After a long time, four friends reunite when each of them receives strange, threatening letters, which they believe are from their long-lost ex-partner, revealing their secrets.
After Jenna returns to town, the girls are forced to face their troubled pasts. They remember blinding Jenna in a scary prank that went horribly wrong. There are inquiries over Alison's passing.
The girls try to revive Alison's memory while looking back at their old and new relationships, but anonymous letters from A haunt them and force them to confront their past.
The girls take their efforts to stop A's threat seriously, but they end up making things more dangerous as they encounter unexpected situations and surprises, most important of which is breaking into Spencer's home and discovering a message on the mirror and a model of a grave on the table.
Ignoring A is a mistake that the girls regret. The girls also deal with the typical issues of adolescence, like emotional or familial issues.
The girls hope to forget the past and enjoy the school dance, but unsettling secrets and memories could spoil their wonderful evening.
After the dance, the girls deal with a lot of issues, and while they all attempt to fix their mistakes. A makes matters worse by sending them an odd letter that leads them to believe that their friend Toby has passed away.
New evidence emerges about Alison's death, worrying the girls, but they continue preparations to honor her spirit, fearing that Jenna insists on giving a speech during the ceremony. At the end of the day, a stranger destroys Alison's memorial.
Tensions rise when the girls are stuck inside a school due to a heavy storm. After discovering an old letter she wrote to Alison, Emily places it in her bag prior to it disappearing. Later, Emily is charged with destroying the memorial.
The girls go camping in an attempt to forget A's threats, but the day does not go well after Hanna learns A's identity, but she is unable to tell the others as A runs her over with a car.
The girls deal with the repercussions of what happened while camping, as Hanna remembers thinking A was Noel, while A sneaks into Hanna's room unseen to write an apology for what he did.
Aria is unhappy that Noel knows about her relationship with Ezra, and Hanna is in a wheelchair as she leaves the hospital. The police learn that Lucas is the one who destroyed the memorial, and the girls are shocked by the persistence of A's warnings.
A is indirectly and unexpectedly helping the girls with different topics for each of them, while a video of Alison and Ian appears, with only the sound of a fight being clear, which raises the girls' suspicions about Ian.
The girls suspect that A might appear at the school's charity event. Hanna and her mother fall into a financial crisis, and the solution is in the hands of A, who leaves her a financial offer. Simone returns to visit the girls, but the surprise turns into a nightmare.
Jason receives news about A, so he shares it with Spencer. A gives Hanna the choice of either revealing Aria and Ezra's relationship or not giving her the money.
Aria learns about Hanna's effort to reveal her affair with Ezra in exchange for money, while Spencer receives an odd cryptic message from Toby.
Aria tries to forgive Hanna for betraying her, while Hanna offers Caleb a room in her basement. On the other hand, the girls are able to translate a message from Toby, which indicates that something bad has happened.
The girls participate in the school play and discover that it frighteningly reflects their lives. Later, they find a cup covered in blood, and investigations prove that it is the blood of a mouse. Four cages appear in A’s house, and each cage has the name of one of the girls on it.
The story of the cup puts the girls in trouble as the police interrogate them, while Spencer's family asks her to see a psychiatrist. At the hospital, Spencer hears the sound of a flute from Room 214, and the police suspect that Spencer had a hand in Alison's murder.
Tension increases between the girls as many problems happen to them, and they learn that there are secrets in the city other than their own. Ian encourages Spencer to run away with him, but Toby advises her not to do so, and new incriminating evidence for Spencer appears.
Spencer is kidnapped on her way to meet Toby but Ian saves her. The girls find videos belonging to Ian that show that someone has been watching them for a long time.
Spencer goes to the church and Ian chases her and plans to throw her from the tower. Someone throws Ian from the tower, and his body disappears. Then the girls receive a final message from A that the problems will not end unless he decides so.