Uncertainty fills the air as Pacey and Joey return to Capeside following their summer-long voyage.
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As a new school year finds Pacey on the verge of flunking out, Henry recruits Jack to break up with Jen; Joey goes to work at the local yacht club.
Newcomer Drue Valentine's smart aleck classroom behavior gets him teamed with Dawson and Joey for a report on Shakespeare's "Two Gentlemen of Verona." So when Pacey wants Joey to go sailing to celebrate his first "A" of the school year, she suggests that he take Jen instead. Meanwhile, when she's charged with conducting one of Andie's college interviews, Drue's mom, Mrs. Valentine, stumbles onto the truth about her mental illness.
As the college application process intensifies, Drue organizes a fake birthday for Jen.
As Dawson discovers that his mom is pregnant, Joey struggles with deciding when to start having sex with Pacey; Jack's sexual orientation causes a problem with his coaching a youth soccer team.
Andie's effort to celebrate her early admission to Harvard ends up endangering her life.
An opportunity for time off before college prompts Andie to try bringing everyone together before she goes.
Dawson, Pacey and Jack are suspected of a senior class prank.
Dawson seeks Mr. Brooks' advice on becoming a director; Joey takes Pacey along to a dinner hosted by an exclusive college.
As Mr. Brooks' revelations about his past inspire Dawson, Pacey is encouraged to push his own relationship with Joey.
Pacey tries to disrupt Dawson's efforts to woo his sister; Drue's mischief ends with him and Joey locked inside a storage closet.
Joey's surprise birthday party for Pacey amplifies long simmering emotional tensions in the Witter family.
Dawson is less than comfortable about meeting Gretchen's friends; Joey and Pacey are enlisted to help Drue get through an important date.
Amid high expectations and emotional ambivalence, the annual Capeside High School Senior Class ski trip has arrived. When a snowstorm forces them to spend the night in a small town along the way, Drue makes sure that the room key assignments pair off him and Anna, Pacey and Joey, and Jen and Jack. Because of Mr. Brooks' failing health, Dawson has stayed behind with Grams. However, a decision to keep Brooks on life support leaves Dawson facing a surprising and difficult choice. And as the Leery's and Grams wrestle with the decision too, back at the lodge, Pacey and Joey confront their own sexual tension.
As Pacey and Joey analyze their first sexual experience, Brooks' death brings Dawson and Gretchen's relationship into focus; a psychologist presses Jen about her past, while Dawson asks Joey if she's had sex..
Following the Senior Class Ski Trip, Pacey and Joey are determined to find someplace where they can continue their sexual relationship without interruption. It's when Pacey suggests that she spend the night with their brother Doug that Gretchen realizes what's happened. And after promising not to say anything, she heads to Dawson's thinking she just might take advantage of his mom and dad's going away for the weekend. Meanwhile, as Drue deviously engineers Joey and Dawson's election as Senior Class Couple, Jen enlists Jack to help her learn more about therapist Tom Frost.
The excitement over Joey's college admission is dimmed when she learns how much it's going to cost.
Senior Ditch Day sends Dawson and Gretchen on a road trip to Maine; Jen takes Joey to New York as support for a showdown with her dad.
As Gail struggles with an overdue baby, Joey worries that she may be pregnant...
While sparking a pair of possible romances, Capeside's senior prom threatens the future of two others.
Gretchen's return to college forces Dawson to make an important decision of his own; Jen balks when Grams wants to sell the house to pay for her college tuition.
Graduation for the Class of 2001 brings friends and family back together as it prepares to drive them apart.
As Dawson prepares to leave for college, he and Joey reunite in order to say goodbye.