Summer is upon the gang and so they move on with their lives to follow their own plans. Joey, back at Capeside, returns to her job as a waitress at the Yacht Club; Pacey gets a new job there as a security guard and runs into Danny Brecher whom has left his wife; Dawson and Audrey are on their way to L.A.; and Jack and Jen to Costa Rica. But a few things change everybody's plans when their flights are delayed. Bessie tells Joey they got an answer from the scholarship Joey thought of applying in France (which Bessie secretly sent in without Joey's knowledge). Also Grams decides to go to Las Vegas with Clifton. Jack meets Eric at the airport, who was just coming back from his hometown where he tried coming out to his parents. Jen tells Jack to go help Eric, as she'll go help herself by going to meet her parents.

The year is 2008. After five years, the gang returns to Capeside for a reunion and wedding after taking different paths in life. Joey is a successful book editor living in New York with her current boyfriend Chris. Dawson lives in Hollywood and is a successful executive producer of his autobiographical TV series, 'The Creek.' He is still single, but has not forgotten the love of his life. Pacey is now the manager to the re-opened restaurant, The Ice House, but still continues his brash lifestyle of dating older women. Jack is now a teacher at Capeside High and dating Pacey's brother Doug, now the sheriff, who is still closeted. Jen lives in New York with Grams and runs an art gallery in SoHo, and is now the mother of a baby girl, while Audrey has gone off to Europe on tour with a band. They all (sans Audrey) meet at Pacey's restaurant, and after a little too much wine they all start bringing back ghosts from the past. They all get dressed and ready for Gail's wedding, and between old memories and new bruises (from Pacey, who was beaten up by some married woman's husband), Joey tries to balance having the two men that changed her life around her. Suddenly, Jen faints and is taken to hospital, where Grams reveals that she suffers from a lethal heart condition. Jen is dying...

With Jen in the hospital, the gang tries not to be too sad about it. Dawson helps Jen make a video for her infant daughter, asking her to never stop loving and dreaming. Jen also asks Joey as her last wish to end the chasing and running and to settle down. Jack tells Jen that she's his soul mate and asks to raise baby Amy for her. Jen finally passes away and while mourning the death of their close friend, the gang has to move on. Doug tells Jack he's willing to spend his life with him and wants to help raise Amy. Joey breaks up with Chris over the phone while she tries to decide whom she will choose: Dawson or Pacey. After Jen's funeral, Pacey suddenly tells Joey that she's "off the hook". Pacey explains to Joey that despite his endless love for her, he can't hold her back any more. Since both Joey and Pacey had troubled and painful childhoods and adolescence's (Joey with her mother's death from cancer and her father's imprisonment for drug trafficking, and Pacey with his outrageously neglectful and abusive parents). But his point is that, as much as Joey wanted, all her life, was to get far away from Capeside and see the world, Pacey seems forever destined to be stuck there just like his alcoholic loser father, and grandfather, and so on. Before returning to New York, Joey sits with Dawson and confesses that even though they may never be together, he and she are soul mates and nothing should ever change that.