Dawson plays detective when Eve's mysterious ways, including breaking and entering and stealing, cause him to wonder about her reasons for being in Capeside, but the secrets he uncovers may drastically change the lives of others close to him. Meanwhile, Joey's misgivings of Rob lead her to crash his date with Andie but her good will backfires on her; and Jack goes against Jen's wishes and sets up a rendezvous for Henry.

In a bone-chilling installment, Dawson recruits Joey, Pacey and Jen to be his guerrilla crew on a documentary for history class about Witch Island, a local spot shrouded in mystery for its reputation for being haunted by witches. They are haunted by tall tales of witches and love lost that has Dawson and Joey questioning their own romance and Jen and Pacey considering a new kind of friendship. Back at school, Andie takes her job on the school disciplinary committee a little too seriously when she tries taking back the halls of Capeside.

Joey questions Dawson's state of mind when he and Pacey decide to lead their friends to a secret location party hosted by a group infamous for their complete and utter debauchery. Back at home, Jack's ex-girlfriend arrives from Rhode Island nursing a broken heart but is unaware of Jack's coming out last year and Jen's first date with Henry is a Valentine's Day she won't soon forget.

Dawson invites Joey, Andie and Pacey to spend Spring Break in the mountains at his aunt's home, but the trip is filled with tension as Joey and Pacey continue to battle about their feelings for each other and Andie becomes intrigued with the gang's childhood friend Will who is visiting. Meanwhile, back in town, Jen becomes surprisingly territorial when another woman flirts with Henry.

After an emotional day filled with love, tears and wedding vows, Joey ultimately must choose between her love for Dawson and her new feelings for Pacey. Across town, Grams talks about love and regret with Jen, while Jack and Andie make a decision to drive all night so that Jen can see Henry one last time.

Joey is looking for a new job and gets one at the Yacht Club pretending to know a very affluent family. She is tricked by her boss's son, Dru, who discovers her lies. Mitch (no also a counselor at the school) tells Pacey he's not going to graduate unless he makes up for his bad grades. Pacey doesn't want Joey to know, but Mitch tells Dawson, who tells Joey, showing that he still cares about Pacey. Pacey and Joey have a fight, and Pacey admits he need help.

Dawson asks Mr. Brooks' advice on becoming a director. Joey takes Pacey to a dinner hosted by an exclusive college.

The morning after, Joey and Pacey discover they've overslept and missed the bus back to Capeside. While they wait for the next one, the couple find themselves confronted with the tensions that accompany the latest development of their relationship. Meanwhile, as punishment for breaking into her hotel mini-bar during the class ski trip, Mr. Kasdan decides to send Jen to a psychologist where she can discuss her "inner teen issues."

Back in Capeside, Joey and Dawson's paths collide and they spend an evening catching up on the past weekend and its many happenings. Sensing a change in Joey's demeanor, he poses the unthinkable question, forcing Joey to consider whether honesty is the best policy. Dawson has to come to terms with Brooks' death and is surprised to discover he is in his will.

Accepted early to USC, Dawson finds his last night in Capeside has arrived much sooner than everyone had originally anticipated. While Dawson looks forward to spending the evening with Joey, Jack and Jen, Mitch has other ideas. Meanwhile, Dawson's not the only goodbye Jen has in store for her, as she bids farewell to the house she's been sharing with Grams. Finally, Joey says goodbye to Dawson in her own way.

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.

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.

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.

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.

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.

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 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.

In Los Angeles, while directing re-shoots on "Wicked Dead", Dawson finds his authority questioned by Heather Tracey and the other producers when Natasha refuses to do a nude scene. As a result, Dawson adopts an aggressive take-no-prisoners attitude, similar to the one that Todd has, to take control of the situation. In Boston, Joey is unable to say good-bye to Eddie who is moving to California to register at a college when she convinces him to help her take Audrey to a rehab clinic in Los Angeles, and the three of them, plus a guy Audrey picks up, drive cross country where the four constantly quarrel with each other. Also, Jen and C.J. set a lonely Grams up with C.J.'s Uncle Bill, who turns out to be quite randy.

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.