The TRUE LOVE SAGA: Joey gave Pacey the advice he needed to help his sort out how to deal with the Tamara Jacobs situation. But along the way, their marine biology project made Pacey see Joey differently. He became infatuated, and in a moment of perpetual insanity, as he claimed it to be, tried to kiss Joey. The next time we see Pacey with any interaction with Joey was their conversation about their fathers. Joey tells Pacey that he needs to tell his father that he hurt him, Pacey counters with the question is that what she did. Joey asks Pacey to "borrow" his dad's truck and take her to the prison so she can see her father. Once they arrive, the guard refuses to let them see him. Pacey gives the guy a twenty and Joey has a heart-felt conversation with her father.

Pacey tells her that it could be the beginning of a friendship. Joey escorts Pacey to pick up Andie from the mental hospital, to find that things are a little on the weird side. Pacey finds out that Andie cheated on him, and turns to Joey. She tells him that he has to forgive her, that if he doesn't, he'll regret it. On the day of a big football game, Pacey and Joey cut class with each other, where the banter picks up. They get caught and sentenced to having to be the school mascot. The two con two younger kids into doing it and Pacey reveals his new endeavor: his boat, True Love. Pacey finds out that he's failing Trigonometry, a class he has with Joey, and tells her he'll do anything if she'll tutor him. Pacey finds himself taking dance lessons with Joey. Dawson suspects him of sleeping with Joey, causing Pacey to question Dawson's motives about his inquiry. Pacey gets angry and leaves, Dawson and Joey then find Jen and Pacey making out in the coat room which sends Joey into what appears to be a fit of jealousy. The B&B opens and Pacey is faced with the realization that he is in love with Joey after watching her sleep the entire night. Pacey, feeling anxiety over the fact that Joey is going out with A.J., gets stage fright. Pacey then tells Joey later that she will find love again, he knew from experience. Joey and Pacey's bantering picks up, and after they all get arrested, Pacey lays into Joey and Dawson for their relationship going round in circles. Pacey then feels bad about what he said. He takes visit to Joey's house the next morning where Joey informs him that she was worried about him. Joey's mural she painted is destroyed by a student, and Pacey seeks him out for vengeance. Pacey told him that he either confessed or prepare to fight. Pacey and Matt Caulfield fight. Pacey becomes a mentor, but not before he spills to Joey that he was only doing Dawson the favor of watching out for her, and that makes her angry. Pacey stands by Joey during her attempts to help out Principal Green. He gets free flyers, gets a rally of people together, and never gets a thank you. Pacey tells Jen that he has fallen for her and she counters with, "Every duck has it's day." Pacey then surprises Joey with her own wall, the side of a building, that she can paint on. He bought it for her. Joey calls Pacey to come pick her up from the college where she was visiting A.J., and he does. Joey tells Pacey what happened. Joey tells Pacey that he knows her like no one else besides Dawson. Pacey pulls over to the side of the road where Pacey kisses her. Joey then begins to push Pacey, yelling at him for doing that. The two are now angry at one another, Joey mad at Pacey for kissing her, Pacey mad for pushing him away. But at the end of the weekend, Pacey has told Joey that it meant nothing, and Joey concurs.

On a trip to Dawson's Aunt Gwen's, Pacey and Joey are forced to face their feelings for one another. The two have to share a bed, making them both feel a little uncomfortable. Later that night, Pacey leaves the room after Joey and Dawson sing their rendition of "Daydream Believer". Pacey tells Joey that he can't compete with their history. Joey says they're supposed to have their own history. Pacey reveals that the only reason he came on the trip was to be near Joey. Pacey gets angry and storms off. Joey tells Pacey that he makes her feel alive. Pacey kisses her again to get interrupted by Dawson's aunt, who tells Joey that she has to tell Dawson. Pacey and Joey have a conversation later where he says that he can't keep giving her the answers. As Pacey is about to leave, she grabs his hand and kisses him.

Joey and Pacey have been seeing each other a week, and they both say that they need to tell Dawson because the guilt is becoming more than either can handle. Pacey says he'll tell him. Pacey crisens his boat. Pacey then goes in search for Dawson, to tell him what's going on. Pacey misses him everytime. Meanwhile, Joey avoids Dawson, until she goes to see him that night. He starts talking about a movie he's watching which goes right along with their situation. Joey leaves and finds Pacey just as he's going in to tell Dawson, she tells him that she needs to tell him. Dawson confronts the two, saying that they aren't friends anymore. Pacey and Joey end things to keep the peace within the group.

Joey and Pacey don't talk for two weeks. Pacey is angry at Joey for this. Pacey is in the boat race going against Dawson. Dawson acts like a jerk and almost gets them all killed. Pacey runs up to confront Dawson, and Joey tells Pacey that she hates him for confusing her, and she hates Dawson for never telling her how he feels and ruining what she could have had with Pacey. Later that day, Pacey finds Joey staring at her wall, and he says he'll renew the lease. He asks her if she could ever love him like a soul mate...she asks him not to give her an ultimatum, he says he understands and leaves her. At the prom, Pacey is pained to see Joey there with Dawson, and during the whole thing, she is feeling horrible for treating Pacey the way she was. Joey danced with Pacey, causing them both to feel things that neither were prepared for. Pacey then plans to leave town and not tell Joey. Doug lets Joey know of Pacey's summer plans and she confronts him on it. He told her that she was getting 3 more months to think. Pacey paints on her wall "Ask Me To Stay", where Pacey tells her that he's not quite ready to give up on them yet. Joey later tells Pacey that she can't give him a reason to stay, and he tells her that she should have made her choice sooner, saved everyone a lot of pain. Dawson then tells her to go to Pacey, and she leaves Dawson. She tells Pacey that she loves him and wants to come with him. They kiss and set sail for the Florida keys on "True Love".