The story begins with a flashback. Alison DeLaurentis and her four best friends, Hanna, Emily, Aria and Spencer, are having a sleepover at Spencer's house before the end of seventh grade. Aria, a fledgling moviemaker, is filming the girls when Ali receives a text message. She excitedly answers it, but won't tell the others who sent it. When she excuses herself to use the bathroom, Spencer mumbles that sometimes she'd like to kill Ali. The other girls secretly agree that Ali can be pushy and mean, but none will admit it out loud. Ali also knows a secret about each of her friends that they have not admitted to anyone else. The girls try to read Ali's texts, but they can't unlock her phone. Ali re-enters the room before they can discover her password.
Spencer's older sister, Melissa, and her boyfriend, Ian, interrupt the girls. Ian joins the girls on the couch as they pretend to be on a talk show that Aria is filming. Spencer, who has a crush on Ian, asks him what his ultimate graduation present would be. He says it would be base-jumping lessons. A friend of his went and said the experience was better than sex. Melissa insists that Ian come help her in the kitchen, and Aria stops the camera. The following weekend, Ali disappears. The police question her friends, asking if they know anyone who'd want to hurt Ali. Although they each hated the way she sometimes treated them, they'd never hurt her. The four remaining friends separate the year after her disappearance, each going her own way, trying to forget the secrets of the past. Four years later, Ali's body is discovered, buried in the backyard of her old house. The police still have no clue who killed her. In the week before Ali's body was found, each of the four friends began receiving texts from a mysterious person called "A." A knows things about them that only Ali knew and seems to be watching their every move.
Spencer's parents insist she start seeing a therapist after Ali's body is found and a schoolmate commits suicide. Spencer suspects they might also want her to talk about why she had an affair with Wren, her sister's college-age boyfriend. The doctor asks her about the stress in her life, but Spencer feels as if things are getting better. It's been three weeks since she's received a text from A, something she doesn't admit to the therapist. The doctor does get her to open up about her relationship with her sister. After the appointment, Spencer's mother surprises her with the news that the essays she wrote for homework have been nominated for a prestigious award, The Golden Orchid. Spencer cringes. The assignment had been due when everything with A and Wren was happening. Feeling overwhelmed, Spencer had plagiarized one of Melissa's old papers and turned it in as her own. Her mother has already called the newspapers and is planning on a big interview and photo shoot to publicize the good news.
Aria is also relieved that she hasn't received any texts from A in the past few weeks, but that doesn't alleviate the tension in her house. A told her mother about the affair between her husband and a student at his college. A also told her that Aria had known about the affair. Since then, her father, Byron, moved in with his girlfriend, Meredith, and the relationship between Aria and her mother has been strained. Aria's also feeling pressure because she started dating her friend Hanna's old boyfriend Sean. Hanna is furious because she still has feelings for Sean. Aria is confused because although she likes Sean, she still has a connection with her English teacher, Ezra. The two had started a steamy relationship before he realized she was his student. They broke up after Ezra read A's text messages about their relationship and thought Aria was playing around with him. The feelings between them, however, are still strong, as Aria discovers one day after class. Ezra is concerned because she seems depressed. Aria isn't sure she can trust him, so doesn't tell him about her family troubles. As she leaves, however, she stumbles. Ezra catches her and the two embrace for a moment.
Hanna and her best friend, Mona, sit in the school's coffee bar and play their favorite game, criticizing the other students for their looks and/or fashion choices. Mona is excited to discuss plans for their "Frenniversary," the annual celebration of their friendship. She's also planning her big 17th birthday party, in which Hanna will play a large role.
Against her parents' wishes, Emily has decided to continue her relationship with Maya. The two meet in the woods when Emily's parents aren't home. Maya tells her that there's a stalker in town, peeping into windows and running through their yards. Emily and Maya share several kisses. Maya admits she'd like to be more open about their relationship, but Emily isn't ready to tell the world she's homosexual.
In the school parking lot, Ezra gives Aria an essay to read concerning The Scarlet Letter, the book they're reading in class. It's the story of a Puritan woman condemned to wear a scarlet letter A on her chest because of her affair with a man. When Aria receives a text from her father, asking if she'll meet with him at his college, it gives her an idea. She asks Sean to drop her off at the school. Then she waltzes in to Meredith's painting class and paints a red A on Meredith's chest before leaving.
Hanna can't wait for her "frenniversary" dinner with Mona. Officer Wilden has other ideas, however. He's called all of Hanna's old friends together to discuss Ali's disappearance, to see if they can remember anything else about that night. He also warns them that someone has leaked one of the videotapes they'd given to the police department to the press. In light of Ali's body being found, the story is making headlines again. Mona calls to find out why Hanna is late and becomes irate when she learns Hanna is with her old friends. Mona doesn't give her a chance to explain before hanging up.
Officer Wilden discusses the suicide note left by a boy in town, Toby Cavanaugh. In it, he said he'd promised to keep Alison's secret if she kept his. Wilden wonders if the girls knew Ali's secret. They won't confess it, but Ali accidently blinded Toby's sister, Jenna, with a bottle rocket. When Officer Wilden answers a phone call, Emily admits she wants to tell him about Jenna. The other girls try to convince her otherwise. Before Officer Wilden returns, the girls all get a text from A warning them to keep quiet about everything or they'll be sorry.
Aria returns home to find her brother watching a news program playing the videotape she'd made of her old friends. It's the film with Ian and the pretend talk show. Her mother comes in carrying groceries, and Aria offers to help. She tells her mother about painting the A on Meredith's shirt, but instead of being happy, her mother is furious. She tells Aria that the heroine of The Scarlet Letter was a sympathetic character. Aria offers to leave the house, since her mother can't stand to look at her. Her mother agrees. Aria has no idea where she'll go, but she knows she wants to try to make her mother happy.
Spencer is struggling to remember exactly what happened the night Ali disappeared. It seems like she's repressing a memory, and the thought frightens her. Her AP teacher announces that she's made the finals of the Golden Orchid. She receives another text from A. A knows she cheated on the essays. A also tells Spencer to attend Emily's swim meet if she wants to know what will happen if she doesn't follow A's commands.
Emily is relieved to have set up an appointment to talk with the police about Ali. She is ready to leave the drama and fear behind her. Her swim coach tells her a recruiter from a university wants to meet with her. When she shares the news with her sister in the locker room, her sister stalks away into a bathroom stall. Confused by her sister's behavior, Emily makes her way out to the pool to watch the rest of her teammates compete. She gets more strange reactions along the way. She soon discovers the reason. A has made copies of a picture showing Emily kissing Maya and has posted them all over the school. Even Emily's parents, who are in the stands watching the meet, have seen the photo. Aria tries to convince Emily to stay at the meet and discover who A is, but Emily is too humiliated.
Sean's parents offer to let Aria stay with them since her mother kicked her out of the house. After dinner, Aria retires to the guest room to get some homework done. She receives an email from A who wonders if she will tell Sean about her relationship with Ezra. Aria hears several twigs snapping outside her window, but when she investigates, sees nothing strange. A news story warns that the Rosewood Stalker has been seen in the area. Returning to her computer, Aria sees A has written again, this time warning her that Ali's killer wanted something from her and is still nearby.
Although Mona isn't returning her texts, Hanna tracks her down at one of their favorite restaurants. Mona has surrounded herself with sycophants she usually makes fun of, but now are acting like her friends. When Hanna questions her about it, Mona explains she wants to have an attending "court" at her birthday party, and these girls will be in it as well as Hanna. They troop off to get fitted for special gowns for the party, but Hanna is left behind because her purse spills open. As she gathers up her things, the waiter comes over to help. He's Lucas, a boy that used to be considered cool in middle school, but is now considered a dork. He tells Hanna that Mona left the check for her to pay. Hanna leaves the restaurant and gets a text. A warns her that one of Hanna's old friends is hiding something and that Mona shouldn't be trusted.
Emily's parents are horrified that their daughter may be a lesbian. They invite a spokesperson from Tree Tops, a group that helps rehabilitate homosexuals, to talk to her. Emily's parents warn her that she either meet with another student in the program and work on changing her behavior, or they will send her to live with an ultra-conservative aunt in Iowa.
Spencer is getting ready for her publicity photo shoot with the local newspaper when she gets a text from A warning that Ali's murderer is right in front of her. All Spencer can see is a picture of her friends stuck in her mirror. Melissa comes in to tell her the reporters are ready for the interview. Spencer again has a strange memory about arguing with Ali, but the details are hazy. The afternoon goes very well, and the reporter is excited to let Spencer know that she will be featured on the front page. A sends a text threatening to tell everyone Spencer's secret.
Maya tries to convince Emily to continue their relationship now that it's been made public, but Emily refuses. She explains her parents' ultimatum, and Maya is crushed. Emily meets with Becka, an alumni of the Tree Tops program. Although Becka seems nice, Emily is confused about how the Tree Tops program works. Becka claims that they help homosexuals to see the cause of their behavior and how difficult their lives will be if they continue in this lifestyle choice. This doesn't add up in Emily's mind because she knows Maya is happier now that she is "out," and there is a lesbian couple that runs a shop nearby who also seem very content. Emily knows she must try the program and asks if she can go out with Becka and her former girlfriend so she can see how they handle their friendship. Becka agrees.
Spencer's therapist helps her understand that her relationship with Melissa has been altered by something that happened in the past — something that made Melissa feel jealous if their parents showed Spencer any love. Spencer, in turn, has compensated by hurting Melissa by taking her boyfriends. Spencer admits she is having weird visions of arguing with Alison. The doctor offers to hypnotize her to see if she can unlock the memory. Under hypnosis, Spencer remembers fighting with Ali the night she disappeared. Ali believed Spencer had read her diary. She also said Spencer wanted to steal something from her. Spencer denied the accusations but remembers shoving Ali. Ali yells another accusation, but Spencer can't hear the words. She wakes out of the memory disorientated. The doctor helps her calm down before she leaves. While Spencer gathers her thoughts in the parking lot, she sees a shadowy figure spying on her from across the street.
Hanna tries to make up with Mona by hiring someone to announce her birthday party, but A transforms the note into a horrible joke. Mona begins telling everyone about Hanna's bulimia problem and how she was arrested for shoplifting. When Mona doesn't deny she's been spreading gossip, Hanna hides in the bathroom. Unfortunately, in her emotional state, she accidently hides in the boys' bathroom. Lucas finds her and offers to cheer her up with a surprise the following day. On her way back to class, Hanna finds a note taped to the back of her blazer that says to feel sorry for her. On the other side, A has typed a message telling Hanna that Mona has had liposuction.
Aria goes to Ezra's office to ask for an extension on a paper. She breaks down and confesses the problems she's having at home. Ezra admits that he went through something similar after seeing his mother kiss a doctor. His parents later got a divorce. The chemistry between her and Ezra overwhelms them both and the two end up kissing passionately. Aria manages to break away. As she leaves his office, she sees a note on his whiteboard. A has seen everything. Another note on the bottom warns that one of her friends killed Ali.
Spencer can't stop thinking about the forgotten argument she had with Ali. She asks her mother if she's ever experienced temporary amnesia. Although reluctant to share the information, her mother eventually tells her the truth. When she was 7, Spencer, her mother and Melissa were victims of an armed robbery outside a museum. When they got home that night, Spencer developed a high fever. She was tested for spinal meningitis, but it turned up negative. She woke from the fever a week later but had no memory of the robbery. Her parents took extra precautions for the rest of the summer, afraid Spencer would relapse. It meant that Melissa had to miss out on several important events her mother had planned to attend with her. Spencer is petrified that this may not have been the only time she's forgotten something important and that she may have been the one to kill Ali.
Lucas takes Hanna for a hot air balloon ride to cheer her up. He tells her about his brother who tried to commit suicide the previous year. Hanna admits her bulimia. Instead of being horrified, Lucas tells her his cousin also suffered from that but got better when she moved away. Hanna finds herself telling Lucas about the harassing notes from A and all the other problems in her life. She admits she and Mona had become friends when they tried to turn themselves into versions of Alison. Lucas is glad she isn't really Ali because she'd been mean to him. Ali spread rumors in middle school that he was a hermaphrodite; that's when his reputation went from being cool to being a dork. Lucas asks Hanna to hang out with him on the night of Mona's party since he hasn't been invited and she's been uninvited.
Spencer and Melissa hang out together in the family's hot tub. Melissa brings up issues she's been talking about with the therapist. She admits she might be purposefully choosing boyfriends who are untrustworthy. She also says that she believes Ian, whom she is dating again, may have been unfaithful to her in the past. If Melissa ever finds out it's true, Ian will be sorry. When Spencer asks what she'd do to the girl, Melissa cryptically answers that maybe she's already done something. Later, A sends Melissa a text with the opening lines of her old economics essay. When Melissa questions it, she learns about Spencer's plagiarism. The sisters get into a violent fight that ends with Spencer pushing her sister down a flight of stairs. As she does, she remembers pushing Ali down during their argument. She passes out before she can remember anymore.
Aria decides not to go to Mona's party with Sean after she receives a call from Ezra. When she arrives at Ezra's house, she immediately feels at home. The two share several glasses of scotch while they talk about themselves. Ezra wants to try and continue their relationship. Aria claims she wants to end things with Sean first, but soon finds herself kissing Ezra.
Hanna believes Mona has been moved by her plea to mend their relationship when she receives a package. Inside is the dress that Mona chose for her special birthday court to wear. Hanna excitedly texts Lucas to tell him that their evening together is off and dons the dress. Even though she'd been fitted for it, the dress is too tight. Hanna manages to squeeze into it, thinking that she must have binged too much over the past few days. Mona is appalled when she sees Hanna at the party. She is wearing the same dress, but it fits her perfectly. Hanna trips and the dress rips. She sees her picture displayed on a giant television screen as she tries to leave. She is grateful when Lucas appears and gives her his jacket to wear before escorting her out of the ballroom. He takes her to a reading room at the nearby college so she can change into some old clothes from his car. Hanna wonders why he was at Mona's party, and he explains that he'd actually been invited, but had told Hanna he wasn't so she wouldn't feel bad. Hanna apologizes for breaking her date with him. The two make out on one of the couches, until an older professor interrupts them. Lucas takes her back to the party so she can get her car. As she drives home, she receives a text from A. This time, however, A didn't scramble her phone number. Hanna realizes it's a local number. A moment later, she remembers whose number it is.
Emily goes ice-skating with Becka and her friend Wendy. Emily is uncomfortable with the obvious history the two have and with the memories it brings up of her feelings for Ali. Before the night is over, Emily discovers Becka and Wendy making out. Becka admits that she thought Tree Tops worked, but seeing Wendy again brought back all her old feelings. Emily asks if they can drop her off at Mona's party. Emily hopes Maya will still be there and they can get back together. She is thrilled when her plan works out, and Maya forgives her. The two sit outside, holding hands and confirming their love for each other. Emily's mother arrives, after receiving a text, and drags Emily home. Her bags are packed and she'll be going to Iowa in the morning.
Aria has a dream about the video she made with Ali and her friends. In it, the dream Ali keeps telling her to look closely at the tape to find the answer as to who killed her. When the dream Ali gets angry because Aria doesn't understand, Aria wakes up. She finds herself in Ezra's bed. He comforts her with kisses, and they talk about moving out of the country together. As she starts to doze off, the police break down the door. They arrest Ezra for sleeping with a minor. As they take him away, Aria finds Sean in the hallway. He called the police after A texted him pictures of Aria and Ezra kissing at school. He tells Aria he packed up her stuff and left it on the porch because she's not welcome to stay at his house anymore. Aria takes her belongings and goes to an all-night diner. She calls her mother to see if she can come home, but her mother doesn't pick up the phone. Desperate, she calls her father, but gets angry when she hears Meredith in the background. Aria decides to spend her time reviewing the video Ali had talked about in her dream. The waitress comments on how sad it is that the news talks about Ali and her friends but never mentions her boyfriend. At first Aria is confused, but when she examines the video again in slow motion, she sees that Ian and Ali touch hands several times. Aria knows that Spencer had a crush on Ian. That information, along with A's clues, lead her to believe that Spencer killed A. She calls Emily to tell her, but Emily doesn't want to talk about it. When Hanna calls at the same time, Emily puts her through so they all can talk together. The connection is garbled, but Hanna tells them to meet her at their usual rendezvous spot at the playground. She knows who A is.
Spencer dreams again about the night Ali disappeared. This time, she sees everything that happened. Ali thought Spencer had read her diary, but Spencer denied it. She and Ali also fought about Ian. Eventually, Ali made Spencer so angry that she pushed Ali into a stone wall. Ali hit her head and fell unconscious. Spencer wakes up to find she is locked in her room. Her father tells her it's for her own good. They've taken Melissa to the hospital. He doesn't let Spencer out. Hanna calls and tells Spencer to meet her at the playground, that she knows something. Spencer is terrified that she's killed Ali and Hanna has figured it out.
As she drives to the playground, Hanna is convinced she knows who A is, but is still unsure how A could have known all her secrets. Hanna waits outside in the parking lot for the others to arrive. She spies an SUV across the lot and wonders if it's one of the girls. Another car pulls in, and Hanna sees Aria hanging out the window. Aria screams for her to watch out, but it's too late. The SUV speeds toward Hanna and hits her.
Emily and Aria call 911. As they wait for the ambulance, Aria tells Emily she believes Spencer killed Ali. Aria then sees Spencer in the trees surrounding the parking lot, looking very odd and upset. Spencer disappears before Emily sees her. Aria receives a text message from A, claiming Hanna knew too much.