The graphic novel begins with a picture of two birds flying against a fall sky. Charlie Spring, a 15-year-old student and Ben Hope, an upperclassman, make out in the library, but Charlie pulls away at the sound of the first bell. Charlie attends his first vertical class—a literature course containing students from each grade. The teacher, Mr. Lange, welcomes Charlie enthusiastically and seats him next to Nick Nelson, a 16-year-old student. Each day, Charlie and Nick pass each other outside of class and greet one another. When Nick’s fountain pen explodes one day, leaving his hands stained in blue ink, Mr. Lange asks Charlie to take Nick to the washroom. There, they joke about their teachers while Nick tries, in vain, to wash the ink from his hands. Charlie ignores both the first bell and a series of increasingly abusive texts from Ben as he and Nick decide in the washroom that they want to be friends. Charlie’s friend Tao Xu cannot believe Charlie is hanging out with Nick, given that Nick is a rugby player and friends with Harry Greene, a student Tao finds off-putting. When Tao accuses Charlie of having a crush on Nick, who Tao assumes is straight, Charlie denies it. Walking home from school, Charlie catches Ben holding hands with his girlfriend. That night, Charlie sends Ben a text message to break things off.  

Charlie is the fastest boy in his year on the racetrack, which Nick notices when he is practicing rugby. Nick is so impressed that he neglects to pass the ball to his teammates. Later that day, Ben confronts Charlie at his locker when he’s on his way to a drum lesson. He demands to know why Charlie cut him off, and when Charlie doesn’t answer, Ben grabs him by the lapels. Nick interrupts and expresses surprise that Charlie and Ben are friends, which Charlie denies as Ben stalks off. Nick tells him he has a question, and Charlie fantasizes for a moment that Nick is gay and wants a relationship. Instead, Nick asks Charlie to join the rugby team. At the second bell, Charlie realizes they have been talking too long, and he leaves for his drum lesson, asking Nick for time to think about the offer. When Charlie does join the team, Nick’s teammates are surprised that he asked Charlie to join, mostly because Charlie is gay. The rugby coach, Miss Singh, tells Nick to spend some time teaching Charlie the basics. Charlie picks up the sport quickly and enjoys roughhousing with Nick.  

Talking to Nick in the locker room, Charlie becomes distracted after getting a text message from Ben. When Ben confronts Charlie in the hallway and tries to flirt with him, Charlie accuses Ben of being selfish and of hiding their relationship out of fear. Infuriated, Ben slams Charlie against the wall and starts kissing and groping him. Nick shows up and pulls Ben off Charlie, and then tells Ben off. Charlie is embarrassed that Nick heard his argument, but Nick reassures him. 

At home, Nick checks out Charlie’s social media profile. Remembering that Charlie got bullied when he came out as gay, Nick messages him to make sure he’s okay. He advises Charlie to stay away from Ben and asks about their backstory. Charlie isn’t sure that Nick really wants to hear it, but Nick reassures Charlie that he cares about him. Charlie shares how Ben first approached him shortly after he came out. They started making out, always in secret, and usually at Ben’s suggestion. Finally, Charlie realized that Ben was just using him and that they had no future. He tried to end their relationship, but Ben would not take no for an answer. Charlie thanks Nick for listening, and Nick replies with a smiley face and a heart emoji.  

Tao confronts Charlie again about the amount of time he is spending with Nick and about how obvious it is that Charlie has a crush on Nick. Tao tries to tell Charlie to abandon his obsession. Later, Charlie sees a picture of Nick’s dog Nellie and gets excited because he loves dogs, so Nick invites Charlie to come meet her. Charlie’s sister Tori catches him trimming his hair before he leaves. At Nick’s house, Charlie immediately falls in love with Nellie, and Nick notices right off that Charlie has cut his hair. They play video games, and when it starts to snow, they head outside to play with the dog. Back inside, Nick realizes Charlie is freezing, so he sets him on a radiator and brings him a blanket. Nick also loans Charlie a hoodie to wear home.  

The two boys hang out again the next weekend, and Charlie offers to give Nick a drum lesson. They share the narrow seat, and Charlie places his hands over Nick’s on the drumsticks, but then Charlie pulls them away. Nick gets bored doing homework, so they start wrestling instead, and again Charlie backs away. When Charlie falls asleep watching a movie, Nick thinks about holding Charlie’s hand, but decides not to. Before Nick leaves, he hugs Charlie. Tori tells Charlie that she doesn’t think Nick is straight. Nick goes home and tries using the internet to discover whether he might be gay.  

Charlie sits the bench as a reserve during a rugby match. He texts Tao to say that he believes Nick might like him back. Tao tells Charlie that Nick has had a long-standing crush on a girl named Tara Jones. Just then, Nick runs over to celebrate the winning score with Charlie, catching him in a twirling embrace. Nick’s teammates speculate that the two are in a relationship. Miss Singh tells them to stop gossiping, stressing that sexuality is a spectrum and that it’s rude to speculate about it. In class, Nick asks Charlie to come to Harry’s birthday party that weekend. The party is loud and crowded, so Nick and Charlie retreat to the bar. Harry finds them there and tells Nick that Tara, his junior high crush, is at the party, then literally drags him away from Charlie’s side to see her. Left alone, Charlie runs into Ben. Tara tells Nick that she’s gay and points out her girlfriend. She asks about Charlie, and then Harry starts to bully Nick about his and Charlie’s sexuality. Nick tells him off and leaves.  

Nick finds Charlie alone at a table and apologizes for leaving him. Charlie confesses that he has just run into Ben and that he finally had the courage to tell Ben to leave him alone. Nick takes Charlie’s hand, and they leave the party. They race down the hallway, then upstairs. Charlie asks Nick about Tara, and he says that he doesn’t like her, but he does have a crush on someone else. Charlie asks Nick if he would consider dating a boy. The two kiss, and images of flowers blossom all around them. They each pull away and then grab hands and kiss again. One of Nick’s friends calls out that Harry is looking for him, and Nick leaves, saying there is something he has to do. Charlie is left alone, apologizing to an empty room.