Over the summer, before Toby moved out of his house and got a loft above a coffee shop. The plumbing is not hooked up yet so he has been showering at Spencer's house. Toby mentions that he was glad that the girls went to her lake house so they wouldn't be suspects in the theft of Ali's body from the graveyard. Later, Toby meets Emily at the Brew. He is renovating the loft upstairs, so he gets to live there for free in the meantime and is happy to be on his own. Emily asks him about Jenna, but he hasn't talked to her since she left for music camp. He asks her if she is doing okay with everything. Emily tells Toby that she spent the whole summer partying and getting drunk. She went to one party and didn't even remember anything the next day. Toby is understanding because he can't imagine losing someone the way Emily lost Maya.
Toby is at Spencer's house looking over some things as she asks him about Jenna. She asks where she went after her music camp got done with, but Toby doesn't know because he already moved out when she left. He tells Spencer that it was awkward living there because his parents acted weird around Jenna, concerned about her since the eye surgery hadn't worked. Toby notices a tense look on Spencer's face so he gives her a back massage. She seems to relax after a while and then when Toby kisses her back, she turns around and they begin to make out on her couch. Then her mom interrupts them. She asks Toby to stay over for dinner and he says yes. Later, he meets Spencer at a coffee shop where he tells her about Jenna's eye drops that he found. One of the bottles had been purchased recently. Toby thought it was weird that if the surgery didn't work, why would Jenna still be renewing that prescription.
Toby surprises Spencer at her house because he didn't want to go to his place due to Jenna throwing a party downstairs. Toby and Spencer discuss how they were the only ones that knew Jenna was faking being blind. Jenna told her parents that she started seeing shadows a few weeks ago and that she was scared people would pity her even more if she didn't get her sight back.
Toby is over at Spencer's house telling her about his new job. Toby notices that Spencer is preoccupied, but she tells him just has a lot on her plate with school. He agrees to let her work, but they end up making out, only to be interrupted by Spencer's dad. Later, Toby takes Hanna to a church party. Ashley and Ted greet them and Ted thinks Toby and Hanna are dating. Toby explains that they are just friends. While Toby and Hanna dance, he asks her why she needed him to accompany her tonight. He knows that the story about the boy hassling Hanna. Hanna admits that it has something to do with Caleb. In the end, Toby calls Spencer, leaving an angry voicemail wanting to know why she lied to him.
Toby finds Spencer at school looking at something. He wants to know why she is avoiding him and why she lied to him about the church party. Spencer was with Jason when he found the anklet that exonerated Garrett in Ali's murder. When Spencer insists that Garrett has to be guilty, Toby reminds her there was a time she thought he killed Ali. Being framed for murder has made him slower to pass judgment.
At night, Toby is at Spencer's house waiting for her. When she comes in, she tells him she needs a ride to her car. Before she can explain what happened, Wilden shows up and asks her why her car was at a hit and run. Toby covers for her by saying he picked her up after work. Wilden appears to buy it and leaves, but Toby wants to know what is going on. Spencer tells him about Jason's accident, but she doesn't want him to tell anyone because Jason could lose everything. Toby agrees not to tell anyone, but he is not happy he just lied to the cops to cover up for Jason DiLaurentis' drunk driving.
Toby goes over to Spencer's house to talk to her about Jason. He is clearly angry that Jason left town with the car that he crashed and left them both lying to the cops. Spencer just wanted to protect Jason and Toby wanted to protect Spencer as well. When Spencer is about to take a phone call, Toby grabs her phone and makes her listen to what he has to say. He knows that she won't tell him anything, so he will make it easy on her, he will find out for himself. Toby then leaves her house going to find answers.
Toby comes back to Rosewood and sees Spencer in town. They run toward each other and hug and kiss in the middle of the street. Spencer is sorry about everything, especially the lies. Toby says he knows who she is, so she never has to be sorry. Toby and Spencer are making out in Spencer's room. He asks if she is ready, she says yes then they move to the bed. Spencer gives her virginity to Toby. Afterwards, they go back downstairs because Toby has to go back to his job. Spencer thinks he took the job to get away from her, but he promises he didn't and says he is right where he needs to be. They tell each other "I love you," before Toby leaves. Later, Mona is talking to someone about how she was disappointed her plan of framing Paige didn't work but glad that Garrett Reynolds is out of jail. Before Mona goes back into Radley she tells the black hooded figure that they'll see each other soon. When the person turns around, we see that it is Toby, and he is a member of the "A-Team." Toby then runs away, disappearing around the corner.
Toby shows up at Spencer's house interrupting Spencer's conversation with Garrett. He wants Garrett to leave and asks Spencer what he wanted. Garrett was going to tell her about what happened the night Ali's body went missing but won't tell her when they are not alone. Toby won't let that happen because he doesn't want Spencer in the same room with Garrett. Spencer hugs him thinking he is just trying to protect her, but during the hug Toby gives an evil look.
Toby and Spencer go to the Brew in their costumes. Toby sees Noel chocking on food so he goes over and tries to help him. Toby and Spencer tell him to calm down and breathe, when Noel pokes a devil up at them. Toby and Spencer go onto the Ghost Train dancing to Cuckoo. After the dance, Toby goes to get a soda when he runs into Jenna who is dressed like a pirate. Toby, covering her other eye, tells her that he liked her better when she was blind.
After Garrett's body got discovered, Toby waits with Spencer and her friends. He tells her that the police wants statements before they can go home. Noel confronts Spencer, Hanna, Emily and Aria telling them to tell the police what happened because they make every mess themselves. Toby gets angry and starts a fight with Noel. Toby pushes Noel into a table making it fall with a body bag coming out of it.
Toby in car chasing Lucas
Toby continues his A duties as he chases someone, on a skateboard, off the road with his car. That afternoon, Toby has lunch with Spencer outside the high school as she tells him about Mona coming back. They also discuss Jenna transferring schools and if it has something to do with two members of the N.A.T. Club being dead. Toby tells her she should let it go but she can't because the police still haven't found the gun that killed Garrett.
After school, Toby goes on a run with Spencer and when they get done, he heats the hot tub up. Toby and Spencer go in the hot tub, and they kiss for a bit before Toby realizes Spencer has something on her mind. She was worried about Jason because he has no one and he doesn't understand that Mona is dangerous. Just then, Spencer hears something as Toby gives her evil looks
Toby and Spencer in hot tub
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At the marathon, Toby goes in the basement where he finds Spencer, Hanna, Emily and Aria getting cornered by Harold. He allows Aria to get past Harold with the paper she needed. When they go outside, Hanna asked how he knew they were there and he saw them go in the back door. Spencer gives him a hug for saving them, but breaks lose when they that someone had started a fire.
Toby helps Spencer study for her quiz off against Mona. Toby tells her that he could go with her to calm her down during breaks, but Spencer doesn't want him to miss his dinner with his boss. Toby realizes that this competition isn't just about college applications anymore and it isn't because Spencer believes Mona is bating her. When Spencer goes to get ready, Toby gets a call from his "boss" where he tells the person that he is leaving Spencer's house.
Emily and Paige after Toby slashed Paige's tires
The phone call turned out to be an A-mission where Toby slashed Paige's tires. He hides behind trees when Emily and Paige come back, but Emily sees the black hoodie and starts chasing him through the woods. Toby hides from Emily as she thinks she lost him.
Toby is with Mona discussing their new plans, but Toby thinks it's too soon to follow through with them. Toby explains that Spencer is still lying to him about A saying that person went away when Mona went to Radley. Mona tells Toby that they need to follow up on their plans because they need to know "she" is in charge.
Emily and Toby at in his apartment
Toby is at his loft working when Emily stops by to give him his drink from The Brew. Toby is going to Spencer's house for a shower while Emily waits for the plumber to fix his shower. Toby sees that Emily is reading Lord of The Flies, which Emily explains that she relates to because Mona being A brought the girls closer together. They then discuss Mona and how if she was still bothering them, they would tell him and Emily would.
Toby gets out of the shower at Spencer's as they discuss how they can't see each other on their anniversary
Spencer and toby at her house
because Spencer has to go to a dinner with her family. They make plans to celebrate it tomorrow as she gives him back his pants. She realizes that there is a hole in them and tells him she can fix it for him because she made her own Halloween costume a couple of years ago. Just then, Spencer's mom comes in and Toby leaves for work.
Toby stops by Spencer's house during his break at work to give her flowers for their anniversary. They kiss as she thanks him for bringing her something. When she goes over to the sink to put them in a vase, Toby sees a key that has an "A" on it and he questions her about it. Spencer says that they are Melissa's, because she has a storage unit. They kiss again and say "I love you", because he has to go back to work.
Later that night, Spencer calls Toby to make sure he is okay because there was a storm coming in. He tells her that he'll make it home before it really hits. But he isn't going home because thinking that Spencer is not home, Toby sneaks into her house as A to grab the key. To his surprise, Spencer is home with the key in her hand because she figured out he was A due to the Radley card she saw. She slaps him for betraying her, but before either of them can say anything else, her mom comes home and Toby flees.
Out of the Frying Pan, Into the Inferno
Revealed in a note conversation between Ali and CeCe Drake, Toby was visited by Alison in juvie who laughed at the sight of him and his doo-rag. She tells him to stop sending the "A" notes, but he has no idea what she is talking about. They talk about Jenna and he says he would like to help the person who is sending the messages. Ali replies with: "I bet you wish you'd kissed me when you had the chance" before Toby still wearing the wearing the doo-rag, signals for the guards to take her out of his room because she couldn't stop laughing. (This means that Ali probably tried to seduce Toby at some point but was unsuccessful - though why she would be interested is anyone's guess.)
Emily is hot on Toby's trail. He finally sends her a text and tells her to stop looking and he will meet her. He sends her information as to where they will meet. Emily shows up at the location and waits for two hours, but Toby is nowhere to be found. Later, Spencer finds a dead body and believes it to be Toby.
It is revealed that Toby is alive. He goes to a restaurant, and sits down at an occupied booth, not realizing the "A-Team" member he is meeting is actually Spencer. He then takes her back to one of his hotels he stays at, and reveals that he joined the "A-Team" to protect her. They reunite with each other and ending up having sex a second time. They later meet up with Mona at the lodge to prepare for Hanna, Aria, and Emily's arrival. Mona asks Spencer to take a "walk" with her in the forest, but instead, Toby says that he will "take care of Spencer." They go off into the woods, where the two see someone walking through the forest with a flashlight. Spencer wants to go see who it is, but instead Toby says that he will go. He leaves Spencer and goes looking for the person, and when he is about to see their face, someone comes up from behind him and knocks him out. That unknown person drops the lighter—which is believed to have started the fire at the Lodge—next to Toby's hand. He awakens to see the lighter beside him, and picks it up.