On Aria's first day back, Aria and Emily seem to be closest to each other. Emily is the first to welcome Aria back to Rosewood, and they are friendly right away, even though they lost contact. Emily comments on Aria's pink hair strip, saying she "wore it well." Emily fills Aria on what she missed while away, including the fact that the other three girls, her former friends, Hanna, Spencer and Emily have all disbanded since Alison's death.Later, in English class, Emily picks up on the weirdness between Mr. Fitz and Aria.
Emily discusses Aria's return home with her own mother, Pam, who makes a comment about the pink streak Aria used to sport in her hair and no less, the fact that her mother used to let her "walk around like that". Emily goes to Aria's house and they sit on a bench. They are the first to tell each other about texts coming from 'A'.
During a flashback it is revealed that Emily and Aria, along with Hanna and Spencer were hesitant to drop a stink bomb in Toby's garage, but Alison eventually convinces them to do it.
Spencer sends an S.O.S. to Emily and Aria, and the girls gather in front of Spencer's vanity, which has been vandalized by "A". The girls sleep over at Spencer's.
Hanna, Spencer, and Emily arrive at Aria's to console her with Chinese take-out and rag mags – thinking she’s sullen from her parents' marriage troubles, when in fact she’s depressed over the breakup with Ezra. At the Homecoming dance, Aria is assigned to the same booth Ezra is working. When given to the opportunity to leave the booth, she takes it. She returns to her friends and they discuss Emily's surprising choice of a date. Later, Aria and the other girls search for Emily and are distressed to discover broken glass and blood in the chem lab, fearing the worst. The next day, Aria and Spencer visit Emily at home to fill her in on Toby's sordid past with his stepsister, Jenna. They try to get Emily to tell the police the truth about what happened last night, but she's not even sure what the truth is.
Aria, Spencer, Emily and Hanna begin to prepare for Alison’s memorial. After the memorial, Jason stops by Spencer's house to thank the girls. They accept his gift - the "Alison" friendship bracelet Alison had been wearing the day of her death.
A huge storm is on the horizon, as Aria, Spencer and Hanna study in preparation for the SAT exam the next morning. Emily is nowhere to be found, though. Soon, they all run into Detective Wilden and have to over for Emily without knowing why. Aria sees Detective Wilden hustle Emily into the library to answer questions. Aria and the other girls follow, and listen as Wilden accuses Emily of destroying Ali's memorial and worse. He reveals a personal letter Emily had written and exposes the secret she had been hiding from her friends - that she was in love with Alison. Emily's friends all stick up for her, then Mrs. Hastings walks in
After Spencer, Hanna, Aria, and Emily are done being interrogated by Darren Wilden, Aria comforts Emily after Emily confesses that she liked Alison as more than a friend. Aria tells her that she knows Alison loved her a lot, even if it may have been just as a friend.
At school, Mona Vanderwaal hand delivers invitations to her "glamping" party. Aria, Spencer, and Emily don't plan to attend until they get a text from "A". Later, the girls are called to the principal's office for questioning by the police. An FBI agent named Agent Cooper arrives; she has been enlisted as the representative of the FBI to assist the Rosewood Police.
At the party, Emily fills the others in on Toby's confession before they start roasting marshmallows and Aria and Emily get their hair done in crazy 80s 'dos.
At school, the girls are decorating for the school's upcoming dance-a-thon, but take a break to discuss whether they should turn the video into the police. Aria agrees with Emily that this video could exonerate Toby.
Aria rouses the girls early in the morning from their sleep at Spencer's house. She's been up all night analyzing the picture that "A" left them. Aria has figured out that the picture was taken from the perspective of Alison's bedroom window. She thinks Alison's brother, Jason, may have taken the picture. Aria proposes talking to Jason, but Emily treats the thought of approaching him with disdain.
Aria joins Emily in her room, rather then spending the day with Ezra. Emily gets a text invite from Paige to a picnic, and Aria gets three texts from Ezra, ignoring each one. After Emily questions her, Aria confides her frustration about keeping "The Jenna Thing" a secret from Ezra. Emily encourages her to confide in him, though Aria isn't as sure, especially given the agreement the girls made to never reveal their secret to anyone.
Worried due to the possibility that the cops might search her house creates a bag full of Ezria mementos and gives it to Emily for safekeeping, so as to protect the privacy of her relationship with Ezra. She leaves one thing out, though - a book by Sherwood Anderson dedicated to her by Ezra.
Later, in the school courtyard, while Aria gives her bag of mementos to Emily for safekeeping in her locker, they overhear Caleb mysteriously speaking on the phone with someone, telling that person that something cannot happen that night. He keeps referring to "her," and it becomes clear after he mentions that he is living in her house that he means Hanna; the other person seems to be saying negative things, while Caleb is defending her. When he gets off the phone, Aria and Emily hide before Caleb can see them. The two interpret the phone conversation to mean that Caleb is talking to another girl in a romantic way.
The next day at school, Emily and Aria talk at their lockers. When Hanna sees Jenna, she walks up to her and surprise slaps her across the face, to Emily and Aria's shock.
In Emily's room, the girls congregate to discuss what Jenna may have been looking for. They also discuss the creep factor in Caleb rifling through Hanna's belongings. But, Aria comes to Caleb's defense, knowing how tempting it is sometimes to go through somebody else's information, such as her boyfriend's web page. Emily suggests coming clean to Ezra about it, but Hanna tries to convince Aria to create a page of her own posing as one of Jackie's past classmates in order to sneakily find out more about her. Aria sets up a fake profile and gets Jackie to accept her friend request. But, thinking better of it, she de-friends her and closes the computer. Going with Emily's advice instead, Aria rents a number of wedding themed DVDs to watch with Ezra. Ezra picks up on the hint, and Aria uses it as a conversation starter to confront Ezra about his past mysterious fiancée.
When with Ezra, Aria gets a text from Emily letting her know that she's found the key, and Aria reports that she has to leave, heading for Emily right away. Thanks to the snowglobe clue, Emily, Aria and Hanna track down a secret storage location. There, they uncover a flashdrive contained in a lunch box. In Emily's room, the girls watch the secret videos in the flashdrive, mostly of the girls in intimate moments.
When Hanna, Spencer, Aria, and Emily come out of the church (when everybody thought they were lying to the cops), Emily mentions how she thinks Ian Thomas' body is on a way to a meat grinder. Aria says, "Oh Em, come on, you gotta quit watching those horror films," clearly worried about Emily. At Emily's house, the girls bring up Dr. Sullivan, who is sworn to confidentiality, and Emily and Aria are the loudest proponents in favor of cluing her in on their secrets.
The girls sit parked in Emily's car. Aria reads Emily's Letter of Intent from Danby and is excited for her friend's good news until she realizes Emily forged the letter. Aria doesn't think it's a good idea.
After Ian Thomas' funeral, Aria walks with Emily, spotting Jason. Emily and Aria talk. Emily forms a negative opinion about Jason, but Aria doesn't seem to feel the same way. but Aria decides to go meet Jason.
At the fashion show, Aria tries to reassure a worried Emily that Samara is not being too touchy-feely with her friend Quinn.
Emily moves into the Marin household. At school, Emily confides in Aria that things aren't going so smoothly at Hanna's place. Aria is concerned, but then Emily lets on that it isn't so bad; she is grateful to be in Rosewood after all. Spencer then walks over and asks Emily if she has gotten an update from Garrett yet about whatever became of their Logan Reed lead. But, Emily says that she has overloaded with swim practice and hasn't had an opportunity. So, Aria and Emily ask Spencer to do it instead. They tell Spencer that she is better at persuading people.
At the hospital, Aria later joins the girls in Emily's hospital room with coffee in hand, and everyone looks on awkwardly as Aria offers the cup of Joe to her friend with a hole in her stomach, which Hanna can't seem to get over. Emily considers telling her dad the truth about the Danby letter. Later, Aria and Spencer return to Emily's room and try to talk Emily out of fleeing Rosewood.
At school, Aria says she is not intimidated by "A", but Emily is hardly comforted. Just then, Jason walks by in the hallway and shares a smile with Aria. Emily is weirded out by their cordiality, but Aria brushes it off before revealing her previous night’s dream and her insecurities about her relationship with Ezra. Emily agrees that Jason is mysterious and wounded and it is understandable why Aria might be attracted to him, but pursuing it would be a bad idea, not to mention her current relationship with Ezra. Emily reminds her that they love each other and just need a way to connect again. Aria asks Emily to keep the conversation to herself. She agrees under one condition - Aria stays away from Jason.
Later, while waiting for Ezra to return to his office, Emily, who is playing cards with Samara's friends, calls Aria to ask her advice about "A’s" blackmails. Aria suggests Emily "bluff" since she is playing cards. In Jason’s shed, Spencer and Emily discover that it is doubling as a dark room. There are developing photographs hanging all around. After shining their flashlights on the photographs, the girls realize that the pictures are all of Aria. But when they enter later, they find the dark room dismantled.
Emily is sitting in the school lunch room when Ariawalks up. Emily says she's been trying to get in touch with her all night; they have to talk. Aria agrees and reveals to Emily that Jason kissed her last night. Emily is not happy to hear this and immediately tells Aria about the pictures Jason had of Aria sleeping (or drugged) in the woodshed, causing Aria to be "officially terrified."
Emily cannot sleep at night, tormented by thoughts of "A". At the first sign of light, she leaves to get into her car and leave, waking Hanna. When Hanna calls Emily, she discovers Emily left her phone in her bag. The Liars gather in Hanna's room and discuss where Emily could have gone. Looking through Emily's phone, Spencer finds a picture of Ezra and Aria kissing sent by "A," along with the caption "Clue Ella in, and I'll let you out." Aria is momentarily concerned the photo was forwarded to Ella, but her friends assure her Emily wouldn't betray her like that, no matter what "A" says.
An episode about life with Alison before the Pilot, a rumour is going around that Emily lost her virginity to Ben Coogan. When Aria hears this, she is ready to march over to his table and set him straight, but Emily pulls her back to her seat and tells them all it's true.
When Emily passes by Aria and Hanna, they both give her the cold shoulder as a part of their plan to fool 'A'. Later, Emily exits the gym after aswim meet, spots the girls, and demands the box Jason gave Aria for all to hear and storms off. Aria and the others feign annoyance. Aria arrives at the greenhouse and apologizes for being late; she dropped a pretty big bomb at home earlier. She helps pick glass out of Emily's hair.
Emily is having trouble focusing on anything with so much going on. She asks Ella if she can postpone the makeup test again because she didn't have time to read the last chapters. Ella agrees to reschedule, then asks Emily if there are more things she does not know about her daughter. Emily says Aria is the same person she has always been; someone to be proud of.
Emily asks Aria for her fake ID for Maya to use. Aria hands it over even though she and Maya don't look alike. Neither of them are worried since the club is in New Jersey.
Aria finds a crumpled note in one of the pockets of "Vivian's" coat, on which a phone number is written. Aria and Spencer want to call it, but Emily is hesitant. Aria says it might give them answers, and Spencer accuses Emily of being scared, which she fiercely denies. To prove this, Emily calls the number, which goes to a computerised voicemail. Aria takes the phone and introduces herself as a friend of Vivian's and asks that they call her back.
At Aria's locker, Aria and Emily discuss what happened with Jenna and Caleb. They wonder where Hanna is, and Emily says that the person still hasn't called back yet. They go into the girls bathroom and Aria calls the number again, planning to leave another voicemail, this time pretending to be Ali. She is caught off guard when a woman answers and asks how Aria got the number. No one there knows anyone called Vivian and tells her not to call back again. Emily considers that perhaps it was just a random number in a pocket, when she is called to the VP's office over the PA system.
Aria tells Emily and Spencer that "A" sent her dad a letter trying to get her caught with Ezra and now her mom is on the hunt to find out who "A" is. Spencer questions why "A" would send a letter like that if she and Ezra are not together anymore. Aria admits that they are actually still seeing each other. Emily accepts this, but Spencer is furious at Aria.
Five months have passed since Aria, Emily, Hanna and Spencer found out about Mona being "A" and Maya's death. The girls are having a sleepover and discussing their summer plans: Aria has been taking photography classes and Emily has been constructing houses in Haiti. Emily has clearly not been taking Maya's death well, excessively drinking and snapping at her friends. Aria wakes up to Spencer missing but this time its Emily who is no where to be found. They find Emily at Alison's grave still drunk, but Alison's grave has been dug up and Alison's remains are gone. With Emily holding the shovel, Aria and Spencer wonder if she had anything to do with it. After Spencer realizes someone is setting them up again Aria and Hanna wipe the prints off the Shovel and bury it somewhere in the woods, while Spencer takes Emily home to get her cleaned up and to burn her clothes.
Emily is in English class with Spencer and Aria as Mrs.Montgomery hands back papers. In her bag, Emily finds a necklace. She takes it out and it says "DEAD GIRLS CANT SMILE." They hear noises outside so the four girls run into the stalls together. Emily says she is sorry again for putting them through this but the girls assure her it isn't her fault. They discuss if they should give it to the police. Hanna and Aria fight over the necklace but drop it in the toilet.
Emily, Spencer and Aria go back into the school hallway where Emily says that she has to make up 4 tests because she went away. Spencer says that she needs a tutor and Aria says that she should ask Ezra. Emily and Spencer joke by saying that would be awkward because she has seen his underwear drawer and she couldn't think of him as Mr. Fitz anymore. The next day, Emily is walking with Spencer, Hanna and Aria as she tells them that her meeting with Ezra was a little weird but she got through it.
Aria calls Emily and looks at the negatives in Lucas's bag. Emily looks up the drug from her flask and finds it's a sedative used to subdue aggressive patients and inmates. One of the side effects is memory loss and Emily realizes she was drugged that night. Aria finds three of the pills in Lucas' camera bag.
Aria and the others discuss about how to tell Emily that Paige has Alison's body and is "A".
When the girls cannot find Aria, Emily starts looking for Aria in the train and finds her in the last second before the box she was thrown in falls of the train. At the end of the ghost train ride Emily, the girls and others stay behind to be questioned by the police.
The girls are talking about Mona at school, and Emily suggests that they all befriend Mona thinking that maybe Mona will tell them something about what happened the night of Halloween, specifically about Aria's dad. Aria leaves and is angry at the girls for thinking that he could be involved. Emily apologizes to Aria later and they walk to class together. Aria tells Emily that she still hasn't told Ezra about his son. They then walk into their history class where Meredith is seen to be their new teacher. During class, Meredith asks Aria a question to which she does not know the answer to as she is texting the rest of the girls. Meredith takes Aria's phone and asks her to stay after class. Aria, however, does not stay alone. Spencer, Hanna, and Emily also stay and Meredith asks them to not stop texting about her history with Byron.
Emily is pouring the patient, Aria, some tea when she makes a comment about it smelling weird. Aria remarks that Meredith says it some herb tea. She and Hanna later go to Aria's house since they haven't heard from her all day. When they get inside, they go to Aria's room, when Meredith appears and tells the girls that she is in the basement. As they walk down the steps, Meredith shuts the door and locks them in.
Aria and Emily talk about not having heard from Spencer. Pam brings Emily a package that has just arrived in the mail from Nate's, or Lyndon's, family. Inside are a bunch of old birthday cards she sent to Alison along with her biology notebook. Later, at Aria's place Emily and Aria talk about the possibility of Alison being pregnant. It's possible the information wouldn't have showed up on her autopsy. They both think she should take the information to the police and Emily offers to go down there. Later at the police station Emily hands in the notebook to Wilden.
Emily, Aria and Hanna are discussing what to do about Spencer, still obviously distraught about her new discovery and break-up with Toby. Aria asks if she has spoken to Toby and Emily replies that she left him a ton of messages. Emily suggests they bring over cupcakes to the Hastings's residence. Aria reminds her to tell Spencer what she remembers about "That night".
Someone in a red coat pulls the liars out of the burning lodge. We see them all of a sudden on the ground outside of the lodge. After they wake up, Mona, Hanna, and Spencer says that Alison is Red Coat. Emily and Aria don't beleive it and tell them it can't be but don't know what to make of everything.
Mona drives up to where the RV is, with the girls in separate cars behind her. The girls arrive and Mona opens the gate to where the RV but the RV is gone, and the girls think that Mona has taken it somewhere else. Hanna and Spencer leave in their car, while Emily and Aria wait. Mona gets into her car and is attacked from behind by a hooded figure with an Ali mask. Emily and Aria see that Mona’s car lights are flashing, so they start walking to the car. Mona finally gets the flashlight and whacks A with it and jumps out of car, and onto to the ground, gasping for breath. Aria and Emily run over to her. Mona’s car starts up and A drives the car and tries to run over the three. They jump onto the rocks and Emily lands on one of them, badly injuring her shoulder.
At Emily's, she and Aria continue checking Alison's stuff, when they discovered the mask that Spencer found. They find a stamp behind the mask, and they decide to go together. Emily, Hanna, and Aria go to that place and meet the owner Hector Lime,and ask him about Ali and the mask, Hector want something in return- Emily's face.
Emily finds Ezra in his classroom and shows him Zoe’s letter. She asks him if it is too positive. He snaps at her, saying some people have real problems to worry about, but before she can leave, he apologizes and tells her that Maggie is taking Malcolm away and to not tell Aria.
In the crawlspace, Aria and Emily wait for Spencer to arrive. Emily tells Aria that she should call Ezra, but doesn’t say why. They find a black button that they think might belong to Red Coat before Spencer finally arrives.
At the hoedown, Aria approaches Emily and Emily tells her to go talk to Ezra. She tells her that Maggie is taking away Malcom, and Aria quickly goes to talk to Ezra.
Aria and Emily returns from a movie. Aria is seen commenting on how she missed half the movie because the dude in front of them was making sales call and that if Spencer was there she would have pegged the dude with her jelly beans. Emily gets a little annoyed to hear Spencer’s name. Aria tells Emily that she was sorry but Emily should not keep holding on to the grudge she felt. According to Aria, Spencer was “just trying to protect” Emily. But Emily thinks that Spencer was trying to control the situation like she always does and she did a mistake by trusting Spencer. They are at Aria’s front door when they hear loud music coming from inside the house. They go in and find that Mike had turned the whole place into a party. Aria orders Mike to get all the people out in ten minutes. She and Emily go upstairs. Aria and Emily finds Mona coming out of Aria’s bedroom. When Mona is asked what she is up to, she says that she was invited by Mike who does not tuck and toll every time Mona walks into a room. Before leaving, Mona comments on Aria’s wallpaper and zips her bag.
Emily goes to Aria's where she is packing to leave Rosewood for Syracuse. Emily tries to stop her but Aria tells her to get out of her way as she does not want help.
Aria calls Emily from Syracuse. She's there for a college visit and doesn't tell Emily about the new guy Riley. When Aria is back from Syracuse, Emily tells her about Mona working for Ezra.
Aria and Emily think that Mrs. DiLaurentis cannot be ‘A’ as ‘A’ knows Ali is alive.
The episode opens with paramedics loading Ezra into an ambulance and taking him to hospital. Noel is being questioned by the police, while Emily, Spencer and Hanna hold Aria back, all knowing that if Aria gets too close, she'll be spending the night at the police station answering questions.
Aria is at the cabin in the woods where Ali supposedly hid, trying to make it look like Ali had actually hidden there. Emily arrives, and Aria is furious with Emily for keeping Alison's text from her. Emily assures Aria that the text wasn't from ‘A’, as ‘A’ is dead, and also tells her that she killed Shana in pure self-defense. Aria says that she still killed someone and she cannot live with that.
Aria, Emily, and Spencer watch the footage of Alison, who is wearing different clothes than what she had just been wearing at dinner. All three girls’ phones start beeping and ringing with an incoming text message, and after reading it, they look up to Hanna who has just arrived. Aria asks if Hanna just got the text that came in, telling her that it’s from ‘A’, but Hanna tells her no. Emily asks if she’s sure, and to check her phone, and after doing so, Hanna says she doesn’t know what text they’re talking about. Spencer passes her phone to Hanna, and she reads it aloud, “New York, New York, it’s a hell of a town. Ali’s keeping secrets, maybe that’s because of Hanna’s big mouth. –A”, before Spencer asks Hanna if she’d care to fill them in.
Hanna, Aria and Emily are walking down the street and Emily questions what Melissa meant when she said Spencer will know everything soon. Aria declares it means what it always means, that no one tells you anything when you want to know it, only when they feel like telling it. Hanna adds that they only tell you enough to make you crazy to know more. Emily then asks whether anyone has talked to Alison in which Aria tells her that Alison calls but Aria does not pick up her calls. Hanna states she has had another bad thought that Alison has left town but A has previously said that she could not and wonders what has changed. Aria suggests that maybe Alison has made a deal with someone else as Alison had previously made a deal with Noel. Emily asks whether Aria is thinking Alison had made a deal with 'A' to leave town and wonders what kind of deal was made. Just at the moment, Lt. Tanner surprises the three liars and states that she is lucky to get most of the girls together at the same time and asks whether they could talk. The three lairs exchanged nervous looks.
In Spencer's bedroom, Spencer is showing Emily and Aria, Melissa's recording. Aria declares that Melissa has killed Bethany Young, however Spencer corrects her saying that Melissa thought Spencer had killed Bethany. Aria adds that the police believe the liars had killed Bethany. Emily adds that when Melissa saw Bethany, she thought she was Alison's clothes however Spencer interrupts saying another pair of Alison's clothes and that there was a duplicate set. The girls wonder whether it was the plan all along for Bethany to take Alison's place in the grave. Emily states that they need to find a way around the picture of A at the hospital. Aria and Spencer are confused and Emily clarifies that she meant Alison not A and that it was a slip of the tongue.
Emily [in Kingdom of the Blind]: I am way more angry than I am scared now.
Aria: Can I borrow some of that?
Aria [in Stolen Kisses]: What should I wear? I need to look insanely sophisticated for this.
Emily: What about a Hello Kitty t-shirt?
Spencer [in Grave New World]: One of us knows how to change a tire, right?
Emily: And you're looking at me cause I'm gay.