Hanna barely survives being rundown by "A", and due to a head injury, she loses her memory of the previous day, thus forgetting "A"'s identity. Emily's parents catch her with Maya at a party and send her to Iowa to live with her strict, religious relatives. She is glad to be safe from "A", but after Emily is accused of threatening her cousins, she runs away.
After being kicked out of Sean's house, Aria reluctantly moves in with Byron and Meredith, who announces that she is pregnant and when Bryon's and Ella's divorce is finalized, they are to be married. While at Hollis College, Aria takes an art class and befriends Jenna, who she suspects could be "A". "A" reveals to Melissa (Spencer's sister) that Spencer stole her essay for the Golden Orchid competition, but the family keeps quiet to protect their reputation. Melissa and Spencer grow closer, and Spencer confesses that she kissed Ian, and that he and Alison were secretly dating. When fragments of her memory from the night Alison died are restored, Spencer is horrified when it dawns on her that she may have accidentally killed Alison.
Emily returns home when she sees her parents on TV, who tell her that they love her and accept her for who she is. Mona and Hanna's friendship is restored, and to celebrate Hanna's recovery, Mona and Spencer plan a party for her. Spencer is surprised to discover that she enjoys Mona's company, and even more so when Mona tells her that she has been receiving messages from "A". Hanna is thrilled that Mona approves of Spencer, and they consider letting her join their clique.
Meanwhile, "A" tells Aria that Meredith has a secret job at Hooters, and she goes there with Mike, only to discover that "A" was lying. Darren Wilden and several other cops are there, and Aria is tempted to tell them about "A". When Mike realizes that something is troubling his sister, he urges her to tell Darren, and she eventually does. On the night of Hanna's party, Aria tells Jenna what happened the night she was blinded and apologizes for not stopping Alison, but Jenna reveals that she and Alison had planned it together to get rid of Toby. Aria asks Jenna about "A", but Jenna becomes scared and quickly leaves, hinting that she knows who "A" is.
Emily and Maya are reunited, but Trista, a girl who Emily had met and flirted with in Iowa comes to visit, their relationship is shattered, and Emily is saddened further when she sees Trista and Noel hooking up. Melissa confronts Spencer about seeing Ian behind her back, which Spencer denies, and when she leaves, Spencer and Mona discover another note from "A" and suspect that Melissa killed Alison because she was jealous of her relationship with Ian. They inform the others, and decide to turn Melissa in. Mona drives Spencer to the police station, and Aria tells Emily and Hanna the truth about The Jenna Thing. When Hanna says that one in four boys sexually abuse their sister, Emily tells her not to believe everything she hears, which causes Hanna's memory to return, and she is horrified when she remembers who "A" is: Mona.
Spencer is hesitant about turning in Melissa, but Mona comforts her and convinces her otherwise. Moments later, Spencer receives a text from Emily, telling her that Mona is "A". When she receives several more from the girls, who are worrying about what Mona will do, Mona realizes that they finally figured it out. While Aria, Emily and Hanna go to the police station to tell Darren that Mona is "A", Mona drives Spencer to Floating Man's Quarry, where she explains that she saw what happened on the night of The Jenna Thing, and when Maya moved in, she found Alison's diary, which contained the girls' secrets. Using the information to her advantage, she got a new phone and became "A" to get revenge on the girls for blinding Jenna. Spencer accuses Mona of killing Alison, but Mona says that it was Ian who killed her, as Alison had blackmailed him about their relationship.
Spencer secretly calls Darren, who overhears her conversation with Mona and learns of their location. Mona tells Spencer that she originally planned to frame her for Alison's murder, but recently grew to like her, and thus decided to frame Melissa to do Spencer a favor. She then offers Spencer her life in return that she becomes "A" with her, as they could pin the blame on someone else. Spencer refuses and Mona attacks her. They fight on the cliff's edge, and in the struggle, Spencer accidentally pushes Mona off the cliff to her death. Aria, Emily and Hanna arrive on the scene with Darren and police, and find Mona's body and an unconscious Spencer. Hanna is shaken with the news that Mona is dead, and that her best friend was in fact her worst enemy all along. Spencer wakes up and tells Darren that Ian killed Alison, and Hanna finds Mona's Blackberry which she used to be "A".
A while later, the truth about "A" is made public, which helps restore the girls' relationships with their families. Hanna still has Mona's Blackberry, and before turning it in, she deletes all the messages Mona sent her to keep her own secrets safe. Ian is arrested and the girls go to his court hearing, where he pleads not guilty. As they leave, the girls are relieved that they can move on with their lives and forget about "A", but Emily catches a glimpse of someone who resembles Alison and is unsure if that will ever happen. The girls have made up now and are closer then ever