Emily struggles to complete a make-up test for English, but Ella completes it and gives her a good grade. Garrett tells Spencer someone has them all fooled, that medical records don't lie. Hanna is still seeing Mona, who is still catatonic. Caleb confronts Hanna who tells him that she's been visiting Mona and they go visiting her together. Mona asks Hanna if she is getting texts again but doesn't answer to any further questions from Hanna. The Liars catch Jenna looking at the earring they planted in the girls' bathroom at school. Jenna is not blind and they decide to keep quiet about this so that they can possibly use her secret against her later.

Lucas starts acting out at school. Melissa is back in town. Veronica tells her daughters that she's defending Garrett because she knows what it's like to have a child accused of something they didn't do. Hanna visits Mona who appears happier and more alert. The Liars think Jenna is pressing Aria to find out how much Emily remembers from "that night". Spencer is convinced Melissa is the reason her mother is defending Garrett. Hanna wonders if perhaps Ian isn't the father of Melissa's baby, but Garrett is. Caleb visits Mona and reads her the riot act. Lucas tells Hanna that Mona may be faking her mental illness as a "get out of jail free" card. The Liars discover Melissa lied about the hospital and was also threatened by "A." When the Liars confront Jenna, she tells them she's been able to see from the first operation because "it was the only protection I had."

Hanna is told by a nurse that Mona has lost her visitation privileges. Maya's cousin Nate drops by to see Emily at work. Caleb tells Hanna about Mona's screaming fit when he went to threaten her. Hanna tells Caleb to stay out of it. At Radley, Wilden shows Wren a court order saying he's allowed to see Mona. Nate tells Emily that Maya told him Emily was her first real love. Wren tells Hanna that Wilden is asking Mona about Alison's remains. Spencer decides to go to Philly and dig up more info about Melissa and her baby. Ashley gets a notice from her dating profile about a possible date. The Liars go to Melissa's apartment to search for her medical records while Spencer distracts her. In a garment bag, they find what looks like a feather that matches the feather the girls got from the Black Swan dress. Caleb tells Hanna that his mother was in a car accident in Montecito which was before revealed in a text by "A". Caleb breaks up with Hanna, tired of all her secrets. Ella tells Aria she knows about Byron seeing Meredith again, but is fine with it. Spencer confronts Melissa and she reveals that she was the Black Swan and that she lost the baby the day after she found Ian's body. She wore the costume because she received instructions from "A" to do so or they would reveal her fake pregnancy.

Aria sees Lucas pounding on the door to get into a photography studio and the girls wonder if perhaps he took the photos at the graveyard. Spencer tells Emily that Garrett is being released to see his mother. Jenna, who has openly revealed she can see again, walks over and hands them invites for her birthday party. Emily's boss is making her work Jenna's birthday party, despite her being a guest. Ezra texts Aria that he's been invited to Jenna's party, prompting Spencer to question the purpose of Jenna's party. Jenna starts flirting with Nate. Ashley meets a man named Ted at the rummage sale and they hit it off. When Hanna starts volunteering to help Ashley, she finds a piece of Emily clothes that she was wearing "that night" Spencer spies on Garrett at the hospital. Spencer sees Garrett writing a card for his mother's flowers. A drunken Paige starts embarrassing herself, eventually falling over and hitting her head. Emily and Nate take Paige to the hospital. Paige comes out with a few stitches but doesn't remember anything. A tox screen found traces of a sleeping pill in her system. Paige gives Emily back the flask. Emily realizes she was drugged 'that night.' Spencer goes into Garrett mother's room and reads the card with the flowers: April Rose has the proof. Aria finds the same pills used to drug Paige and Emily in Lucas' camera bag.

Garrett's case may be closed due to lack of evidence. Ted invites Hanna to a "Thank You" party for all the volunteers at the church. Jason tells Spencer he found April Rose - not a person, but an antique shop. Hanna and Toby arrive at the church party while Spencer and Jason arrive at the antique shop. Aria finds thousands of dollars in Ezra's sock drawer while he's in the bathroom. Spencer finds an anklet that belonged to Alison that had gone missing. Emily arrives at the party and sees Holden. Emily sees the same eye tattoo from her flashback on his wrist. Holden shows her that it is erasable and it is for some sort of club/party. Holden tells Emily that he used to see Maya there. Emily tells Hanna about her conversation with Holden. Spencer's father tells her that an important evidence in the Garrett Reynolds case was turned in last night, and he knows she turned it in. It turns out the police have been looking for the anklet for two years. Traces of Alison's blood was found on it, along with someone else's blood. Then, Spencer receives the following text message: Hey Spence, I have one more surprise for you. Garrett isn't their killer. -A

Detective Wilden is on the case. He thinks Hanna is guilty since her blood type matches the blood found on the anklet. Aria makes a trip to Radley to see if she can get Mona to crack about her possible co-conspirators. Shortly after Aria leaves, Hanna decides they should break back in to try to talk to Mona alone without a chaperone around. Mona leads them into the abandoned children's wing of Radley where she hums to herself repeating the same thing over and over again. Hanna realizes later on that Mona was trying to tell them through a code that someone's "NOT SAFE", that "MAYA KNEW", and the address to Maya's website (MAS Sugar) which the girls did not know about. The girls meet a girl named CeCe who reminds them a lot of Ali. It turns out that CeCe and Alison were friends and she used to date Jason. Spencer sees Jason's car crashed into a tree. She drives him home and leaves her car at the scene of the accident. When the cops knock at Spencer's door, she and Toby lie to protect Jason, though Toby does not understand yet. When Spencer explains, Toby becomes frustrated and leaves.

Byron tells Aria that Meredith got the teaching job at Rosewood High. Emily and Nate go to the old boat House, Maya's favorite spot in Rosewood. Toby is still angry with Spencer. Paige tells Emily that she was with her a part of the time when she was drunk on "that night". Spencer is looking for help about getting into Maya's site, and goes to Caleb. Meanwhile, Wren tells Hanna that Mona might be moved to a facility in Saratoga for added security because the hospital thinks she's been passing her meds to a visitor. Hanna is forced to convince the board to let Mona stay in Rosewood. Spencer and Aria think that Veronica is trying to hide evidence that Garrett has killed Maya. Caleb helps Spencer with Maya's site and is able to hack into it. Aria meets Dianne Fitzgerald, Ezra's mother, who doesn't approve of Aria's family's reputation and tells Aria that she is responsible for ruining Ezra's career. Spencer, Aria, and Hanna watch random videos from Maya's website. Emily is in many of the videos. In one video, Maya says that she has to face her fears.

Aria shows Spencer a photo of Maya's arm with the same black eye tattoo that Holden had. Caleb gives Hanna a piece of paper with the log-in information for Maya's site. After Caleb leaves, Hanna gets a text saying "The Apple Rose Grille at closing time. Go alone or Caleb pays -A" Hanna confesses to Emily about having been able to hack into Maya's website a few days ago. Hanna gives Emily the log-in information to see for herself. CeCe, Aria, and Spencer arrive at a party, which turns out to be at Noel Kahn's cabin. Once they try to get into the party, Aria and Spencer see that they have to get stamped with the same black eye tattoo that Holden and Maya had on their wrists. Tension rises when Aria and Spencer face-off against Noel and Jenna, respectively, in a game of "Truth." The police have a court order that demands for Hanna to take a sample of her blood to see if it matches with the blood from Alison's anklet. Ashley rekindles her relationship with Ted. While Hanna goes to the Apple Rose Grille as told by "A," Hanna runs into Caleb who reveals that he sent her the "A" text to see if she would come. Hanna spills everything that happened with the new "A" and Caleb insists that he helps. Wes, Ezra's brother, tells Aria that Ezra got a girl named Maggie pregnant in high school. Aria confronts Ezra about this and she also tells him that his mother offered her money to end their relationship.

Aria continues to question Ezra about his past with Maggie. Ella begins dating Zack, the owner of the Rear Window Brew where Emily works. Hanna tells Emily that Caleb knows about "A" and now they are pretending to not be together. Emily finds two pictures of Maya in the daytime with a sign behind her and when she puts them together, it says "The Kahn's." Spencer talks to Noel and he says that she wasn't just a random guest and that they had a texting relationship. Paige stops by the coffee shop and Emily tells her to stop by her house later so they can watch a movie. Spencer sneaks into the boy's locker room and breaks into Noel's locker and checks his phone for texts from Maya. Emily and Hanna go to the Kahn's cabin to investigate. While searching the cabin, Hanna finds a hidden door and inside, she determines that Maya must have been staying in the secret room. Emily and Hanna find Maya's bag filled with personal belongings. "A" comes and locks Emily and Hanna inside the cabin. Spencer gets a new email from BLOCKED saying "Stay out of my locker!" and a video from the security camera at the cabin the night that Maya died. Later, after they manage to escape, Emily finds Nate sitting on the steps in front of her house. After Emily shows him the bag of Maya's things, Nate starts to cry and kisses Emily when she tries to comfort him. Paige walks by, sees them, and cancels her date with Emily. Spencer discovers in the video that Maya arrived at the cabin at 10:04PM. At 1:14AM, Noel and Jenna arrive at the cabin. A few seconds after Noel and Jenna enter the cabin, Maya exits the cabin and is grabbed by a mysterious figure in the driveway.

Ted comes to Hanna's house with a flash drive that contains the N.A.T videos, which was left in the church, rather than Ian taking it. CeCe reveals Alison's and Paige's violent past to Spencer. CeCe tells Spencer that Alison may have been scared of Paige. Later, Spencer is attacked by a snake in the dressing room, but is rescued by CeCe. Emily calls Hanna and says that the knife they found in Maya's bag is missing, though the bag is still there. Hanna and Spencer help CeCe with the boutique's trunk show while Emily shows up with Paige. Spencer and Hanna search through Paige's bag for Maya's knife. Aria visits Maggie and realizes that she has a seven-year old son, Malcolm. Emily realizes that Spencer and Hanna have gone through Paige's purse. She leaves upset with Paige. However, Spencer and Hanna have found the proof they needed - the earring from Ali's grave. They think that Paige dug up Ali's grave and may be "A". Paige confesses to Emily that at one point, Alison's bullying drove her to suicidal thoughts. Hanna's mom destroys the N.A.T. videos, but Hanna tells Ted that she did it. When Paige goes inside Emily's house, Jenna appears and warns Emily to be very careful who she spends time with.

Garrett's trial starts. Emily is at odds with her friends who suspect Paige is "A." Toby and Spencer have sex. Mona escapes Radley. Maggie visits Ezra, making Aria uncomfortable. "A" sends a text to the Liars, telling them to meet at Ali's grave at the Rosewood Cemetery at 10pm with Maya's bag, but without Emily. Emily tells Paige about the new "A." Paige receives a text from "A," telling her come to the Rosewood Cemetery at 10pm. Emily and Nate head up to the Lighthouse Inn. She gets a call from "A," in a distorted voice, who says, "You have one minute. Get out." It is revealed that Nate is Maya's killer and that his real name is Lyndon James. Lyndon opens a closet revealing a bound Paige and tells Emily he is planning to kill Paige using the knife from Maya's bag. Emily escapes and reaches the top of the lighthouse where she fights Lyndon and ultimately fatally stabs him in self-defense. Caleb arrives and puts his gun down to comfort Emily, but as they embrace, a dying Lyndon uses the last of his strength to shoot Caleb. Paige tells the police that someone had sent her a text telling her to go to Alison's grave at the cemetery, but Lyndon had gotten her before she could get there. Caleb survives his shooting and undergoing surgery but Lyndon is dead. Spencer lets Paige know that she is sorry for thinking she was "A." Veronica tells the girls that Garrett is now a free man thanks to Emily. The girls get a four-way call from "A," saying "Emily, I owe you one." In conclusion, the second "A" Team member is revealed: Toby Cavanaugh.

Mona is out of Radley and back at Rosewood High. The Liars do not trust Mona. Someone plants a cow brain in Mona's locker kept up with a knife. Mona is appalled and whispers something to Lucas. The Liars worry that people will think they were involved, including Mona, who instantly assures them she believes them, and wants to earn back their trust. When Lucas goes to Hanna's house later to return the rest of the money he owed Caleb, he tells Hanna that Mona had been sneaking out of Radley for a long time. Emily recognizes the new janitor as the front desk clerk from the Lost Woods Resort. The Liars investigate his office during the fundraiser and find Alison's diary. Proof of Alison's blackmail against Byron is found in the diary. Aria rips out that page and keeps it. Mona regains trust from the school when she posts an apology video on the school's website with help from Jason DiLaurentis. Meredith, now the Liars new history teacher, is injured in a fire at the fundraiser.

Aria remains suspicious of Byron. Mona tells the Liars that Harold, the janitor, has pursued her and she declined his sexual advances. They doubt her honesty. When the girls go back to investigate Harold's office further, a hooded figure rushes out. Hanna recognizes the person's shoes - it is Lucas. Lucas tells her he was looking for something but when Hanna offers to help him, he blows her off. Andrew Campbell proctors as Mona and Spencer face-off for team captain of the scholastic decathlon. Mona wins and Hanna shuns her for it, suspecting that her intentions continue to be sinister. On the way to a swim team party, Emily and Paige chase after a hooded figure after their car tires are slashed. Aria confronts Meredith about Byron's involvement with Alison on the night of her murder. Mona follows Byron late at night at Hollis and makes a mysterious phone call.

In Alison's biology notebook, Emily, Aria, and Hanna discover a conversation between Alison and a friend where Alison talks about a "beach hottie." Emily turns to CeCe for answers about the beach hottie but CeCe claims Ali never told her who it was. Spencer continues to struggle with the idea that Toby is on the "A" Team. "A" sends Spencer a text as Aria and leads Spencer to believe that Ezra broke up with Aria when he finds out that Aria knew about his son with Maggie. Spencer confronts Ezra who is unaware that he has a son. Emily asks Hanna to keep an eye on Paige when she starts acting weird. Hanna follows Paige to a lesbian bar and assumes the worst when she sees Paige and Shana having a friendly conversation. CeCe tells Emily that Ali thought she was pregnant during the summer they spent in Cape May. Later, Emily sees a picture of Wilden at the police station indicating that he was also in Cape May that summer with Ali and CeCe. Ezra heads to Delaware to meet his son for the first time and asks Aria not to call him.

While Ezra is away, Aria discovers that Ezra's brother, Wes, was placed under academic suspension for hitting on his physics teacher and Mrs. Fitzgerald tried to cover it up. On a final trip to Caleb's aunt's house before it is sold, Hanna determines that Caleb's uncle may actually be his biological father. Emily seeks Dr. Sullivan to help her deal with confounding emotions over killing someone in self-defense. Dr. Sullivan suggests hypnotherapy, which results in confusing Emily further. The private investigator Spencer hired to follow Toby tells her that he traced the "A" key to a single unit, but it turns out to be a dead end. Jason, Aria, Emily, and Hanna gather at the mausoleum to say a final goodbye to Ali after the police release Ali's remains to the DiLaurentis family. Spencer rushes in shortly afterward and spills the beans to Jason about Ali being pregnant with Detective Wilden's child at the time of her murder. Emily recalls seeing a person in a black hoodie digging up Ali's grave and abducting Emily. Emily remembers more of what happened "That Night". She remembers seeing Red Coat while being attacked by a member of the "A-Team." She remembers that Red Coat had blonde hair. Emily says that she (Red Coat) is the one in charge.

Spencer continues on a downward spiral from her break-up with Toby. Andrew Campbell kicks Spencer off the scholastic decathlon. Emily tries to talk to Spencer but Spencer refuses. Hanna talks to Jamie and gets confirmation that he is Caleb's biological father. Hanna persuades Jamie and Caleb to meet in Rosewood. Hanna also convinces Ashley to talk to Ted about hiring Jamie for the church restoration project. Jason and Emily search his dad's office for photos of Ali and Wilden, proving they were together in Cape May. After Wes and Aria arrive to help CeCe with a photo shoot at her boutique, CeCe leaves to get dinner. CeCe calls them later and lies about her car being towed. Later, Wes kisses Aria when she invites him to sleep on her couch. Jason and Emily find a picture that reveals Ali standing between Wilden and CeCe. They take the picture on their way out, but they get trapped in an elevator. Emily escapes, but Jason does not and plummets to the ground. At the hospital, Jason tells Emily he lost the picture. As the girls reunite at the hospital, they discover Jason has disappeared.

The hunt is on for discovering the identity of the girl in the red coat. Hanna comes clean to Ashley about knowing CeCe and that she and her friends found out about an illicit relationship between Ali and Wilden. Spencer accepts a dinner date from Wren. Afterward, they share a kiss outside the restaurant and are seen by the mystery girl in the red coat. Spencer tries to follow her but loses sight of her after turning a corner. Mrs. Fitzgerald continues to try to come between Aria and Ezra. Paige, Emily and Hanna go to the Rosewood Costume Shop looking for answers from Shana. When Spencer returns home, she heads into the steam shower and gets trapped by "A." Having received a text from Spencer earlier asking her to come over, Aria comes to her rescue. Once safe, Spencer tells Aria to call Emily and Hanna because she knows who is helping Mona. Emily goes to CeCe's apartment and finds her packing to leave Rosewood. Before she leaves, CeCe tells Emily that Melissa took the picture of Ali, Wilden and CeCe in Cape May and that she is not completely sure about what is true about Ali and Wilden. Wilden threatens Ashley and Hanna. Ashley runs over Wilden with her car. She and Hanna return to the scene of the crime and find Wilden's body missing. Ashley and Hanna are caught on film, oblivious to the camera in Wilden's car recording them.

Spencer reveals to Aria and Emily that Toby is helping Mona. Aria returns to Ezra's apartment to find he has returned...with Maggie and Malcolm. Emily and Hanna arrive at Toby's apartment and find a parking pass with the name "E. Lamb," Toby's alias for Radley. Spencer receives a bouquet of flowers and a card that reads: Someone close to you will pay for your loose lips -A. Later, Emily goes to Toby's place again and talks to a guy who worked with Toby. He says Toby left but never said where he was going. While Aria babysits Malcolm, he accidentally cuts his chin. Aria worries she may not be a fit parent and contemplates breaking up with Ezra until he gets everything sorted out. Spencer follows Mona heading into the woods. Spencer finds a body in the woods with Toby's tattoo on his hip wearing a helmet. Mona yells "he's dead" before Spencer identifies the body. She chases Mona but loses sight of her. Hours later, Emily is waiting for Toby after he texted her to meet up but Toby doesn't show. Emily catches a glimpse of the girl in the red coat in her rear view mirror. Hanna and Aria push Wilden's car into Lake Rosewood after it shows up in Hanna's garage with footage of the night Ashley hit him. Spencer is found the next morning in the woods, completely catatonic. She is admitted to Radley.

Spencer is held at Radley for a 72-hour observation and assessment. Spencer befriends a male nurse. She notices the name on his badge, E. Lamb, is identical to Toby's alias for Radley. E. Lamb tells Spencer that Radley has experienced a recent dilemma involving staff I.D. badges and visitor guest passes. Hanna and Ashley are blindsided when Detective Wilden approaches them at the church where they are meeting Ted for coffee. Emily is surprised when Shana invites her to coffee, only to introduce her to Olympic gold medalist Missy Franklin. Emily learns that Shana is also a swimmer, which Paige neglected to tell her. Aria lies about her relationship with Ezra in order for him to be reinstated at Rosewood High. Mona pays Spencer a visit in Radley and offers her a spot on the "A" Team for the second time. Ashley says goodbye to Hanna and heads to New York for an annual seminar. As Ashley drives away, Wilden pulls up in his car. Wilden confronts Hanna and demands to know where his car and keys are. Wilden promises not to bother Hanna and Ashley anymore as long as Hanna complies with his demand. During a group therapy session at Radley with Dr. Sullivan and other patients, Spencer confides that her friends can no longer count on her.