The story opens with a flashback to a spring sleepover four years ago. Alison DiLaurentis and her friends — Hanna, Spencer, Aria and Emily — are giving each other makeovers and trying on each others' clothes. The girls gossip about others in their sixth-grade class. As Ali passes a window, she sees Toby Cavanaugh, her creepy neighbor, staring in at them. Toby is a year older. He smirks at the girls before running away. Toby has no friends, and the only person he talks to is his stepsister, Jenna. Ali and her friends don't like Jenna because they think she's a dork.
Ali makes a plan to get back at Toby. When he isn't wandering the neighborhood, he's up in his tree house. Ali wants to steal one of the bottle rockets he keeps at the base of the tree and shoot it into the tree house window to scare him. The other girls aren't sure it's a good idea, but Ali doesn't back down. The friends watch as Ali steals a bottle rocket then backs away from the tree house so she can aim it through the window. They hear a loud explosion then see sparks in the tree house. Soon the tree is on fire. Ali runs back to her friends and tells them it wasn't her fault. When the fire department arrives, Spencer tries to tell them what happened, but Ali stops her, and the two hide behind a bush. The others watch from the window as a paramedic carries someone from the tree house. It isn't Toby, but Jenna. Ali convinces the others that no one saw her with the bottle rocket. As long as they all keep quiet, the cops will suspect Toby because it was his bottle rocket. In the morning, three of the girls are surprised and confused because Toby confesses to the crime.
The incident comes to be known as "the Jenna Thing." Jenna is blinded by the fire and sent away to a special school. Toby is sent to a reform school in Maine. Ali makes her friends string bracelets. As she ties them on each girl, they have to swear to never tell the truth of what happened. A year later, Ali vanishes.
Ali's close circle of friends disbands soon after she disappears. Now, three years later, the four friends reunite at Ali's memorial service. Her body was discovered a few days previously, buried under a concrete slab in her backyard. The girls have been receiving mysterious text and email messages from someone calling herself "A." This mysterious person knows secrets from their past that only Ali knew, but also appears to be spying on their present activities. All the girls receive a message at the memorial service claiming that A is still around and knows everything. They are surprised to catch a glimpse of Toby and Jenna Cavanaugh at the funeral. The girls are afraid of discussing the Jenna Thing in public, so they agree to meet up at a playground.
As Spencer heads to the meeting, she recalls something else from the night that none of the others know. When Spencer and Ali were outside, Toby ran up to them, claiming he saw Ali with the bottle rocket. Ali told him she saw what he had been doing in the tree house, and she'd tell his parents. She forced Toby to admit to lighting the bottle rocket. He promised to get even with her one day. Spencer worried that Toby would tell on them until Ali admitted what she saw him doing in the tree house. Ali made Spencer promise not to say anything about the bottle rocket or Toby, threatening that she'd find a way for Spencer to take the blame if she did. Spencer wonders if "A" could be Toby since he is the only other person who knows the truth of that night. As he lived in her neighborhood, he might have been able to spy on her to learn the other secrets about her. Such as in seventh grade she'd kissed her older sister's boyfriend, and this past year, she and her sister's new boyfriend had made out in Spencer's bedroom.
The old friends rendezvous at the school playground. Each admits to receiving incriminating notes but won't reveal their content. Only Ali knew all their old secrets, but as Ali is dead, they all wonder whom she could have told. Spencer suggests that A could be Toby, but as she won't admit that he knew about the Jenna Thing, she can't convince the others. They agree to call each other if they get any more messages so they can compare notes. As Spencer drives home she gets another text. This one says it doesn't blame her for not telling the others the truth. After all, she wouldn't want her friends to get hurt.
Hanna's friend Mona offers her a ride home from the park. Mona wonders if Hanna has taken one of her mother's valiums, as she's so flighty, but Hanna doesn't tell her that she is distracted by all that's happened over the past week. Hanna hasn't told her friend how her previous boyfriend, Sean, broke up with her after she tried to seduce him at a party and how she was arrested for taking his car and crashing it. She also does not mention the texts from A. Mona wonders who they will take to Foxy, the annual charity ball, but Hanna doesn't think she'll even attend. Another surprise waits for her when she returns home. Her father, whom she hasn't seen or spoken to in years, is in the kitchen with her mother. Worried about Hanna's recent trouble with the law, her mother called for help. Although the charges for car theft were dropped, Sean's father is asking that Hanna do community service at a rehabilitation clinic. Her parents insist on her cooperation even though she doesn't want to do it. Hanna resists the temptation to binge on food as her mother takes a call from work and her father gets a call from the beautiful daughter of his girlfriend.
Emily meets her friend Maya at an inn. Maya's family had moved into Ali's old house. Unnerved by the discovery of Ali's body in their backyard, the family is staying at the inn until publicity dies down. Maya invites Emily up to her room while her parents are away on a day trip. The two share a kiss on Maya's bed, but Emily is aware that the window is open and people can see in. Maya asks Emily to be her date to Foxy. Emily excuses herself to the bathroom before she gives her friend an answer. As she struggles with her feelings, she receives a text from A who wonders if Emily is going to tell people about her new love or wait for A to do it for her. Emily tells Maya she just wants to be friends before rushing out of the inn.
Aria arrives home from the memorial service to find her parents arguing in the kitchen. Her parents' marriage had been in trouble in the past. In seventh grade, Aria and Ali had caught Aria's father kissing one of his students. Neither girl had ever told anyone about the incident, but texts Aria received from A intimated they knew the secret. Aria's family had spent the last two years in Iceland, and her parents had seemed to fall in love with each other again. Since returning, however, the old dysfunctional habits have returned. Aria offers to take her younger brother to a bar for a drink to get their minds off the trouble at home. Unfortunately, while they're at the bar, they spy their father flirting with Meredith, the same girl he'd had an affair with years before. Aria's brother flees the bar before she can follow him.
Spencer can't stop thinking about the possibility that A is Toby. She remembers seeing him on a train a year after the Jenna incident. He glared at her, and Spencer felt he was threatening her. A week later, Ali disappeared. Spencer is relieved to get a text from Wren, the old boyfriend of her sister, Melissa. Spencer's family isn't talking to her since Melissa spied Wren and Spencer kissing passionately in Spencer's barn bedroom. Shortly after, the barn bedroom was given to Melissa, and Spencer was forced to move back into the house. Even after Ali's funeral, neither her parents nor her sister will offer her sympathy.
Emily's swim coach convinces her not to quit the team by offering her the chance to be team captain. Although Emily doesn't enjoy the sport anymore and hates the idea of running into her old boyfriend, who's also on the team, she can't resist the chance to be captain. She agrees not to quit. In the hall, she runs into Ben, her old boyfriend. He teases her about Maya, but Emily tries to convince him she was drunk when he saw them kissing at a party. He asks her to prove it. He pushes her against the water fountain and runs his hand up her chest. Toby Cavanaugh interrupts Ben's attack. Although grateful for his help, Emily believes he might be the person sending her the threatening texts.
Aria takes the long way home from school, trying to work out what do about her father's affair. Her car stalls out in a deserted area, and it is raining. She fights against a panic attack as she walks toward a farmhouse, hoping to use their phone to call for help. (She has forgotten her cell phone at home.) Hanna's ex-boyfriend, Sean, stops and offers her a ride. She asks to use his phone instead, but has another attack when she can't reach anyone at home. Sean has her breathe into a paper bag to calm her. As they talk, Aria is pleasantly surprised by his love of philosophy and his compassion. She admits her father's affair to him after he promises to keep her secret, and he tells her one of his own. He tells her that he belongs to a virginity club, but now isn't sure he wants to wait until marriage before he has sex.
Spencer discovers that her parents have canceled her credit cards when she tries to pay for books at the store. She realizes they must have done it after she'd tried to apologize to them for her affair with Wren. In her frustration at this latest insult from them, Spencer calls Wren, even though she'd originally told him they couldn't continue their relationship. She spends the night at his apartment after calling her parents to say she's staying at a friend's house. By morning, she loses her virginity to him. When she returns home to change for school, her sister comes in to talk. Melissa has decided to try and make peace with her. Melissa says she's talked to their parents about loosening up on their treatment of Spencer as well. Andrew, a boy from school, calls to see if Spencer wants him to bring her notes from the classes she's missed. To hide her relationship with Wren, Spencer asks him to go to Foxy with her that Saturday.
In an effort to win back Sean, Hanna attends a virginity club meeting. She's shocked to learn that abstaining from sex means not engaging in any sexual behavior, not just intercourse. She approaches Sean after the meeting to apologize to him for her behavior. At first, he acts cold toward her, but by the end of their talk, Hanna feels she may yet have a chance to win him back, as long as she plays by his rules.
Toby steps in to rescue Emily again, this time after she falls from her bike. She finds herself attracted to him, even with all the mystery and controversy surrounding their past. Maya has been calling and texting, but Emily ignores her friend's attempts to contact her, unable to cope with her homosexual feelings. Toby and Emily talk again during a swim meet. Emily is surprised that Toby seems to be experiencing the same feelings of not fitting in that she does. The two share a tentative kiss. When Toby returns to the meet, Emily receives a photo message from A. It's a picture of Emily and Maya, looking into each other's eyes and closing in for a kiss. The text under it threatens to spread the picture around the school.
Hanna and her father try to reconnect even as her dad prepares to get remarried. He asks Hanna to be at his wedding, suggesting they talk through any issues she may have with his choice. As a kind of peace offering, he's arranged for the two of them to spend the weekend together in Philadelphia. They'll dine at an exclusive restaurant and stay in a suite at the Four Seasons Hotel. Hanna realizes that she'll have to miss Foxy and her chance to win Sean back, but she agrees to spend the weekend with her dad. A text from A threatens to tell her father about her involvement with the Jenna Thing unless Hanna does exactly as A says.
Maya confronts Emily about why she's been avoiding her. Because she isn't ready for the school to know she has homosexual feelings for Maya, Emily tells her that she's attracted to Toby. Emily also admits that she didn't quit the swim team, and as the captain of it, she'll be going to Foxy. She plans on asking Toby to go with her. Maya is hurt and warns Emily that she can't change who she is.
Spencer continues her affair with Wren. Normally a straight-A student, she falls behind in her classes. She regrets asking Andrew to Foxy as it means she can't see Wren until Sunday. She also wonders how she'll finish the paper due in her AP economics class by Monday. A sends an email urging her to cheat in order to get the paper done by doctoring one of Melissa's old papers and submitting it as her own. Spencer receives another email warning that A plans to hurt her and/or Wren as payback for what she did in the past.
A has warned Aria to tell her mother about her father's affair. A also directed her to check out the yoga studio where her father's girlfriend, Meredith, works. Aria plans on taking a private class with her so she can talk about the affair but is spooked away when she sees Spencer at the studio. After spending the next day stalking Meredith on the Internet, Aria is ready to get away. Sean calls and asks to take her out. The two drive to a desolate lot on a hill. Sean pulls out a thermos of Captain Morgan rum and they talk. Sean asks Aria to go to Foxy with him, and she agrees, although she's not sure whether they are going as friends or as a date. Aria admits she went to Meredith's yoga studio to talk to her but didn't go through with it. Sean offers to drive her to Meredith's house. When Aria confronts her, asking her to stop seeing her father, Meredith admits that she knows she's hurting his family but that she and Aria's father are in love and won't stop seeing each other.
Hanna spends her Friday afternoon sitting in the bleachers during a soccer game, but she is unable to focus on what's going on because she's worried about A's identity. Sean takes a moment to talk to her after the game. She tells him she's not going to go to Foxy, and he tells her he probably won't, either. He says that they should go out for dinner during the week to talk about the way their relationship ended, and Hanna agrees. Two other girls question her about her breakup with Sean. Hanna tells them that she broke up with him. She spies a note next to her on the bleachers. It's from A and instructs her to tell the girls that she tried to seduce Sean at a party and that she forces herself to throw up several times a day. If she doesn't do it, A will tell everyone, including Hanna's father, about her involvement with the Jenna Thing. She blurts out the words rapidly so the girls aren't sure what they've heard before Hanna runs away.
After speaking with Meredith, Aria breaks down in Sean's car, and he takes her home and tucks her into bed like a child. Aria is appalled, believing Sean must think she's crazy. Sean picks her up the next night to go to Foxy. Aria is so embarrassed by her actions the night before that she avoids him when they get to the dance. Sean finally takes her out to his car so they can talk about Aria's weird behavior. Instead of being angry, Sean is compassionate and wants to help her get through this trial. The two make out in his car until Aria sees a note on the windshield from A.
Emily attends Foxy with Toby, but the evening feels all wrong, like she's holding hands with her sister. She ditches Toby to go to the bathroom. A Tarot card reader offers to tell her future, but Emily refuses. The woman calls out that something life changing will happen to her this night and that Emily must return to the one she loves. Before she can get back to Toby, Ben attacks Emily again. He pushes her up against a wall and puts his hand up her dress. He tells her he'll stop if she admits she likes it. If she doesn't, he'll tell the school she's a lesbian. Emily knees him in the groin and escapes. She runs into Maya, who's seen the incident. Maya expresses concern and then whispers that she will wait as long as it takes for Emily to come back to her.
Hanna is excited about spending time with her father until she realizes that his girlfriend and her perfect daughter, Kate, will be with them as well. She's amazed to find Kate much friendlier than the last time they'd met. When her father presses her to explain more about her "volunteering" at the clinic and the new abstinence club she's joined, Hanna is appalled. She runs to the bathroom where she receives a text from A. It tells her to go to Foxy because Sean is there with another girl. Kate waits outside in the hall to make sure Hanna is OK. Kate offers to tell the adults that Hanna received a call from someone in the virginity club who needs help, allowing Hanna to run to the dance and work things out with Sean. Kate also spies the Percocet in Hanna's purse and asks to have a packet. Hanna gives it to her and heads off to Foxy with new hope that having Kate as a stepsister might not be too bad after all.
Spencer is unnerved by a visit from Officer Darren Wilden on Saturday morning. He questions her about Ali's disappearance, wondering if she has any information to give that she didn't share with the police in the past. Spencer still can't admit what she knows about Toby because of her promise to Ali. That night she attends Foxy with Andrew but can't enjoy herself. Wren hasn't returned any of her calls, and she's too worried about what A might do to her or Wren. Unfortunately, when Wren finally does call her back, Andrew overhears the conversation. He runs off when he learns that Spencer was using him because her family wouldn't like her real boyfriend. She follows Andrew back into the dance to try and apologize. Before she can find him, she spies Emily being escorted by Toby. Spencer fears that Toby has come to get revenge on them all for what they did to him and Jenna.
Hanna confronts Sean and Aria at the dance, creating a scene. She ends up crying in the bathroom. It's then she realizes that A must be at Foxy because the text told her Sean was with someone else. Spencer finds her and Aria, and she confesses that she believes Toby is A. The three discuss the texts they've gotten since Ali's funeral with Spencer, admitting that one sounded like a threat against them. She also tells them that Toby had seen Ali light the bottle rocket. They all come to the conclusion that Toby must be A and seek to find Emily before he can hurt her.
After the incident with Ben, Emily finds Toby and asks if he will take her home. Seeing that she's upset, he agrees. In the car, she admits to having feelings for Maya but being afraid that the kids in school will make fun of her for being gay. Toby pulls over to the side of a deserted rode as a storm rages outside. He confesses that the evening had been hard for him because the kids all acted so nice even though they'd teased him when he was younger. Emily realizes how much anger he still holds against her and the other girls as he continues to talk about the past. She also realizes that he knows that Ali was the one who hurt Jenna. When he makes a comment that he's glad Ali is dead, Emily concludes he must be A. She flees the car by going out into the storm.
While Aria and Spencer try to figure out a way to warn Emily, Hanna has to get back to her father in Philadelphia. She thinks she's going to be able to slip into the hotel room while the others are at the theater, but instead, she finds them waiting for her. Kate didn't lie for her; she told her mom and Hanna's dad that Hanna left for Foxy. She also told them Hanna made her take the Percocet. Hanna's father is furious. Hanna realizes Kate played her for a fool to try and keep her out of their lives. Hanna's mom arrives to take her home. Hanna pleads for a chance to explain what's been going on to her dad, but he refuses to listen. He doesn't even say goodbye to her when she leaves.
Emily makes it home and locks the doors. Her parents are gone for the weekend, and her sister hasn't returned from her date. Spencer calls to warn her about Toby, and Emily tells her she came to the same conclusion. The storm knocks out the phone line before they can say anything else. Toby appears at Emily's back door, asking for a chance to explain. Emily is petrified, thinking he's come to kill her, too. She tells him that she knows what he did. Toby panics and runs away. Emily remembers that he has her purse in his car, which means he has the keys to her house. She tries to call the police, but the phone is still out. She grabs a baseball bat for protection and waits to see if Toby will return to kill her.
In the morning, Spencer calls Wren, hoping for sympathy. Instead, he tells her that he wants to break up with her. He admits that he's been seeing someone else. Spencer is devastated. Her sister, Melissa, asks her how the evening went, and Spencer can't lie anymore. She admits she's been seeing Wren but that things are over now. Melissa isn't surprised by the news. She's been with Wren all weekend. Someone anonymously warned her that Wren was sleeping with Spencer. Melissa gloats that she won Wren away from Spencer without even trying, and she admits that her plans are to dump him.
Hanna wakes up to find Officer Darren Wilden coming out of her bathroom, wearing only her towel. Confused at first, she soon remembers that he's sleeping with her mother. Hanna tries to convince him that Toby murdered Ali, but he tells her Toby was already investigated and has an airtight alibi for the night Ali disappeared. His police walkie-talkie interrupts their conversation with the news that another body has been found in town. He won't give her any details before he leaves, but Hanna is convinced the body must be Emily's.
Aria's home life is ruined after A sends a letter telling her mother everything — about the affair, the fact that Aria kept it secret and even that Aria visited Meredith at the yoga studio. Aria's mother is devastated by the news, and Aria's father moves out. Aria's mother blames Aria for keeping the secret for so long. Spencer calls to see if Aria has heard from Emily, as there are police cars in Emily's driveway.
Aria, Spencer and Hanna converge on Emily's front lawn, trying to find out what's happened. Officer Wilden tells them to go home, but the girls are desperate for news. They are beyond relieved when Emily comes out to talk to them. She explains that Toby's body was found in the woods nearby. He committed suicide by overdosing on pills. Spencer admits that Toby always knew about their involvement in the Jenna Thing. Hanna tells them that Toby couldn't be Ali's killer because he had an alibi.
Toby's sister, Jenna, arrives. Her guide dog leads her over to the group of girls, and she asks if Emily is there. She gives Emily back her purse and also a note that Toby had written to her. When Emily had said she knew what he'd done, he believed she meant about what he'd once done to his stepsister, Jenna. Only Ali had known his secret, and he took the blame for the bottle rocket to keep her from telling it. Seeing Emily's fear of him made him believe his secret was known. He killed himself, convinced he couldn't change.
Emily is confused by the note. She and Hanna apologize to Jenna for their teasing when they were younger. Jenna forgives them before she leaves. Spencer finally admits everything she knows about the accident that blinded Jenna. When Ali aimed the bottle rocket at the tree house window, she saw Toby inside, molesting Jenna. Ali had been so shocked that she had bumped the bottle rocket out of position. Toby chased them and told Ali that he would tell the police what she did, but she blackmailed him with the knowledge that he molested his stepsister. Emily is distraught that her actions may have led Toby to kill himself. All of the girls realize that Ali blackmailed each of them with the secrets she knew about them as well. The girls leave Emily's house, knowing that Toby didn't kill Ali, but still believing he was the person sending them texts as A. Emily soon discovers they're wrong, however, when she receives a new text from A telling her that nothing is over.