Emily was saved by Toby from being sexuality assaulted by her boyfriend Ben Coogan, to which she breaks up with after. She is wary of him at first of the once-troublesome boy but starts to warm up to him after a few conversations with him and they begin to date, however, things go sour on the night of a dance at Foxy when she and Toby talk about Alison. He bitterly states that he's glad she's dead and makes a few other remarks that lead Emily to believe he's "A", an anonymous entity who has been terrorizing her and her friends with dark secrets only known by Ali. She tries to escape from him after telling him she knows his secret. The next morning, she learns that Toby killed himself. In the last letter addressed to Emily, he discusses his guilt over molesting his stepsister Jenna Cavanaugh. That was the big secret he thought Emily knew.
Emily and Toby meet the same way in the book, though she see's him in the school halls earlier, at Noels party Emily and her friends discussed Toby saving Emily. The others warn her not to trust him and stay away from him, after the party Maya drives Emily home to her house, where she spots Toby sitting on his porch steps alone. She sees him fiddling with motorcycle parts and approaches him. Not quite sure how to state it, she thanks him for saving her in the locker room from Ben, and Toby smiles back silently.
The next day Emily then heads to her chemistry class, where she sees Toby standing alone. He lets her know that he's transferring to her chemistry lab, then comments on the scarf that she is no longer wearing and compliments her on it. To Emily's chagrin, the chemistry teacher assigns Toby as her lab partner, and Emily lies that she is okay with it. When Emily opens her lab book, she is shocked to find the photo of her and Maya kissing from Noel's cabin party. She shuts it immediately, hoping no one else saw it. Did Toby see it?
The next day after English class Toby is seen opening his locker, a ton of shaving cream falls out, and some guys are heard laughing loudly in the background, the perpetrators of the prank. Emily watches silently before turning around.
That night, while walking outside her house, Emily rips up the photos of her and Maya kissing and places them deep in the dumpster. Toby catches sight of her and strikes up a conversation. Emily asks Toby if he saw the pictures in her lab book. It seems that he has, but Toby says he's cool with her not wanting people to know. Toby uses it as a teaching moment to speak to Emily about not being the person people want you to be, but being the person you want to be.
The next day in chemistry lab, Emily asks Toby where he was the night before (slightly suspicious that he might be "A"). He replies that he was at The Grille doing homework, where he normally studies to get away from Jenna and her noisy machines. Emily and Toby’s surprising friendship grows even stronger, as both begin to take an interest in each other. Emily appreciates Toby's artwork on his lab notebook. They discover they have the same taste in music and agree to meet later at The Grille.
Emily and Toby are scheduled to meet, but when Emily arrives at the cafe, she sees Spencer and Hanna. Too embarrassed to socialise with Toby in front of them, she reluctantly blows him off. They fill Emily in on the Jenna lipstick situation. Later, the waitress hands Emily the mixed CD Toby has left for her. Hanna, believing that Maya made it for her, encourages Emily not to bullied by pursuing a non-conventional relationship. However, Emily takes this to heart regarding Toby.
Later the next day at the Grille, an upset Toby tries to ignore Emily when she comes to sit with him, but gives in when she presents him with a mix CD of her own. She apologies for blowing him off, and he accepts.
At school, Maya and Emily aren't very warm towards each other either; Maya says she isn't going to homecoming, but at least the girls agree to hang out at some point. Next, Toby surprises Emily with tickets to Homecoming. She’s nervous to accept because of what her friends may think, but can’t deny her burgeoning attraction to him either.
At the dance, Toby and Emily arrive at the door. Emily calms Toby who is nervous about making an appearance; when they finally do, the other PLLs, not to mention Maya, are not thrilled. Emily is particularly surprised by Hanna's reaction, as she had seemed so supportive of Emily following her heart. Hanna then confesses that she had thought Emily was referring to Maya, but before they can continue their conversation, Toby appears.
Then, Emily approaches Maya and accuses her of saying something to Hanna, who gets offended by Emily's attitude and defensively insists that Hanna had said something to her. She accuses Emily of not being okay with who she is and confirms her suspicions when Emily can't look her in the eye and deny her feelings for Maya. Toby picks up on Emily's hurt and realises that he isn't Emily's first choice of a homecoming date.
Later, Toby whisks Emily away to the Chem Lab to confide in her privately about his big secret. Just then, Emily receives a text message claiming that Toby killed Alison, making her more and more unsettled. As Toby tries to explain, she pushes him into the cabinet of beakers, injuring him badly before hurting herself as she runs away and trips on the train of her dress, hitting the hard floor and falling unconscious. Toby drives an unconscious Emily to the hospital and drops her off at the emergency room.
The next day, Emily is back inside her room, recovering from her wounds. Aria and Spencer come to visit and quickly inform her of Toby's sordid past with stepsister Jenna to keep her from contacting him again. Emily does not quite believe that Toby killed Alison and had intended to kill her as well. Why take her to the ER if he meant to kill her?
The ship got a lot of fans as Emily and Toby started to become friends, in the book they dated but because Emily is a lesbian in the TV series, they didn't date and instead became close friends. Nonetheless the ship, whether romantic, platonic or friendship has a lot of fans.