During the summer, Pacey and Audrey rocked Los Angeles and spent time with her next door neighbors, the Osbournes, and Jack Osbourne even tags along with them to interview at Worthington. Jen spent her time in New York and got ecstatic to learn her parents are separating. Jack got dumped by Eric, but got over it. Joey spent her summer in Capeside doing a lot of reading, working and romancing. On their first week back at Boston Bay College, Jen is shocked to run into find that Grams Ryan has decided to go back to school. At Worthington, Joey experiences nothing but bad luck when she decides to enroll in an intermediate writing class taught by the liberal, but manipulative and cynical, Professor Greg Heston who does not hesitate to ridicule and embarrass Joey in front of the class with her lack of knowledge of the current book topic. Pacey and Jack move out of Grams' house and Pacey tries to get the perfect apartment, owned by a feisty, punk rock British woman, named Emma Jones, who works as a waitress in the local bar Hell's Kitchen. Also, Dawson is working on a new movie, a horror film titled "Wicked Dead" with him as the assistant director and the hack Todd Carr as director. When he finally gets together with Joey, he is the only one to have remembered her 20th birthday.

After spending their first romantic night together, Dawson and Joey decide not to discuss it, because every time something happened between them they always ruined it by over discussing it. Dawson even shows Joey the set that he's working on which resembles his own house in Capeside. Meanwhile, Pacey starts on his new job as a stock broker which was set up by Audrey's father and during Pacey's first day he deals with his ambitious, but oily and pig-headed boss Rich Rinaldi. At the same time, Jack finally gets himself and Pacey the dream apartment Pacey was chasing so hard to get, with a little deviousness against Emma. During a heated argument with Grams, Jen accidentally meets a very cute guy, named C.J., a fan of Jen's defunct radio show who invites her to a counseling center that he works at. Also, Joey is hired as a waitress as the local bar, Hell's Kitchen, to get some extra cash for herself.

Joey's worst nightmare comes true when she accidentally sends a very personal e-mail she wrote for Dawson to the entire student body. The next morning, Joey's e-mail is the topic of virtually all campus discussions when Professor Hetson cruelly decides to debate it with his students just to see Joey squirm at the talk. Meanwhile, Jack makes an attempt to get to know his cultural professor, Mark Freeman, better, but he pays no attention to Jack. Pacey, while struggling to survive the first days on his new job, closes a very important deal for the firm, which his wheeling-dealing mentor Rich Rinaldi takes full credit for. Eddie, at student in Joey's reading class and whom works as the bartender at Hell's Kitchen, persuades Joey to confront any challenge that Hetson throws and not show any weakness because the stern and misogynistic Hetson thrives on it.

Dawson's former girlfriend, Natasha, (whom Dawson met and dumped during his summer in L.A.) returns as the new lead actress for the movie and now he has to deal with the consequences of dumping her over the phone. The production orders some food from Hell's Kitchen and Joey delivers it on the set, forcing her to see Dawson. Natasha gets angry and jealous when she sees Joey and has Todd fire Dawson by saying she will not work unless Dawson goes. But Natasha soon realizes Joey has hurt Dawson much more than he hurt her. When Eddie confronts Joey about her uncertainty, she decides to "follow an impulse" and kisses him. Meanwhile, Pacey ditches Audrey and goes to a strip club party with his bosses. Audrey runs into him and goes to a party with Jen and Jack, where she gets drunk and almost sleeps with a guy, if it weren't for C.J.'s stopping her. Also, Jack is disappointed when Professor Freeman tells him his wife is pregnant, and later makes a move on Jack.

Heather Tracy, Dawson's movie producer, arrives on the set and threats to shut down production on the film if the lead, Natasha, isn't replaced. The egotistical Todd doesn't do much to save her job and it's up to Dawson to keep the film from being canceled altogether. Back at Worthington University, Eddie has an argument with Professor Hetson over him criticizing Joey's presentation and he storms out of the class. Joey leaves after him, and then she discovers he's not a student after all. Meanwhile, Emma asks Audrey to be the new lead singer of her all-girl punk rock band, Hells Belles, which will perform at Hell's Kitchen. But Pacey continues working late hours and misses Audrey's debut performance. Also, Jack confronts Professor Freeman after he gives Jack's paper a C- which Jack thinks was the result of an argument the previous day.

On Halloween night, Todd throws a costume rave on the sound stage where Dawson thinks he sees the ghost of a famous Hollywood actress whom was murdered, while he also sees Todd and Natasha becoming more friendly. Jen is encouraged by Jack to call C.J., but she thinks he's gay after he shows up at the rave with another guy. Jack has a talk with C.J. and finds out the guy he's with, David, is gay, but not him. But C.J. also confides in Jack that he's not interested in Jen either. Meanwhile, Joey is stuck babysitting for Professor Hetson's annoying and headstrong 15-year-old daughter, Harley. Eddie helps her by taking them to a haunted house, where he and Joey kiss. Also, Audrey breaks up with Pacey at the costume rave after she overhears him talking to Emma that he doesn't love Audrey anymore.

Audrey gets a little too drunk before a concert with 'Hells Belles' band at Hell's Kitchen, and ends up making a scene and trashing the place. C.J., who was there on a "non-date" with Jen, tries to give her a little comfort and end up taking her back to his place. Meanwhile, Jack attends Professor Freeman's book signing and tells him the moment for Jack to make his move has passed as Freeman informs him that he has quit teaching to concentrate on his writing career. Jack then goes to invest his relationship with David, who waited all night long for Jack to show up at the bar. Joey feels bad for not being there for Audrey and has an argument with Eddie. When Eddie comes over to Joey's dorm to hand her Audrey's wallet that was forgotten at the bar, they decide drop their little game and go on a date. Also, Pacey's firm partners go down to New Orleans to celebrate a business deal, and Pacey has a big disappointment when he learns that the girl he's with is a call-girl bought by Rinaldi.

Dawson gets concert tickets for the band 'No Doubt' for the entire gang. Joey asks Eddie to go with her, but she forgets their tickets. But they sneak backstage anyway with a little help from Eddie's father who works as a maintenance man in the building. Jen sets Pacey up to meet Audrey at the concert hoping they'll reconcile. Everything goes well at first until C.J. confesses to Jen that he and Audrey slept together the night before, and he later confronts Audrey about her relationship with Pacey. Pacey learns about it and starts a fistfight with C.J. in which they get thrown out of the concert, as well as Jen, Audrey, Emma, Jack and David just for being with them. At the same time, Dawson misreads his tickets that are for Saturday's concert, and he and Natasha end up in jail after a policeman catches them making out in the parking lot, and Todd has to bail them out.

A big movie star, named Max Winter, arrives on the set to act with Natasha, and the flirting between them upsets Dawson. Pacey takes Emma to an office party where she finds out that Pacey is using her to win a contest among the office employees to see who brought the hottest date. Meanwhile, Joey has an upcoming Hetson final and Eddie offers his place for her to study. In the morning, they talk and end up having sex, which causes Joey to be late and she ends up missing the exam. Professor Hetson refuses to let Joey take a make up test and outright gives her an 'F'. Later that evening, Hetson comes to the bar and immediately starts an argument with Eddie where, in a very cruel tone, he tells Eddie how much he despises a loser like him taking up Joey's time. The hot-tempered Eddie falls right into the trap by punching Hetson in the face, and he gets instantly fired from Hell's Kitchen for it. Admired by Eddie's actions and stand against the mean Professor Heston, Joey then tries to cheer Eddie up and admire him for his noble act by taking to a local ice skating rink where they declare their love for each other.

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.

During a typical five-day work week, Joey is incessantly trying to reach Eddie while dealing with Harley Hetson showing up at Hell's Kitchen every day after cutting school. When Harley persuades Joey to see Eddie, she is devastated after finding out that Eddie has moved out of his apartment without saying a word. But Joey manages to persuade Harley to behave like an adult, and she also finally stands up to the intimidating Professor Hetson to help him look after Harley once in a while. Meanwhile, Pacey begins skipping work by hanging out at the Boston Aquarium with Emma. But any romance between Pacey and Emma is quashed when Rich Rinaldi buries Pacey with more paperwork, making him miss his lunch date at the aquarium with Emma. Jen starts working as a peer counselor with C.J., but her personal interests get in the way of her work. Jack and David both get tested for HIV which leads to them talking about their sexual pasts. Dawson and Todd fly to Los Angeles after photography on Todd's movie, "Wicked Dead" finally wraps up. But Heather Tracy and the executive producer, Larry Newman, want Todd to re-shoot the entire ending. After Todd refuses, due to his pride and ego, he gets fired and Dawson is ordered to step in as director. Also in L.A., Audrey goes back to her roots by hanging out with her party-loving friend Jack Osbourne.

Harley tries to encourage Joey to make up with Eddie after they find him now living with his parents in nearby Worcester, and even gets him to return to her with a made-up story about Joey being pregnant. Meanwhile, Audrey returns from L.A. with a more positive attitude. After apologizing to her friends, Emma takes Audrey back in the band Hell's Belles for a big concert. But Audrey cannot stay away from liquor in which she performs drunk, and passes out on stage, and Emma fires her from the band. Meanwhile, Pacey is invited by Rinaldi to an exclusive party for the best stockbrokers and gets a promotion of handling a mysterious account led by the shady pharmaceutical entrepreneur Roger Stepavich to handle the client's major pharmaceutical company. All is well until a mysterious woman tells Pacey that all that good might have some bad, which raises suspicions on Pacey about Rinaldi's true intentions towards him.

In Los Angeles, while directing re-shoots on "Wicked Dead", Dawson finds his authority questioned by Heather Tracy when Natasha refuses to do a nude scene. Frustrated in this work, Dawson (at Natasha's advice) resorts to an aggressive, Todd-like attitude to get the crew to listen to him. Meanwhile, Joey is unable to say good-bye to Eddie, who is moving to California to register at a college. She convinces him to help her take Audrey to a rehab clinic in Los Angeles, and the three of them, plus Bob, drive cross country where the four quarrel with each other. At a gas station, Audrey steals their car, forcing Joey and Eddie to walk, and they manage to work out their differences. They find Audrey in the parking lot of a bar and save her from an attempted rape by a guy she met there. Back in Boston, Jen and C.J. set a lonely Grams up with C.J.'s Uncle Bill, who turns out to be quite randy.

In Los Angeles, Dawson visits Audrey at the rehab clinic where he spots a big time film producer, named Toni Stark, and follows her into a therapy session hoping to talk to the woman who'll direct Dawson to better contacts. Meanwhile, Pacey throws a party at his place to celebrate his new success at his job as well as purchasing a new super-sized TV set and is surprised when Joey, still sulking over the departure of Eddie, lets loose by getting drunk and setting up a spontaneous game of spin the bottle. Jen catches the reformed alcoholic C.J. with a drink which leads to them arguing, and making up by having sex for the first time. Also, Emma tries to stay in the country to get her green card by courting a stoner to marry her until Jack offers to marry Emma. But in the end, Emma decides that it's not worth it and decides to leave.

After agreeing to pose as Pacey's date at a business party, Joey demands to be taken home. Pacey makes a quick stop at a local K-Mart to buy some snacks and condoms for another date for later that night, and they accidentally get locked inside the store. They're forced to spend the night there and talk about their friendship and relationship, past and future, which eventually leads to a kiss.

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.

Joey agrees to be Pacey's temporary secretary over his recent promotion. But they both have second thoughts when their mutual jealousy leads to disaster in the office over a reporter, named Sadia, the same woman whom met Pacey at the office party (in the 'All the Right Moves' episode), as well as Joey not getting along at all with the pig-headed and callous Rich Rinaldi. Meanwhile in Los Angeles, Dawson sells his idea for a coming-of-age movie, but when the studio heads Heather Tracy and Larry Newman want to change the movie into a teen sex film, Dawson must decide if he should take the lucrative deal or stick with his original concept. Also, an open-minded Grams is the intermediary that brings Jen and C.J. back together.

Dawson asks Pacey to help him invest for his first independent film and then returns to Capeside to write his next script. But Gail asks Dawson what will he do in case his plans of becoming a successful director fall through. Meanwhile, Pacey escorts Joey to Harley's school dance where they have a perfect time despite Harley's date, Patrick, picking a fight with another guy. There, Joey tells Pacey she can't have anything to do with him because Eddie is back from California during a break before he starts college in the fall. Also, Grams tells Jen she has been diagnosed with having breast cancer, and Jen sees her entire world fall apart with the possibility of Grams's death.

Audrey returns to Boston from rehab in L.A. and tries to make peace with everyone while the gang see their relationship problems exposed to a large audience when they all become patients of Dr. Drew Pinsky and Adam Carola's counseling center benefit at Boston Bay. C.J. is trying to find out why Jen inadvertently dumped him that very morning, while Eddie wants to know why is Joey opposing to have sex with him, while David thinks Jack is flirting with another guy. All and all, Jen ends up walking away from her hosting duties, leaving Audrey in charge. She tells C.J. about Grams' disease and C.J. assures he's there for her. Joey finally gives in and asks Eddie back to her place. But David and Jack don't have happy ending for David refuses to believe Jack was just being nice and asks for some time off.

Joey aces Professor Hetson's final exam and ends the semester with a C+, and Joey is finally relived that her ordeal with Hetson is over. However, she decides she wants him as her advisor after she chooses English as her major. Eddie proposes they go backpacking through Europe before going their separate ways to college. Reluctant at first to jump so suddenly on such an intense trip, Joey decides to go, only to find a goodbye note from Eddie, this time for good saying that she deserves someone better than him. Elsewhere, David finally breaks up with Jack, who ponders if he was only with David to prove to himself that he could hold a steady relationship. Meanwhile, Pacey continues dating Sadia and selling stocks. But things change drastically, first when Sadia leaves him by returning to her fiancée. Then the biotech stocks that he and Dawson were investing in go bankrupt. Pacey then asks Rinaldi to borrow some money, but the cold-hearted Rinaldi refuses. Frustrated and angry, Pacey finally snaps and punches Rinaldi in the face, who instantly fires Pacey.

Pacey, now jobless and penniless, returns to Capeside where Dawson invites him to be a producer on his autobiographical film. Pacey accepts, but can't work up the courage to tell Dawson that all his money is gone. With classes at Worthington over, Joey says goodbye to Audrey who has to stay behind to attend summer classes to make up for her absences, with Jack Osbourne tagging along. Joey also returns to Capeside to see Dawson where they have minor argument with about how she wanted him to be the most significant person in her life and somehow he became her only one night stand. Back in Boston, Jen invites her mother, Helen, over to Grams' house where she wants her to tell Helen about her cancer. While introducing C.J. to Helen, Jen witnesses C.J.'s Uncle Bill storm into the house and yell at Grams, revealing everything by saying that she shouldn't give up on her life just because she has cancer. Jen suggests that they all move to New York to live with Helen. Also, Audrey decides on a low-key change for herself by playing an old-fashion acoustic guitar at Hell's Kitchen, and Pacey finally tells Dawson about losing all his money in his poor stock investments.

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.