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.
Pacey gets a job at a bar and meets an attractive Hispanic waitress named Karen. Although Karen has a very non-friendly boyfriend, that doesn't stop Pacey from feeling attracted to her. Dawson arrives to visit Joey, and is misled by Audrey when she decides to set her sights on him herself. Jen's compassion gets her to help Charlie and be on the college radio station.
Dawson is hit with tragedy after he heads home to Capeside to break the news to his parents that he is dropping out of USC to be with Joey, who is in shock herself after she realizes Pacey has been in Boston for weeks.
Lifelong friends Dawson, Joey and Pacey put past grudges behind them in the wake of the tragic death of one of their fathers. Along with Jack, Jen and Grams, each tries to find the words and actions to comfort their friend.
Dawson takes Joey up on her invitation for a weekend in Boston, but the two have reservations once there. Meanwhile, Jack is surprised when his boyfriend Tobey shows up unexpectedly forcing Jack to choose between fraternity hell week and spending time with Tobey.
Dawson is having trouble with anxiety attacks since his father's death, so he tries to escape reality on a night of debauchery with Jack and his fraternity brothers, which ends with Dawson's accusing Joey of causing his father's death.
Meanwhile, Jen seeks revenge on Charlie; Audrey's mom visits; and Pacey makes a discovery about Danny.
Jen helps Dawson go to the shrink he ran away from last week. Dawson still thinks that the whole idea of sharing his thoughts with a complete stranger is weird, but he is surprised with how much he learns from it. Back home, he has to handle the problem with his father will, which does not include Lily. Meanwhile, Joey is working on a project about old love letters written by an obscure writer, and with the help of Audrey's audition tape for "The Real World: Ibiza", she manages to catch something no one of the fellow students caught. Pacey confronts Karen about the risks she is taking for having an affair with Danny, and Karen is hurt when Danny's wife shows up at a dinner party and he blows her off completely.
Dawson takes Jen on a road trip to a small film festival in New Hampshire where his documentary is being honored. The spotlight is intoxicating for both of them as they share one of the single most momentous events in a boy's life.
Meanwhile, Jack brings Joey and Audrey to a frat party under false pretenses; and Pacey takes Karen on a non-romantic date.
After watching scary movies, Joey, Pacey and Jack talk about their creepiest experiences and urban legends. Joey shares her story of how she was almost attacked by the librarian on Halloween and saved by the creepy man she was running from. Jack tells the story of when he was helping clean the frat house basement and found a guy strapped, who later he found out to be a ghost. Pacey reveals that he was chased by a black car while giving Karen a ride home, but there was nobody driving the car. Grams arrives and says she has the scariest story: the time when Jen got locked out of the radio booth.
Pacey offers to cook for the gang on their weekly dinner (an event they always plan on doing but always fail to). Jen and Dawson return early and decide to keep what happened between them, but they are caught by everyone making out at the door. The dinner goes on in a very awkward way for everyone as Audrey and Dawson worry about Joey. But surprisingly she seems to be fine with it. Charlie also drops by, causing some tension for Dawson. At the end, they all decide that keeping their long lasting friendships is more important than having a weekly dinner, and Joey confesses to Pacey how she really feels about the whole Dawson-Jen thing.
Joey and Audrey go to a nightclub to celebrate both Joey's grades and fall break. There, Audrey tries to convince Joey to have some real fun. Charlie is also there and he hits on Joey, who turns him down for what he did to Jen. But Charlie doesn't give up so easily and dares Joey to do something wild. She accepts the dare and goes on the stage to sing with the band. Excited about it, she kisses Charlie. Meanwhile, Pacey sees himself hanging out with Audrey after he joins the ladies at the club to celebrate his new promotion. And Dawson and Jen go back to Capeside, where they have their first fight over what Dawson will do with his life. At the end he decides to move in to Grams's attic in Boston and move on with his life.
Dawson and Jen realize that living together is not as much fun as they hoped to be. Between ruined toothbrushes and bathroom overcrowding, they're getting on each other's nerves. Jen faces a new challenge at work after she turns her regular show into an advice show. She mainly gives advice to other girls with problems, and makes statements on men that hurt Dawson's feelings. She comes home expecting a fight, but Dawson surprises her saying he won't fight or lie or cheat on her. Meanwhile, Melanie (Pacey's summer flame) shows up offering Pacey a job working with her uncle's new boat around the Greek Islands. After a lot of thinking, Pacey decides not to go, since he has developed a successful life in Boston working at the Civilization. Jack moves into the fraternity house and gets his own room, but has some problems staying there after he discovers he was supposed to be rooming with another guy who felt uncomfortable living with a gay guy. And Joey decides to give Elliott Sawyer another
It's Dawson's first day in his new film school. Oliver (the somewhat obnoxious filmmaker Dawson met on the film festival) starts showing him around and wastes no time in asking Dawson to direct a movie he wrote. Reluctant to direct someone else's work, Dawson starts giving notes to Oliver on the script, and ends up accepting the job, thanks to Jen's incentive. Jen, on the other hand, is having some problems of her own. Her current state of happiness from the wonderful relationship with Dawson is reflecting on her on-air performance. Now she has to go back to the sharp-tongued, edgy advices she used to give instead of the romantic, love-themed ones. Meanwhile, Elliot finally has the courage to ask Joey out, but Joey makes second plans for a gathering with professor Wilder. She makes a fake excuse not to go out with Elliot, and her evening takes an unexpected turn when she and professor Wilder kiss. Elsewhere, Jack is reprehended by his brothers for being on academic probation. Irritated
Directing Oliver's movie is not an easy task. First, Dawson has to deal with Audrey's (who took the leading part) complaints about Oliver's kissing skills. Then he has to recast the other lead role after watching the footage and discovering that Oliver stinks as an actor. Now they have to find someone who can act, is hot, charismatic in less then 6 hours. They can't think of anyone but Charlie, who fits the profile like a glove (for Jen's desperation). During the shooting Audrey has a crisis and locks herself in the bathroom because she kissed Pacey and felt like she was betraying her best. They have to call Joey (who was over at Professor Wilder's house to solve their issue) for help, and after her blessing Audrey is back on the set so they can finally finish the shooting. Meanwhile, Jack is fed up with his brothers and decides to move out of the fraternity house after he and Eric have a moment and later Eric accuses him of trying to kiss him to the other guys.
Joey is held up and forced to clean up her account by a street mugger, who is accidentally run over by a car just after mugging Joey. The merciful girl from Capeside stands by her aggressor, checking up on him and trying to get an ambulance and get him to the hospital after seeing the similarities between him and her own father. When the cops and paramedics arrive, Joey faints and is taken to the hospital. After recovering, she accidentally meets the mugger's estranged wife and daughter. Joey stands by her dying mugger as she tries to learn more about her own father. After his death, she makes a choice of sparing the guy's little daughter's feelings by telling her he jumped in front of the car to save her life.
Jen and Audrey are tempted to risk their new relationships with Dawson and Pacey after interviewing a couple of cute musicians. Meanwhile, Pacey's caught by surprise when he realizes Jack has taken him to a gay bar, and Dawson's curious upon seeing Joey's reaction when she catches Professor Wilder on a date.
Charlie asks Joey to sing with his band at a distant club, which requires Pacey to give them a ride. Pacey and Charlie hate each other, and it takes a patient Audrey to keep them from going at each other's throats. Joey is nervous and isn't well received by the audience, until Charlie helps her with a duet. Still, he doesn't give up putting his moves on her. Audrey and Pacey, on the other hand, seem to be more and more in synchrony. Meanwhile, Dawson, Jen, Jack and Grams drive up to Capeside for Lily's 1st birthday, and Dawson finds out his mother has a significant other. Meanwhile, Jen confesses to Jack that she wants to break up with Dawson, while he is conflicted with the possibility of loving Joey again.
Oliver tells Dawson he's arranged a screening for their movie, which is yet to be finished. Dawson freaks out, but Joey comforts him saying the movie is brilliant. Everybody attends to the screening and solve their conflicts while waiting for it to start. Dawson meets a handful woman, and after exchanging insults she reveals herself to be Amy Lloyd, movie critic for Boston Weekly, whom Oliver secretly invited for the screening. She storms out of the theater, and it's up to Dawson to bring her back. They go out for coffee, have a heart-to-heart talk and even make out! Meanwhile, Joey is scared about her feelings towards Charlie and goes to Jen for advice. Jen says it doesn't matter if the guy is a jerk; at the end of her life there might always be a Clifton Smalls (the new African American boyfriend of Grams). Pacey asks Audrey how many men she's slept with, and she tests him by saying 27, then 57, when it was really only 5. Pacey passes the test and tells Audrey he's in love with her.
It's Spring Break and the gang goes down to Miami to party! But not everything is a reason to celebrate. Audrey and Pacey go through their first relationship test when Audrey's high school boyfriend (and her first true love) shows up with tickets for the M2M concert at an MTV event. She is torn with the memories of the past, and eventually kisses Chris, who confessed to Pacey still being in love with her. Nevertheless, Pacey stays cool about it and asks Audrey to be his official girlfriend after she confesses she loves him not Chris. Meanwhile, Dawson and Oliver hit to road to NY to meet a film agent who's interested on their movie, but never make it there. Dawson starts to tell Oliver his story with Joey and decides to surprise her in Miami, looking to reactivate their romance. But when he gets there, all he finds is a suicidal Jack (who's failing out of school and is suffering with the fact that Tobey's got a new boyfriend) and Pacey, who tells him his story with Joey is over. Charli
Charlie's band lands a deal for a tour and Charlie asks Joey to go with him, but she doesn't want to leave college in the middle of the semester. Charlie then decides to quit the band and stay with her, which freaks Joey, who thinks they're jumping too many steps. She breaks up with him so he can go with his band on tour. Meanwhile, Oliver and Dawson finally get to NY to meet with an agent, but Oliver ruins the meeting. Dawson threats to end their partnership and begs for another chance. Civilization is sold and Alex Pearls takes over as the new manager. She promotes Pacey as head chef and fires Audrey. Pacey tries to get Audrey her job back, but all he gets is an inadvertent kiss from Alex.
Pacey's new boss proposes more professionalism in the workplace and promises to leave behind her attraction towards him, even offering Audrey her job back. Audrey suspects something is going on between them and refuses to return to Civilization. Later, Alex drops by at Pacey's and Audrey walks on them talking about their kiss. She storms out in anger, leaving the future of their relationship unknown while Pacey struggles with the growing attraction he feels for Alex. Meanwhile, Dawson runs into Amy Lloyd, the movie critic, and they end up in bed together. After sex, they talk about movies and she lends him her movie. Joey and Jack focus on studies, and while she has problems concentrating, he has to catch up an entire semester and even goes back to the fraternity house asking for help. Luckily, Eric (the same guy that caused Jack his expulsion) shows up at Grams with the needed notes.
Pacey leads a revolt against Alex at Civilization. Dawson, Joey, and Audrey return to Capeside, leaving Audrey to wonder about their pasts. Joey decides to see her father for the first time since his latest incarceration, while Dawson finally pays a visit to his father's grave. Jack and Jen wonder how they'll spend the summer.
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.