake that she cheated on him, and he breaks up with her. Cooper, however, is confused by the rumor about him, which is not true—he is relieved that Simon didn’t reveal his true secret. Meanwhile, though Nate and Bronwyn are total opposites, they begin talking secretly with one another.
The next day, the cafeteria is plunged into chaos when an anonymous post made to a new blog—About This—purports to be written by Simon’s killer, and reveals the secrets hidden on the unpublished About That post. A voice on the loudspeaker summons Addy, Cooper, Bronwyn, and Nate to the office, where their principal, Principal Gupta, offers them the chance to reveal what’s going on in a “safe space.” None of them say anything, and instead glumly head back to class. That weekend, Bronwyn and her sister Maeve visit the public library. Maeve has found a way to hack into Simon’s old app using the public computers; there is an encrypted file in the queue, and Simon’s username is connected to a series of strange posts on the forum 4chan. The next morning, a newspaper article affirms that Bronwyn, Cooper, Addy, and Nate—the “Bayview Four”—are all officially “persons of interest” in the case.
The media begins hounding the four students, and Nate and Bronwyn try to protect each other from being harassed by the news as they leave school one day; they are nursing a crush on one another despite having been told by investigators to stay away from one another, as well as Addy and Cooper. Addy befriends Janae—a Goth girl who was close with Simon and now spends her days crying in the bathroom—after her popular friend group snubs her in the wake of her cheating scandal. Maeve and Bronwyn continue their research and find out that Simon often hung out on forums that glorified gun violence; Simon even expressed support for school shooters. As more and more major news outlets begin covering the Bayview Four, Cooper and Keely break up. Investigators find a comment on one of Simon’s old About That posts—a nasty exposé about Maeve’s drunken behavior at a party—which reads Fuck off and die, Simon. The comment was written by Bronwyn, and she comes under scrutiny. Cooper, who has to switch clothes and hats with his friends to avoid being harassed by the media, escapes the news crews and drives out to San Diego where he meets with his male lover, Kris. Nate and Bronwyn kiss for the first time, admitting their intense feelings for one another.
Bronwyn admits she doesn’t trust Janae, but Addy continues trying to befriend her—especially since other girls in class are turning against Addy. One evening, Cooper is called down to the police station. He meets with his lawyer and an investigator, who reveals the police have finally unencrypted the queued file on About That—it contains a post concerning Cooper’s sexuality. Investigators tell Cooper he is now a more “significant person of interest” than the others, since it seems as if someone switched the posts and made sure Simon wouldn’t be around to switch them back. Cooper comes out to his parents, knowing that the information will leak; sure enough, just a few days later, Cooper’s secret leaks to the school via the About This blog, and the only person who stands up for Cooper is Nate. Bronwyn is so proud of Nate that she kisses him in full view of the whole school; Addy brings Cooper over to sit at their lunch table, where the “murder club” defiantly bands together at last. The media coverage in the wake of Cooper’s outing begins to shift, with many prominent news people like Mikhail Powers suggesting that the investigation has been unfairly focused on the Bayview Four, and has now invaded their private lives with little evidence to suggest that they are responsible.
One morning, Maeve calls Bronwyn downstairs—Nate has been arrested in connection with the murder. As Bronwyn scrambles to bring Nate’s mother together with a local pro-bono lawyer, Eli Kleinfelter, who can represent Nate better than a public defender, it emerges that school received an anonymous tip informing them that Nate had drugs in his locker; when officials searched it they found no drugs, but did find a bag containing the nurse’s supply of epi-pens. Bronwyn knows that Nate has been framed and is desperate to find the truth. Even as Cooper and Addy—relieved to be “off the hook”—are happy just to be out of the limelight, they agree to help Bronwyn continue to search for the answer to it all. As the “murder club” combs through the About This posts, they spot an anecdotal detail that none of them recognize; only Addy knows what it means, because she mentioned it offhand to Jake months ago. With his friend Luis’s help, Cooper tracks down one of the cars involved in the accident in the parking lot the day of Simon’s murder; it belongs to a student at another high school named Sam Barron. Bronwyn confronts the student, and he reveals that a Bayview student paid him a thousand dollars to fake a car crash. Bronwyn shows him a picture of Jake, asking if it was Jake who paid him off; Sam gravely reveals that Simon Kelleher himself paid him.
The murder club meets at a coffee shop to go over the new information they have. Cooper’s boyfriend, Kris, comes with them, and his outsider’s perspective is helpful in putting together a few strange details; he suggests that Simon committed suicide, and that Jake is simply some kind of “accomplice.” This accusation distresses Addy, but several days later, she can’t shake the feeling that Jake is involved. She asks Cooper to drive her to Janae’s house. Janae admits that she has “massively fucked up,” and retrieves from her bedroom a sheaf of papers—Simon’s manifesto, detailing his desire to shake up his school unlike every other mass-murderer in America and bring four people down with him in an unforgettable way. Janae reveals that Simon—who always longed to be popular but faced rejection from the popular crowd at every turn—orchestrated his own death and framed Cooper, Bronwyn, and Nate, whom he hated for three separate reasons, to go down with him. When Jake learned an embarrassing secret about Simon at a party (that Simon rigged the prom court in his own favor in a desperate grab at popularity), Jake asked to become involved; having already learned about Addy’s infidelity, he wanted to bring Addy down too. The evidence found in Nate’s locker was planted by Janae; Janae was supposed to stick Addy with it all, but after Addy showed her so much kindness, she couldn’t bring herself to do it. At that very moment, the doorbell rings; it’s Jake, whom Janae reveals comes by often to cajole her into keeping quiet about their plan, which Janae has been feeling worse about. Addy suggests Janae let Jake in and act as if nothing is the matter—she’ll record their conversation from the next room, and then she and Janae will bring the evidence to the authorities. As Addy records Jake, however, her phone goes off with a message. Jake, enraged, pursues Addy out of Janae’s house and into the woods out back, where he grabs her, smashes her head on a rock, and tries to kill her by choking her. Cooper comes to her rescue at the last minute and manages to get her—and Janae—away from Jake.
Nate is released from the holding facility; when he hears that the rest of the “murder club” had been working so hard to clear his name, he feels he isn’t deserving of their kindness, and retreats into himself. Jake, meanwhile, is incarcerated and charged with numerous crimes; Cooper becomes a national hero, and is confused by the alternating love and hatred he’s received from the media. Addy suffers a skull fracture but makes a full recovery; she moves in with her sister, Ashton, escaping her vain mother’s influence and making a fresh start away. Bronwyn, meanwhile, confronts Nate, who has been avoiding her since his release; she tells him that she still wants to be with him, but he claims they’re too different and that their feelings for one another were just fleeting.
Three months later, Bronwyn plays in a High School Spotlight concert at the San Diego Symphony; all her old friends and new friends attend, and she plays beautifully. After the performance, she is surprised to see Nate pulling up on his motorcycle; he reveals that he snuck into the performance and watched, and, urged on by Addy, now wants to apologize to Bronwyn for convincing himself that she was better off without him. Though Bronwyn tells him that things can’t just go back to the way they used to be, Nate suggests they begin repairing their friendship; Bronwyn accepts his invitation to a movie, and smiles rapturously for the first time in months.