All of the gang's lives go through changes. After Andie begins seeing her dead brother Tim in the last episode, Jack and Pacey agree to call Mr. McPhee not realizing that he'll want them to be treated in Providence, not Capeside. All are stunned at the new changes and Andie and Pacey must decide if Andie's mental wellness is more important than being together. Jack also must decide whether or not to go with Andie or stay. Dawson while helping Mr. Potter extend the Ice House interviews him for a film project about his changed life, but has it changed? Jen decides to make a change so she calls her mother and inquires about returning home or visiting and is told it is inconvenient right now.

Dawson returns from spending the summer in Philadelphia with his mother, and on his way home meets a beautiful young woman who brings trouble to his otherwise ho-hum life. Meanwhile, Joey, who has frozen Dawson out all summer, realizes she is still reeling from their unexpected break-up when she sees him again, but may have found an unexpected new friend for their junior year; Jen gets more than she bargained for when she takes on the fascist head cheerleader; Mitch accepts a new position as Capeside High's varsity football coach; and although Pacey tries to be brave, he has had a lonely summer without Andie.

Dawson is recruited by his dad and Principal Green to produce a film for the football pep rally, but the stars of the film end up being Dawson and his lady friend Eve, not the Capeside Minutemen. Meanwhile, Pacey has enlisted Joey for assistance in bringing Andie back to Capeside, but their long-awaited reunion doesn't go exactly as Pacey had intended; and Jack comes to an unexpected understanding with his father who has returned to Capeside to be with Jack and Andie.

Father and son are at odds when Dawson moves forward with a news piece for his mom's Philadelphia station using Mitch's star player, Jack, as his subject matter even though Mitch is vehemently opposed. Meanwhile, Joey and Pacey find themselves in cahoots when they must pay the price for ditching class; Andie jumps to conclusions and panics about the reasons Principal Green wants to meet with her; and Jen goes to great lengths to remove herself as head cheerleader but is shocked at the end results.

Dawson is torn about telling Jen the scandalous secret he has about Eve and even more distressed when his mom unexpectedly returns from Philadelphia. Meanwhile, Andie accuses Joey of sabotaging her chance to reunite with Pacey; and Jen shocks the entire town with the entertainment she has hired for the Annual Homecoming Queen Gala and shocks the very shy Henry even more when she asks him to be her escort.

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.