After arriving in Boston to visit, Dawson sees great complications in his past relationship with Joey, who decides to drop out of Professor Wilder's writing class. But the line is incredibly long, which takes Joey all day and all the time she had to spend with Dawson, who ends up being guided around the campus by Audrey whom he confides in with his problems. Meanwhile, Jack pushes Jen into talking to Charlie, who works as the campus radio DJ, and after their first date, she ends up sleeping with him. Also, Doug pays Pacey a visit at the Boston docks and tells him about a job he can get for him at a restaurant, called Civilization, in which the chief, Danny Brecher, is a friend of Doug's. Reluctant at first, Pacey eventually gives in and gets the job after his latest girlfriend, Melanie, is forced to pay for their evening out since Pacey has no job or money.

Dawson goes back to Capeside to inform his parents of his decision to drop out of USC and stay in Boston. Mitch reprehends him and tells him he belongs in California, but Dawson's decision is made. Meanwhile, Jack is accepted on the Sigma Epsilon fraternity house and has doubts if he should go because they want him because he would be filling a quota of being a gay member. Joey finds Pacey working at the restaurant and goes pay him a visit on the boat where they have a nice conversation about their current lives. Pacey, bored of just peeling potatoes at the restaurant, has to put up with one waitress, named Karen Torres, and her bad mood in which he later finds out because he got the kitchen job she wanted. Also, Jen and Charlie try to go through 12 hours without sex so they can learn more about each other.

With Dawson still staying in Capeside, Joey tries to get his mind off his father in which they end up going to Professor Wilder's book party where Dawson has an emotional twist which makes him storm out of the party. Meanwhile, Jen sees Charlie with another girl and makes a scene out of it, but turns out it was his sister. Embarrassed, she decides to make up for it and bring him a fruit basket, and catches him kissing another girl. Tobey makes a surprise visit for Jack, who gives more attention to his fraternity brothers and he ends up breaking Tobey's heart. Also, Pacey still tries to establish a good working environment with Karen and learns that his boss, Danny, is cheating on his wife by meeting a mystery woman aboard his boat.

Dawson goes to Boston to see a shrink for his anxiety attacks. Instead of calling Joey right away, he decides to go party with Jack and his fraternity friends. Jen decides to get back at Charlie for cheating on her by teaming up with the other girl, Nora, to get revenge. Meanwhile, Audrey's overbearing mother, Kay, arrives from Califoria for a visit, and all she does is drive Audrey insane by judging her and making her feel bad. Joey sees herself caught up in the middle of the mother-daughter argument and makes an intervention in order to save her roommate. Also, Pacey discovers that the woman Danny has been cheating on is Karen when he recognizes a necklace she wears which was in Danny's possession.

Jen helps Dawson go back to the psychiatrist, Dr. Rachel Weir, whom he ran away from. 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 in Capeside, Dawson has to handle the problem with his father's will, which does not include baby Lily. Meanwhile, Joey is working on a project with Professor Wilder about old love letters written by an obscure writer, and with a little help of Audrey's audition videotape for "The Real World: Ibiza," she manages to catch something not one of the fellow students caught. Also, Pacey confronts Karen about the risks she is taking for having an affair with Danny, but she refuses to listen to him. Later, Karen is hurt when Danny's wife shows up at a dinner party the restaurant holds, and he completely blows Karen off.

Dawson's therapist advises him to go to New Hampshire (where his documentary film of Arthur Brooks is being honored) and take a friend with him since he's been feeling so estranged from them. He takes Jen (who gets heartbroken after finding out that Charlie is trying to reconcile with his other girlfriend, Nora, and not her) and they pretend to be a couple, getting a very romantic honeymoon suite. Meanwhile, Jack brings Joey and Audrey to a frat party and Joey finds out they're only there for the fraternity brothers to score with them. Also, Pacey takes Karen on a non-romantic date and they accidentally sleep together, in which she reacts confused, quits her job, and hits the road.

Joey and Audrey go out to a nightclub to celebrate both Joey's straight-A grades and the winter break from school. 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 in which she accepts a dare to go on stage to sing with his band. Meanwhile, Pacey sees himself hanging out with Audrey after he joins her and Joey at the club to celebrate his new promotion when Danny makes Pacey the assistant chef at restaurant Civilization. Also, Dawson and Jen go back to Capeside to visit his mother where they have their first fight over what Dawson will do with his life.

Dawson and Jen realize that living together isn't as fun as they thought it would be; Jen turns her regular show at work into an advice show.

Summer is upon the gang and so they move on with their lives to follow their own plans. Joey, back at Capeside, returns to her job as a waitress at the Yacht Club; Pacey gets a new job there as a security guard and runs into Danny Brecher whom has left his wife; Dawson and Audrey are on their way to L.A.; and Jack and Jen to Costa Rica. But a few things change everybody's plans when their flights are delayed. Bessie tells Joey they got an answer from the scholarship Joey thought of applying in France (which Bessie secretly sent in without Joey's knowledge). Also Grams decides to go to Las Vegas with Clifton. Jack meets Eric at the airport, who was just coming back from his hometown where he tried coming out to his parents. Jen tells Jack to go help Eric, as she'll go help herself by going to meet her parents.