Toby makes a minor appearance when he walks Jenna into Alison DiLaurentis' funeral, then later leaves with her.
Jenna walks in school with Toby in tow. He receives uneasy glances from all the students. After swim practice, Ben Coogan—Emily's boyfriend—sneaks up on her in the girls locker room and tries to fool around with her. She tries to push him off nicely, but he gets violent and more forceful. Just then, Toby came to the rescue and wordlessly pushes Ben off of Emily. He pounds Ben into the locker until Ben bleeds, while Emily shouts for Toby to stop. In a flashback of the night of The Jenna Thing, It is revealed that Ali threatened Toby to take the fall for them.
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Toby becomes Emily's lab partner, much to Emily's dismay. Toby notices when Emily slams her lab book shut, though he doesn't know that it is because of the photos planted there. That night, Toby catches sight of Emily 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 about her secret. 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."
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The next day Emily questions Toby about his whereabouts the previous night. He tells her that he was studying at the Grille all night. He then asks her where she was and she tells him she was at a friend's house. The duo stay after class to finish their experiment. They agree to meet later at the Grille and hang out. However, Emily brushes him off out of fear of what her friends will think and sit wit her friends instead. The next day, an upset Toby tries to ignore Emily when she comes to sit with him, but gives in when she presents him with a mixed CD of her own. She apologizes and he accepts.
There's No Place Like Homecoming
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Toby surprises Emily with tickets to homecoming. Later, the girls discover Toby’s tattoo – "9/01 Free at Last", on his left side, This makes them suspicious—especially Spencer—that he may have had something to do with her disappearance. At the dance, Toby whisks Emily away to the Chem. Lab to confide in her privately about his big secret, which the other girls have just uncovered. The girls realize what Alison had blackmailed Toby with in order to force him to take the blame for "The Jenna Thing" - she knew about Toby's sexual relationship with his step-sister. As Toby tries to explain, in a creepy threatening manner that she clearly is not responding well to, she pushes him into the cabinet of beakers. Emily then flees with Toby hot on her trail, but she trips on the train of her dress and is unconscious.
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Toby drives an unconscious Emily to the hospital and drops her off at the emergency room. After that, Toby flees Rosewood, without telling anyone—including Jenna and his parents—where he is going. A day later, Emily sees cops in front of the Cavanaugh house, with a shaken Jenna in tears, sitting on the front porch as the police leave. She sees a wrecked motorcycle, but is too afraid to ask if Toby is alive or not.
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A new piece of evidence leads the police to announce that Toby is officially wanted for the murder of Alison DiLaurentis. Toby appears in Emily's car and explains that he gave Alison the sweater while he thanked her helping him get away from Jenna. He also tells her that he is leaving Rosewood, as he will most definitely be convicted of Alison's murder—whether he is guilty or not. Toby tells her to meet him at the Rosewood Church at midnight, before he leaves for good. However, the police discover Toby's whereabouts as he waits for Emily.
Toby has been released from jail due to insufficient evidence, but with one caveat: an ankle monitor, keeping him all too close to step-sister Jenna. Emily sees Toby sitting on his stoop wearing his house arrest anklet and heads over to tell him that she wasn't the one who turned him into the cops. Later, Jenna reveals to Toby that it was actually she who turned him in, telling him that it would look as though he was guilty of murdering Alison if he left Rosewood, Toby quietly and defiantly responds by saying, "you can chain me to this porch, and I'd still never touch you like that again." Jenna responds by slapping him.
The girls, aside from Emily, still don't trust Toby despite being cleared of killing Alison. Later, Toby is walking across the street and the townsfolk is be mean and judge him. After some little kids run away from him, truly frightened, he runs into an alley to cry not knowing and Spencer is watching and pitying him.
Spencer shows up on the Cavanaugh's doorstep, telling Toby that she is his new French tutor. When he asks why, she responds that she is taking AP French, They sit down on the porch, and she hands him the French translation of "Catcher in the Rye," having seen him reading the book once before. She explains that the best way to learn another language is to read a book you have already read in English in another language. Toby questions her motives and listens as she apologizes for suspecting him and begins a friendship with her.
Spencer visits Toby's home again, but finds the door open when she knocks. Toby warns her not to snoop as Jenna remembers exactly where she places things and will know if things are touched. Toby had been on the phone with the District Attorney and therefore couldn't speak up right away as soon as Spencer arrived. He lets her know that the charges are being dropped, as the blood evidence they collected was corrupted. Thus, Toby is no longer under house arrest for the murder of Alison DiLaurentis. He can have his tracking anklet removed as soon as he goes to the Rosewood Police Department. Spencer offers Toby a ride to the station, and he accepts, leaving Jenna rebuffed when he turns down her ride in a taxi with him.
The next morning, Toby goes to Spencer's house. In her kitchen, Spencer makes Toby breakfast, and he hands her Jenna's phone, which he stole the night before, (and he than confides that he is frightened of what Jenna's reaction will be if/when she discovers he took it). Spencer reassures him that everything will be fine, and uses the opportunity to ask Toby why Alison had been so sure that Toby was the one peeping on them, but Toby firmly denies that he ever spied on anyone; the only thing he can make of Alison's assumptions is that she had something against him, though he is clueless as to what.
Spencer and Toby form an unlikely alliance as the two grow increasingly suspicious of Jenna and her ties to a mysterious room at a local motel. Toby is staying at the same motel to escape Jenna's wrath, as she knows that he took her phone and believes that he touched her snow globe. While dropping Toby off, Spencer hears flute music coming from room 214 - which was the same numbers in the braille message. When she peeks through the window into the room, she sees a bag from "Neufelds," the same exact bag Ian mysteriously gave Jenna during their strange encounter at the high school. The duo stake out the motel and find out what Jenna is up to and eventually the two fall asleep together. In the morning, they realize that it was a set up, but begin a relationship nonetheless.
After Spencer becomes a person of interest in Alison’s murder, she continues an unlikely relationship with Toby, who is all too familiar with the feeling of being wrongly accused and suspected by the police. He coaches Spencer accordingly, urging her to serve the cops coffee in a bold move acknowledging their presence, yet not being afraid. Later, Toby and Spencer spend comforting time alone, sitting alone in his house discussing running away and what that feels like. Toby asks her to call him first if she ever gets the urge to runaway again. She agrees and they hold hands.
Toby is working on his motorcycle, when Spencer comes by. Toby knows that Spencer is innocent, but when he sees a cop car pull up closely, he suggests that she leave and offers to visit her in her home later. He picks up on the fact that her parents would rather he not come around, though. So, they agree to meet up at the festival at 7 PM instead. Jenna comes out of the house, then, and calls Toby to drive her to school. It is unclear whether she overheard their date plans. At the festival, Spencer gets locked in fun house due to a fake text from "A." She is shaken, but unharmed. Her family leads her home, but Spencer stops following when she catches sight of Toby. Despite her mother's wishes to come along, she runs straight into Toby’s arms and kisses him.
Toby is at Spencer's house, reading a book while she is doing her homework. Spencer says she likes having him here with her. Toby opens a window and turns her coach around. He calls her over and she sits on his lap while he puts his arm around her, enjoying that they have each other. After awhile, Spencer gets a text from her sister, saying that she needs a ride home from the church. Toby tells Spencer that he'll keep Jenna busy like she wants him to, but he wishes he was going with her. She tells him that he's helping her by finding out if Jenna's involved in all of the bad stuff, or not. She then tells him that he is her safe place to land, and that she wants him to stay safe, and they kiss again.