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.

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.