The Pilot opens at night in a barn, where Hanna, Aria, Spencer, and Emily are having a sleepover. Suddenly, the lights go out. They hear creaking noises and go to investigate, but it turns out that their best friend Alison is just playing a prank to scare them. The five girls gossip and trade secrets before falling asleep.
When the girls wake up, there are only three of them lying on the floor. Aria goes in search of the other two, and runs into Spencer, who tells her that Alison is missing. Aria tells him that she heard a scream during the night.
Flash forward one year later, and Aria has just come back to Rosewood from a year abroad in Europe. She is still upset about Alison's disappearance (No one ever found her), but her mother encourages her to rekindle her old friendships. Aria's father checks in to make sure that she feels okay about Alison, but Aria sees through his questions and reassures him that she's "still keeping his secret".
After dropping her brother off at lacrosse tryouts, Aria happens upon Ezra at a Bar and Grill. He is about to start a teaching job, and he assumes that she is a college student. Aria tells him that she wants to major in English. The two feel an instant connection, and soon they're making out on the bathroom counter.
In the next scene, Hanna is shopping with former-nerd Mona. Hanna sees Spencer across the mall, tells the salesman she'll "be right back", and runs off to catch up with her friend still wearing a pair of sunglasses. She and Mona eventually leave the mall with their stolen loot: a scarf and Hanna's sunglasses.
Aria's father drops her off at school, saying that he still loves her mom and hopes she'll forgive him. We see a flashback in which Alison and Aria are trying to ditch Mona and they accidentally catch Aria's father having an affair with another woman in his car.
Back in the present, Aria is greeted by Emily. They walk into their English room, and Aria realizes that Ezra from the Bar and Grill is their new teacher. They awkwardly stare at each other for a few moments before he comes to his senses and introduces himself as Mr. Fitz. Aria suddenly receives a text message reading "Aria: Maybe he fools around with students all the time. A lot of teachers do. Just ask your dad. -A"
In the next scene, Emily and her mother are talking about Aria's return and Alison's disappearance. They notice that new people are moving into Alison's old house, and Emily brings a welcome basket to her new neighbors. The new girl's name is Maya St. Germain, and she shows Emily pot.
Spencer has just finished converting the old barn into a loft, and she's excited to move in for her junior year - but her sister Melissa arrives with her fiancé Wren, and she claims that as a couple, the two need their privacy more than Spencer does.
Aria goes to talk to Mr. Fitz. She wants to continue their relationship, but he tells her that everything has changed now that he's her teacher and walks away.
Emily walks Maya home and tells her the whole story of Alison. The two share an almost-kiss - and later that day when Emily gets out of swim practice, she finds a note in her locker that reads "Hey Em! I've been replaced - you've found another friend to kiss! -A"
Back at the Spencer's house, Wren has just gotten out of the Jacuzzi and asks Spencer if she has a towel. The two discuss her field hockey practice and his running team at Oxford before he offers to massage her shoulders to get rid of the aching. Melissa shows up though, and they quickly move apart. Later, Spencer looks out her window to see Wren and Melissa moving into the barn - and she receives an email that reads "Poor Spencer. Always wants Melissa's boyfriends. But remember, if you kiss I tell. -A". We see a flashback in which Melissa brings home a different boyfriend, Ian, and Alison threatens to tell her that Spencer kissed Ian. Spencer tells her that if she tells her sister anything, she'll tell everyone the truth about "the Jenna thing". Spencer sees a flash of blonde hair out the window and thinks it's Alison.
Emily and Aria are sitting on a porch swing talking about the mysterious notes they've both received from 'A'. Neither one of them is willing to discuss the notes in detail since they refer to personal secrets. Both girls suspect that Alison is sending them.
When Hanna and her mother sit down to dinner, Hanna receives a text message from Spencer that reads "WE NEED TO TALK!!!" The doorbell rings and it's the police - with video footage of Hanna stealing the sunglasses from the mall. They take her and her mother to the police station, where her mother talks to the officer. Hanna is about to take a handful of the candies sitting on the table next to her when she receives a text message that reads "Be careful, Hanna. I hear prison food makes you fat. -A".
Hanna's mom takes her to their car and tells her off, explaining that Rosewood is a small town and she can't afford to ruin her reputation this way. She tells Hanna to deny everything because she will take care of it for her.
Emily goes to Maya's house and Maya tells her that Alison's body has been found. Spencer, Hanna, and Aria stand together as Hanna reaffirms that they've all made a promise to keep "the Jenna thing" a secret.
Later that night, Hanna is at home watching the news when her mother enters the house with the police officer that showed up earlier. She sleeps with him in return for his silence about Hanna's crime.
The next day is Alison's funeral, and Aria is looking out the window when Ezra shows up. He apologizes for being a jerk to her at school and she tells him that she doesn't want to get him in trouble. As she walks away, he grabs her arm and kisses her.
The four girls sit together in the front row at Alison's funeral, and realize that they've all received messages from 'A'. They turn around and see Jenna, who is blind, being led into a seat. Mrs. DeLaurentis explains that she didn't know that Jenna and Alison were friends, and Spencer tells her that they weren't.
After the funeral, Emily, Spencer, Aria, and Hanna are approached by a detective who tells them that because the case has changed from a missing person to a murder, he needs to go over each of their statements from a year ago to find out what happened to Alison. It is obvious that they are hiding something. The episode ends with all four girls receiving the same text, which they read out loud, "I'm still here, bitches. And I know everything."