Dawson is a freshman film student in Los Angeles, while Joey starts college at an Ivy League university in Boston. Instead of focusing on the new lives they have worked a lifetime for, they find themselves distracted by the distance between them and their unsettling last kiss.

As summer approaches, everyone gets ready for various travels. Dawson prepares to head out for LA with Audrey, while Jack and Jen get ready for their Costa Rica vacation. Left behind in Capeside for the summer, Joey and Pacey lament their fates - until they make a crucial last-minute decision that changes everything.

Dawson returns to Boston after working as an assistant director in Los Angeles over the summer and reunites with Joey who has spent a relatively angst-free summer in Capeside. Audrey and Pacey return from L.A. with a surprise passenger, Audrey's childhood friend Jack Osborne.

Dawson & Joey's reunion leads to an evening of truth and intimacy, which is ruined when Dawson receives a phone call from another woman. Pacey gets a job interview that could change his life. Sparks fly between Jen and CJ, a handsome new peer counselor she meets at school.

Joey's worst nightmare comes true when she accidentally sends a very personal e-mail she wrote for Dawson to the entire student body. The next morning, Joey's e-mail is the topic of virtually all campus discussions when Professor Hetson decides to debate it with his students. Meanwhile, Jack makes an attempt to get to know his cultural professor, Mark Freeman, who pays no attention to Jack, a little better. Pacey, while struggling to survive the first days on his new job, closes a very important deal for the firm, which his wheeling-dealing mentor Rich Rinaldi takes full credit for. Eddie, a student in Joey's reading class, whom also works as the bartender at Helle's Kitchen, persuades Joey to confront any challenge that Hetson throws and not show any weakness since Hetson thrives on it.

Dawson finds himself in an awkward situation when he is put between Joey and the intoxicated leading lady of his film. Audrey allows herself to be taken in by another man's charm.

Dawson's manages to 'get the girl' when a producer visits the "Wicked Dead" movie set to fire Natasha and close down production. Audrey is excited when asked to be the lead singer of Emma's band but is crushed when Pacey misses the gig. Joey demands the truth from Eddie.

When Dawson assists Todd in throwing a blow-out Halloween party, Todd and Natasha have Dawson believing he is seeing the ghost of a legendary film actress. Jen becomes suspicious about C.J., and Joey gets stuck taking Professor Heston's daughter to a haunted house with Eddie.

Dawson comes through with No Doubt concert tickets, but he and Natasha's first public date ends in a brush with the law. Joey and Eddie have to sneak into the concert, while Pacey come to blows with CJ at the concert when it is revealed that he slept with Audrey.

Natasha is drawn to a handsome new actor who arrives to the set. Meanwhile, Joey spends the night at Eddie's apartment but misses Professor Heston's final exam. Pacey invites Emma to his office party and sparks between the two turn to passion.

Dawson and Gail invite everyone back to Capeside for Christmas, but Dawson confronts Natasha about her one-night stand; Joey's happiness with Eddie turns sour when her father expresses his disapproval; Jen spends her time consoling a dumped Grams and Audrey gets loaded.

Back in LA, Dawson is asked by the studio to direct re-shoots but is conflicted about being disloyal to his mentor. Meanwhile, Joey hasn't heard from Eddie since Christmas and finds his apartment empty; Pacey starts skipping work to spend time with Emma; Jen's insecurities as a peer counselor are compounded when C.J. is assigned to train her.

Joey agrees to be Pacey's temporary assistant but their mutual jealousy leads to disaster in the office. Dawson sells his idea for a coming-of-age movie, but when the studio wants to change it to a teen sex film, he must decide whether to stick with his original concept.

When Dawson gives up his dream of making his film, a strong-minded Joey rallies the old group back to Capeside to help Dawson begin production before pursuing her dream of traveling to Paris. Jen, Jack and Grams must say their goodbyes and leave for New York.