When a major hurricane strikes Capeside, all the principal characters take refuge in the Leery home, including Joey's very pregnant older sister Bessie and her boyfriend, where Jen's overly religious grandmother does not hide her bigotry towards them. Also, Dawson rages at Jen about her past and at Joey for not confiding in him about her mother's philandering. But when Mitch learns about Gail's affair, he angrily storms out of the house, leaving a tormented Dawson to deal with the fallout. Meanwhile, Pacey takes shelter at Tamara's beach house with his brother Doug, a local policeman, where he ruins his brother's chances to hook up with Tamara by secretly telling her that Doug is gay.

Capside is abuzz with rumors of a teacher's indiscretion, rumors that could prove fateful for Pacey and Tamara. Pacey then takes it upon himself to go before a school board hearing to admit to personally fabricating the rumors to clear Tamara. Meanwhile, Joey and Jen get a life lesson when Bessie is aided by an unlikely source, Grams Ryan, when she goes into labor and gives birth to her baby in Dawson's living room, with Dawson videotaping the whole thing.

At her sister Bessie's persuasion, Joey goes to visit her father in prison. Dawson tags along and leading them to spend the night in a motel where he finally reveals his true romantic feelings for her, while Joey debates going to France for a semester abroad to escape from her troubled home life in Capeside. Meanwhile, Grams tries to persuade the atheist Jen to act through prayer as her comatose grandfather is admitted to the hospital. Also, the sarcastic Pacey continues quarreling with Doug over Pacey's failing grades, which all emits from Pacey's extremely low self-esteem.

During a late-summer heat wave, Dawson plays detective when Eve's mysterious ways, including breaking and entering at Grams house, cause him to wonder about her reasons for being in Capeside and he gets Pacey to help him. But Eve is too slick for Dawson's inept detective ways and throws him off balance every time. Meanwhile, Joey's misgivings of Rob lead her to crash his date with Andie at the movies which leads to him firing her. Also, Jack goes against Jen's wishes and sets her up for a rendezvous with Henry.

Joey questions Dawson's state of mind when he and Pacey decide to lead her and their friends to a secret location party on a golf course hosted by Matt Caulfield, a wealthy and snobbish student connected to a clique of spoiled rich kids from school, infamous for their complete and utter debauchery. Meanwhile, Jack's ex-girlfriend, Kate Douglas, arrives from Rhode Island for a visit while nursing a broken heart, but is unaware of Jack's coming out. Also, Jen's first date with Henry is a Valentine's Day she won't soon forget when he passes out after donating four pints of blood to pay for their romantic dinner at a fancy restaurant.

Joey is chosen to be part of a group of students to paint a school mural, but when hers is defaced before the unveiling, Dawson offers words of encouragement while Pacey takes action and risks suspension when he goes in search of the culprit whom he suspects to be Matt. When Andie's PSAT scores rank among the best in the country, she feels tremendously guilt-ridden and gambles with everything she has worked for by telling Principal Green about the previously stolen PSAT test. Also, Pacey moves in with his brother, Doug, when their divorced sister and her kids move back into the Witter house and take over Pacey's room.

Pacey hopes that an overnight camping trip by taking Dawson to their favorite childhood camping spot will help ease the pain when he prepares to tells Dawson about his romantic feelings for Joey. But their plans get interrupted when Buzz and two of his friends come along. When Dawson brings up memories about their loyal friendship, Pacey chickens out and decides not to tell Dawson. Meanwhile, Joey deals with the emotional fallout from her kiss with Pacey by spending a girls' night out with Jen and Andie. But to Jen's surprise, they stumble upon a 15th birthday party for Henry at the local roller skating rink that she was not invited to. Also, Jack clashes with his father when Ethan arrives at his house for a visit in which Ethan gets caught in the middle when Mr. McPhee bonds with him and not Jack.

In this unusual episode that replays the same day's activities from three different perspectives: after Pacey unveils his new sailboat, named 'True Love', he and Joey vacillate on the ways to tell Dawson about their feelings for each other. But each time they decide to tell Dawson about them being romantically involved, they chicken out. But when both Pacey and Joey get together and decide to tell Dawson about them, Dawson's angry reaction is what they hoped they wouldn't get: Dawson reveals that he already knows when Jen had earlier that day told him about Joey and Pacey after assuming that they told Dawson. Meanwhile, Andie, who thought she was over Pacey enough to date, accepts a date with Capeside visitor Will, but their first date is ruined when she also learns about Joey and Pacey now a couple. Pacey also leaves the trouble-making Buzz with his brother Doug for the entire day as Andie deals with her feelings for will, Also Jen deals with Henry who wants to take their relationship to the next level.

Pressured by two parties, Joey ultimately must choose between her love for Dawson and her new feelings for Pacey who's planning a summer getaway by sailing down the coast on his new boat, 'True Love.' Meanwhile, Grams talks about love and regret with Jen over the departed Henry, and encourages her, with Jack and Andie tagging along, for an all-night drive to Ohio so that Jen can see Henry one last time. They then take Jack to Boston to see Ethan who tells him that he has returned to his boyfriend. Mitch and Gail decide to get remarried and have the ceremony at their house with Dawson as the best man and Joey as the maid of honor. At the end, Dawson encourages Joey to make a move to follow her own path, and she runs off to join Pacey on his boat, leaving Dawson emotionally beaten and alone once again.

Pacey and Joey return from their summer vacation at sea where they have to deal with Dawson's feelings, who has been deeply hurt for the past months while he and Jack made money by painting houses. At first, he doesn't want to talk to either one of them, but at a drive-in theater, Jen convinces him to talk to Joey. Meanwhile, Pacey's other older sister, Gretchen, arrives in Capeside after taking time off from college and moves in with Doug, making Pacey homeless since he does not want to live with Doug or their hostile parents anymore. So, he asks Joey to let him crash at her B&B house for a while. Dawson confides in Jack about Gretchen, for whom he had a secret crush a few years ago. Also, Andie meets two French guys during a beach outing where she becomes attracted to one of them.

A sailboat owned by Capeside High's pompous Principal Dave Peskin, with "Class of 2001" written on the sail, and with his pet dog aboard, is found in the school swimming pool as part of a major school prank. As a result, Mitch Leery and Principal Peskin are after the guys who did it in which Dawson, Pacey, Jack and Drue are main suspects. Since, the dog that was on the boat instantly recognized Jack, Pacey had access to the yacht club and Dawson had access to the school keys. Each one has alibis for that day; Jack was at the soccer field with Jen to help plan a game. Dawson was cleaning Mr. Brooks parlor where he discovers that the that the old man was a former filmmaker from the 1950's. Pacey was with Doug on a routine police patrol where they squabbled about Doug's well being. Drue, despite his denials, is revealed as the culprit. But at the end, Joey finds out that Dawson, Pacey and Jack all teamed up to pull it off and to get Drue into trouble.

Joey decides to help throw a surprise 18th birthday party for Pacey at his parents house, not knowing about Pacey's 'birthday curse'. The party goes haywire from the start as Joey finally sees why Pacey hates his dysfunctional and annoying family so much; his domineering, drunkard father; his overbearing, delusional mother; and his divorced sister Kerry and her three children, make everyone feel uncomfortable, and Doug later joins in and gets them to embarrass Pacey with stories from his past. Meanwhile, Dawson becomes upset when he feels that Gretchen doesn't want anyone to know about their growing romantic relationship and postpones their first real date to go to the party. Also, Jen is paired with Tobey for a community service project that evening of being the town's designated driver for drunken college kids.

As Senior Ditch Day arrives, Joey is excited to find herself accompanying Jen on an excursion to New York City under the auspices of attending a college meeting. But it's not long before Joey realizes that they're there for an entirely different reason. Jen is there to meet her estranged father, Theo, where she reveals to him the roots of her self-destructive lifestyle. Meanwhile, eager to infuse their relationship with a bit of spontaneity, Gretchen and Dawson take off on their own road trip. But what starts out as unpredictable fun turns into one debacle after another when they get stuck in the middle of nowhere with a flat tire. Back in Capeside, Pacey and Drue find themselves the only seniors in school on Ditch Day. That evening, they set out for some real fun, drinking at a bar which leads to both of them getting arrested for underage drinking, leaving Pacey in serious doubt as to what his future will hold for him.

As graduation day approaches, Joey has a tough time preparing her commencement speech, and Dawson helps her find some bittersweet inspiration. Pacey wonders if he's going to graduate at all and worries that his last final will be the toughest one. He walks out of it after his teacher makes a rude comment on him, costing him his diploma. Meanwhile, Andie McPhee returns to Capeside for the cap and gown ceremony, and is surprised to meet Jack's new boyfriend, Tobey. Pacey spends some quality time with Andie and decides he must get out of town to search for his feelings. After a friendly talk with Doug about his future, Pacey privately says his goodbyes to Doug, and then leaves town, vowing never to return. Also, Drue temporarily moves into Jen's house after being kicked out of his home by his mother after an argument. Drue then tells Jen that before they both graduate and go their separate ways to college, he convinces her to help him pull a hilarious senior prank for old times sake by setting off the school sprinkler system during the ceremony. But they get caught by Principal Peskin whom forces them to listen to his awful violin playing skills for three hours as their final detention of punishment.

After arriving in Boston to visit, Dawson sees great complications in his past relationship with Joey, who decides to drop out of Professor Wilder's writing class. But the line is incredibly long, which takes Joey all day and all the time she had to spend with Dawson, who ends up being guided around the campus by Audrey whom he confides in with his problems. Meanwhile, Jack pushes Jen into talking to Charlie, who works as the campus radio DJ, and after their first date, she ends up sleeping with him. Also, Doug pays Pacey a visit at the Boston docks and tells him about a job he can get for him at a restaurant, called Civilization, in which the chief, Danny Brecher, is a friend of Doug's. Reluctant at first, Pacey eventually gives in and gets the job after his latest girlfriend, Melanie, is forced to pay for their evening out since Pacey has no job or money.

Dawson goes back to Capeside to celebrate Christmas and brings Natasha and Todd with him where Dawson can't get past the fact that he saw Natasha and Max together, and Todd's drunkenness bothers Gail. Joey also arrives back in Capeside with Audrey, where Eddie later arrives with a Christmas tree to celebrate. There Eddie meets and has an argument with Joey's father, Mike Potter, who worries that Eddie might not be good for Joey since he's now unemployed and doesn't go to college. Pacey also comes back to spend time with his brother Doug who does not like the expensive gifts and constant, lavish spending Pacey is doing after making a lot of money at his stock trading job. The gang, as well as Jen and Grams, gather to have Christmas dinner at the Leery household which goes disastrously wrong where a drunken Todd makes an embarrassing thanks, but not as embarrassing as Audrey's, whose drinking problem has gone so out of control that she lashes out on everyone, and wrecks Pacey's new car.

Professor Heston orders Joey to baby-sit for Harley to make sure she does her homework. But Joey ends up serving as relationship counselor when she finds Harley's boyfriend, Patrick, hiding in the house and he starts to drool over Joey. Meanwhile, Dawson pays a visit to his past when he's asked to speak on Mr. Gold's class at Capeside High about how it is to be working in L.A. Dawson has a student, named George, show him his movie in which he realizes that he's moved on from the teenager he once was. Pacey also returns to Capeside when his father is admitted to the hospital after suffering a heart attack where Pacey has an argument with Doug about the way Pacey's been treating the family by shutting them out, and resents the new lifestyle Pacey has.

As Dawson abandons his lifelong dream of becoming a filmmaker and works to pay off his huge credit card debt, Joey decides that Dawson must realize his dream, and rallies everyone she knows to help him begin production on his movie, which is the autobiography of his life. Joey forcibly recruits Harley and Patrick to play the roles of Joey and Pacey, and George volunteers to play Dawson, while Audrey volunteers for the role of Miss Jacobs. Gail even calls Todd Carr to assist with the production and Doug Witter for security, whom is now the acting sheriff since Mr. Witter is too sick to work anymore. Meanwhile, Pacey is newly inspired to raise the funds that are needed by going to various local businesses to raise money and at one meets a crush from his past, Christy Livingston. As filming wraps, Jen, Jack and Grams say goodbye to everyone as they leave for New York City where Jen and Jack transfer to NYU. Joey acts an a mentor to get Dawson and Pacey to make up while she finally achieves her life-long dream of going to Paris.

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.

A sailboat owned by Capeside High's pompous Principal Dave Peskin, with "Class of 2001" written on the sail, and with his pet dog aboard, is found in the school swimming pool as part of a major school prank. As a result, Mitch Leery and Principal Peskin are after the guys who did it in which Dawson, Pacey, Jack and Drue are main suspects. Since, the dog that was on the boat instantly recognized Jack, Pacey had access to the yacht club and Dawson had access to the school keys. Each one has alibis for that day; Jack was at the soccer field with Jen to help plan a game. Dawson was cleaning Mr. Brooks parlor where he discovers that the that the old man was a former filmmaker from the 1950's. Pacey was with Doug on a routine police patrol where they squabbled about Doug's well being. Drue, despite his denials, is revealed as the culprit. But at the end, Joey finds out that Dawson, Pacey and Jack all teamed up to pull it off and to get Drue into trouble.

Joey questions Dawson's state of mind when he and Pacey decide to lead her and their friends to a secret location party on a golf course hosted by Matt Caulfield, a wealthy and snobbish student connected to a clique of spoiled rich kids from school, infamous for their complete and utter debauchery. Meanwhile, Jack's ex-girlfriend, Kate Douglas, arrives from Rhode Island for a visit while nursing a broken heart, but is unaware of Jack's coming out. Also, Jen's first date with Henry is a Valentine's Day she won't soon forget when he passes out after donating four pints of blood to pay for their romantic dinner at a fancy restaurant.

Professor Heston orders Joey to baby-sit for Harley to make sure she does her homework. But Joey ends up serving as relationship counselor when she finds Harley's boyfriend, Patrick, hiding in the house and he starts to drool over Joey. Meanwhile, Dawson pays a visit to his past when he's asked to speak on Mr. Gold's class at Capeside High about how it is to be working in L.A. Dawson has a student, named George, show him his movie in which he realizes that he's moved on from the teenager he once was. Pacey also returns to Capeside when his father is admitted to the hospital after suffering a heart attack where Pacey has an argument with Doug about the way Pacey's been treating the family by shutting them out, and resents the new lifestyle Pacey has.

Dawson goes back to Capeside to celebrate Christmas and brings Natasha and Todd with him where Dawson can't get past the fact that he saw Natasha and Max together, and Todd's drunkenness bothers Gail. Joey also arrives back in Capeside with Audrey, where Eddie later arrives with a Christmas tree to celebrate. There Eddie meets and has an argument with Joey's father, Mike Potter, who worries that Eddie might not be good for Joey since he's now unemployed and doesn't go to college. Pacey also comes back to spend time with his brother Doug who does not like the expensive gifts and constant, lavish spending Pacey is doing after making a lot of money at his stock trading job. The gang, as well as Jen and Grams, gather to have Christmas dinner at the Leery household which goes disastrously wrong where a drunken Todd makes an embarrassing thanks, but not as embarrassing as Audrey's, whose drinking problem has gone so out of control that she lashes out on everyone, and wrecks Pacey's new car.

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...

As graduation day approaches, Joey has a tough time preparing her commencement speech, and Dawson helps her find some bittersweet inspiration. Pacey wonders if he's going to graduate at all and worries that his last final will be the toughest one. He walks out of it after his teacher makes a rude comment on him, costing him his diploma. Meanwhile, Andie McPhee returns to Capeside for the cap and gown ceremony, and is surprised to meet Jack's new boyfriend, Tobey. Pacey spends some quality time with Andie and decides he must get out of town to search for his feelings. After a friendly talk with Doug about his future, Pacey privately says his goodbyes to Doug, and then leaves town, vowing never to return. Also, Drue temporarily moves into Jen's house after being kicked out of his home by his mother after an argument. Drue then tells Jen that before they both graduate and go their separate ways to college, he convinces her to help him pull a hilarious senior prank for old times sake by setting off the school sprinkler system during the ceremony. But they get caught by Principal Peskin whom forces them to listen to his awful violin playing skills for three hours as their final detention of punishment.