Since a very young age, Dawson, Joey and Pacey had been very close friends. Dawson and Joey were perhaps especially close, and as they got older, this close friendship began to develop into a romantic involvement. Meanwhile, Pacey and Joey's relationship became one characterized by playful banter and merciless teasing. Despite these hostile appearances, however, Pacey and Joey often seemed more alike than they thought themselves to be. With Joey firmly established as Dawson's soulmate, and Pacey firmly placed by Dawson's side as his underdog-ish sidekick, a romantic relationship was out of the picture (or at most, acknowledged only as a catalyst for the ballad of Dawson and Joey.

In their junior year of high school, the dynamics of this delicate triangle shifted. After Dawson and Joey's relationship came to an end, Dawson became interested in pursuing other objects of affection, leaving Joey heartbroken. Pacey, sent on behalf of Dawson, offers what he can to comfort her. When Pacey is also left heartbroken by his own first love, the two begin to develop a sincere friendship, beyond just bantering, and beyond just a mutual attachment to Dawson. At the same time, Pacey begins to work on fixing up a boat, which he decides to name "True Love." After his first heartbreak, Pacey decides that the idea of True Love is unattainable, and so names his boat after it.

As the two of them start spending more time together, Pacey makes the painful discovery that he has fallen for, as he puts it, the worst person he could possibly ever fall for. Rather than make any huge declarations, Pacey stands quietly by, defending her honour when her mural is defaced, and buying her a wall to challenge her to meet her potential. When Joey gets her heart broken again by an older college boy, she calls on Pacey to help her and bring her home. She tells Pacey that he and Dawson are the only two people who really know her. At this point, Pacey decides he can't stand quietly by any more, and demands that Joey confront her feelings by kissing her. After several outbursts and conflicts about consequences, as well as hopeless denials, Joey finally acknowledges her more than platonic feelings for Pacey. The real challenge, though, is how the two of them are going to break the news to their good friend Dawson, who has finally decided he's ready to have Joey become a special part of his life again. When he finds out, the friendship the three of them had is torn apart. Pacey and Joey attempt to reject their feelings for each other, but it proves exceedingly difficult, and when Dawson recognizes this, he sends Joey to explore her feelings for Pacey. Joey catches Pacey just as he is about to sail the True Love out for the summer. She joins him and the two sail off into the sunset.

Over their senior year, Pacey and Joey go through the ups and downs of their relationship. It is always evident that they both care very deeply about each other, but things like their insecurities and future goals begin to cause problems. Despite these problems, the two become very close, and what was thought by some to be a simple, passing interest gradually becomes one of the most significant (if not the most significant) relationship in both of their lives. Joey, who had always thought her first time would be with her best friend Dawson, takes that step with Pacey. Eventually, Pacey's insecurities about Dawson and especially himself become too much, and he explodes at Joey during their senior prom. After some cooling off and a great deal of regret over what was said, they both realize that what is left of their relationship cannot be maintained through their quickly diverging paths, and that what is best for both of them is some time apart, even though they both still love and miss each other.

Over the next year, the two are slowly able to rebuild their friendship. They both explore other relationships. Joey with her professor, Eddie, and Pacey with Joey's roommate, Audrey. When Joey learns about Pacey and her roommate, she finds herself in a similar situation that the one she and Pacey put Dawson in year ago. Rather than oppose the pairing, however, she takes the higher road and gives them their blessing. It soon becomes clear, even to Audrey, and Pacey and Joey are not over each other.

As more time goes by, Pacey begins to admit to himself (and at one point, to an intoxicated Joey) that he never did get over her. Despite their diverging paths, they still managed to stay directed towards each other. After spending a night alone, locked in a K-mart, Pacey gives Joey a sincere professing of his feelings; that he has always loved her, but rather than force her to make any difficult decisions, he has just accepted his feelings as a fact of life. Joey asks for some time to think about what to do next, to which Pacey obliges. Soon after, the two begin enjoying each other's company at dinner, and situations of a date-like quality. Pacey even hires Joey as a temporary assistant for him, which turns out to be disastrous when the pent up sexual tension between them manifests itself in embarrassing grope-fests in his office. Pacey tells her that he needs to fire her, for his concentration's sake, but the two agree to spend more time together outside work. They then face another obstacle: the return of Eddie. While Pacey is certain about wanting to reunite with Joey, Joey is less sure. When she tells him about Eddie, he is heartbroken, and the two part ways once again.

Five years later, after the two have settled into their separate paths, Joey returns to Capeside to visit her old friends. She has left her relationships with Dawson and Pacey both unsettled and decides that she will make her decision once and for all. But more than that, she has always known who she has wanted to be with, but instead of being brave enough to make that decision, she has always fled. Pacey tells Joey that he understands if her decision doesn't include himself, because the simple act of being in love with her is enough for him. But Joey does not want to run from her choice any longer. She chooses Pacey, and the two watch the televised incarnations of their little trio together, in the final scene of the series.