On Dawson's advice, Joey attempts to heal the wounds of her romance with Jack which has been left shattered by rumors and innuendo. Meanwhile, Jack and Andie's father, Joseph McPhee, arrives in town for a get-together which brings out old family tensions which leads Jack confronting his innermost secrets. For the first time in his life, Pacey stands up for what he believes in when he takes on the mean-spirited Mr. Peterson. But the consequences of his convictions are more than Pacey could have imagined when he's suspended from school and Peterson makes his personal agenda to fail Pacey with unethical means. Pacey then sets out to ruin Mr. Peterson by investigating and challenging his authority with a code of conduct book over his teaching methods. Also, Jen thinks that Ty may not be the guy for her when she sees little amusement in his stereotypical comments especially over Jack's true sexual orientation, while Grams is surprisingly understanding and supportive.

Concerned for Andie's well being, Jack phones their father who arrives back in Capeside where he announces that he intends to take both Andie and Mrs. McPhee to Providence for treatment in a mental hospital. Both Jack and Pacey are stunned at the news which leads to Pacey and Andie to decide whether her mental wellness is more important than being together. Jack also must decide if he wants to go with Andie and their mother, or stay alone in Capeside. Meanwhile, Dawson is preparing his film class' final exam by videotaping all individuals involved as well as helping Joey's father, Mike Potter, extend the Ice House for Bessie. After being shunned by everyone, Jen wonders where she'll live after her parents tell her by phone that she is not welcome to come back to New York.

Dawson is recruited by Mitch and Principal Green to produce a film for the football pep rally, while the mysterious Eve continues to temp Dawson. Meanwhile, Pacey enlists Joey's help for help in bringing Andie back to Capeside. But Pacey's and Andie's long-awaited reunion doesn't go exactly as Pacey intended when a guilt-ridden Andie tells him about a fling she had of her own and as a result, Pacey breaks up with her. Also, Jack is asked to join the football team, the Capeside Minutemen, and then comes to an unexpected understanding with his father who has returned to Capeside after moving his struggling business to live near Jack and Andie. Also, head cheerleader Jen has a meeting of minds with the new Capeside quarterback; the rookie freshman Henry Parker.

Pacey hopes that an overnight camping trip by taking Dawson to their favorite childhood camping spot will help ease the pain when he prepares to tells Dawson about his romantic feelings for Joey. But their plans get interrupted when Buzz and two of his friends come along. When Dawson brings up memories about their loyal friendship, Pacey chickens out and decides not to tell Dawson. Meanwhile, Joey deals with the emotional fallout from her kiss with Pacey by spending a girls' night out with Jen and Andie. But to Jen's surprise, they stumble upon a 15th birthday party for Henry at the local roller skating rink that she was not invited to. Also, Jack clashes with his father when Ethan arrives at his house for a visit in which Ethan gets caught in the middle when Mr. McPhee bonds with him and not Jack.

Pressured by two parties, Joey ultimately must choose between her love for Dawson and her new feelings for Pacey who's planning a summer getaway by sailing down the coast on his new boat, 'True Love.' Meanwhile, Grams talks about love and regret with Jen over the departed Henry, and encourages her, with Jack and Andie tagging along, for an all-night drive to Ohio so that Jen can see Henry one last time. They then take Jack to Boston to see Ethan who tells him that he has returned to his boyfriend. Mitch and Gail decide to get remarried and have the ceremony at their house with Dawson as the best man and Joey as the maid of honor. At the end, Dawson encourages Joey to make a move to follow her own path, and she runs off to join Pacey on his boat, leaving Dawson emotionally beaten and alone once again.

Andi gets early acceptance into Harvard, exciting Jack and their father. But accomplishing what should be the biggest thing in her life doesn't make her happy. She decides to explore different paths in her life by going to a rave with Jen and Jack. Andi steals an Ecstasy pill from Jen, which reacts badly with her anti-depressant. Meanwhile, things get awkward during the party when Gretchen brings along Pacey, Joey and Dawson, who is growing more attracted to Gretchen. Also, Mitch and Gail decide to keep their baby.

While Andie is recovering from her near-fatal drug overdose, Jack blames Jen for the incident, while Jen blames the deranged Drue for her life falling apart after he turns everyone, including Grams, against Jen by saying that she deliberately slipped Andie the ecstasy. Andie's father tells her that it would be better if she were to spend the rest of the year in Italy with her aunt, since she already has the credits required for an early graduation. Meanwhile, Joey is conflicted when she must ask Dawson to say a good word for a college acceptance form. Also, Dawson continues painting the misanthropic Mr. Brooks' house and realizes that the old man has his own personal life problems with his estranged family.