Pacey and Joey return from their summer vacation on "True Love". Now they have to deal with Dawson's feelings, who has been deeply hurt for the past months. At first, he doesn't want to talk with neither one of them, but Jen convinces him to talk to Joey. Meanwhile, Pacey's older sister, Gretchen, arrives in Capeside and moves in with Doug, making Pacey homeless. But he won't live with his parents anymore, and so he asks Joey to let him crash at her house for a while. Dawson tells Jack about Gretchen, for whom he had a secret crush a few years ago. Andie meets 2 foreign guys, and she is attracted to them. Dawson and Joey talk, and he says he'll be ok, but it takes one day at a time. Everybody is wondering if Pacey and Joey did it while on the trip, and they don't confirm or deny. But Joey secretly tells Dawson nothing really happened.

Joey is looking for a new job and gets one at the Yacht Club pretending to know a very affluent family. She is tricked by her boss's son, Dru, who discovers her lies. Mitch (no also a counselor at the school) tells Pacey he's not going to graduate unless he makes up for his bad grades. Pacey doesn't want Joey to know, but Mitch tells Dawson, who tells Joey, showing that he still cares about Pacey. Pacey and Joey have a fight, and Pacey admits he need help.

Pacey is happy for his good grades, and decides to sail for celebration. Dawson, Joey and Drue are assigned for a work and Joey can't go with him. Instead, Pacey takes Jen with him. What they didn't know is that a huge storm was coming, and suddenly they have to face it. Andie is having an interview with Drue's mom for college, but her medical records get in her way. Mrs. Valentine worries about Andie's mental stability and denies her the spot. When the storm get bigger, Andie takes control of the situation and guides everybody to rescue Jen and Pacey, who admit to each other their biggest regrets in life. Jen regrets never being in love, despite her feelings for Henry, and Pacey regrets the destruction of his friendship with Dawson. Dawson and Joey go on a small boat to rescue them, and Dawson saves Pacey's life. He apologizes to Dawson for all his attitude over the past months.

Everybody starts to think about their future, and how they are getting into college. Joey's concerned about Pacey not having grades good enough to get into college. Drue makes everybody think it's Jen's birthday so he can make a party. Andie takes over Jack's applications and drives him crazy with her obsession over it. Gretchen is applying for a job as bartender at Mrs. Leery's restaurant, and doesn't exactly tell what happened (or what will happen) with college.

Gail drops a bomb at Dawson saying that she might be pregnant. Joey seeks advice from Jen, now that she has the feeling sexual intimacy with Pacey is approaching. Jen tells her to go to the clinic as prevention. Jack is in an awkward situation when a girl is making moves on him, and he feels pressured to tell her he's gay.

Andie gets accepted into Harvard in advance, but accomplishing what should be the biggest thing in her life doesn't exactly makes her happy. She decides to explore different paths in her life by going to a rave. In the party, Drue gives Jen drugs, and she gives it to Andie. She tries ecstasy, which has a reaction with her anti-depressives and makes a disastrous combination, which almost leads her to death. Mitch and Gail decide to keep their baby, and things get awkward during the celebration when Gretchen brings Pacey and Joey with her.

While Andie is recovering from her near-fatal drug overdose at the party, Jack blames Jen for the whole incident and is not talking to her. Jen blames the deranged Drue for her life falling apart when he turns Grams and the whole town against Jen by telling everyone that they intentionally gave Andie the drugs. After Andie comes home from the hospital, her dad tells her it would be better if she went to spend the rest of the year in Italy with her aunt, since she already has the credits required to an early graduation. Andie decides to go and plans a goodbye dinner with the whole gang. She tells them how important life is, and the valuable time they might be wasting with useless fights between natural best friends. Jack and Jen get things straight, and Andie plays a little trick to bring Dawson and Pacey together.

Dawson, Pacey and Jack are all prime suspects in the masterful senior prank against Principal Peskin, but after their interrogations reveal seemingly air-tight alibis, another culprit surfaces.

Dawson asks Mr. Brooks' advice on becoming a director. Joey takes Pacey to a dinner hosted by an exclusive college.

Joey can't find a moment alone to study or deal with her feelings. Dawson's collaboration with Brooks begins, rejuvenating his film making spirit. Jen takes Jack to a "Gay-Straight Coalition" meeting but she seems to fit in with the crowd more than Jack does.

Pacey and Dawson finally start hanging out together again when Dawson tells him that he has feelings for his sister, Gretchen. Pacey doesn't like the idea, so when he and Gretchen go on a road trip to her ex boyfriend's house to pick up her truck, Pacey tries to get them back together. However, after being there for awhile, Pacey realizes that the guy he's trying to get back together with Gretchen is not who he thought he was. Back in Capeside, Joey has her fair share of problems when she gets locked in a storage closet at the Yacht Club with none other than the loathsome sociopath Drue Valentine, which is later revealed that he set the thing up to avoid going to New York to visit his estranged father. Meanwhile, Dawson observes the feelings growing between Mr. Brooks and Grams and fears that Grams will get hurt when she finds out that Mr. Brooks, like her last husband, is terminally ill.

Joey decides to help throw a surprise birthday party for Pacey with his mother, not knowing about Pacey's 'birthday curse'. The party goes haywire as Pacey's family makes everyone feel uncomfortable, and Pacey a loser. Dawson becomes upset when he feels that Gretchen doesn't want anyone to know about their relationship and postpones their first real date to go to the party.

The senior trip is coming up and Joey needs to get the time off from work -not an easy task seeing that Drue's mom is her boss. However, she decides to give her a few days off.... if she agrees to go on a double date with Pacey to accompany Drue and a wealthy girl named Anna Evans and make sure that Drue behaves himself. Of course this isn't an easy thing to do, and during their night out, Joey starts to get concerned over all the attention that Anna is bestowing on Pacey. Dawson has his own problems when he and Gretchen go out with her friends and he realizes the span in between their ages. Jack also (finally) gets some positive attention from Tobey.

While the rest of the class is on the ski trip, Dawson stays behind to care for a near-death Mr. Brooks, but he's overwhelmed when he's asked to make an impossibly hard decision. Dawson is given the responsibility to decide whether to cut off Brooks' life support. Meanwhile, there's a lot more than skiing going on when the senior trip doesn't go exactly as planned. The evening takes an unexpectedly romantic turn for best friends Jack and Jen... After spraining her ankle Jen gets drunk and nearly sleeps with Jack. while Pacey and Joey find their own ways to keep warm on the cold, snowy night, taking their relationship to the next level.

The morning after, Joey and Pacey discover they've overslept and missed the bus back to Capeside. While they wait for the next one, the couple find themselves confronted with the tensions that accompany the latest development of their relationship. Meanwhile, as punishment for breaking into her hotel mini-bar during the class ski trip, Mr. Kasdan decides to send Jen to a psychologist where she can discuss her "inner teen issues." Back in Capeside, Joey and Dawson's paths collide and they spend an evening catching up on the past weekend and its many happenings. Sensing a change in Joey's demeanor, he poses the unthinkable question, forcing Joey to consider whether honesty is the best policy. Dawson has to come to terms with Brooks' death and is surprised to discover he is in his will.

The results of the Senior Polls have ramifications for Dawson, Joey, and Pacey, as the three try to ignore the tauntings of pollmaster Drue Valentine. While Pacey and Joey try to eke out some time alone together, Dawson finds his night alone with Gretchen more awkward than he'd expected. Gretchen learns that Joey lied to Dawson about sleeping with Pacey and is angry and Joey is forcing her to lie to her boyfriend. Meanwhile, Jack's suspicious when Jen drags him on some mysterious errands, and his suspicions are confirmed when he realizes just what she's up to.

Joey receives some good college news. But while Joey glows, Dawson is forced to face a crushing rejection. Joey's elated mood, however, is tempered by a sobering realization due to the fact her sister runs a B&B she can't afford to pay the fee. ...until Dawson proposes a surprising solution, loaning her the money Mr. Brooks left for him in his will, increasing her guilt for lying to him about sleeping with Pacey. Meanwhile, Jen and Jack have nothing but options when it comes to college. While Jack's convinced that New York is the place to go, Jen isn't so sure she's ready to return to the Big Apple. A therapy session forces Jen to confront her past.

As Senior Ditch Day arrives, Joey is excited to find herself accompanying Jen on an excursion to New York 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 finally talks to her father, for the first time since she left for Capeside. Jen reveals she saw her father in bed with another woman before she left. Meanwhile, eager to infuse their relationship with a bit of spontaneity, Gretchen and Dawson take off on a road trip... But what starts out as unpredictable fun turns into one debacle after another after 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. Having had enough, they set out for some real fun, drinking at a bar in the best Drue style, leaving Pacey in serious doubt as to what his future will hold for him.

As Gale's delivery date approaches, the girls throw a baby shower for her...but it's an experience that throws Joey for a loop when she realizes it's possible that she could be pregnant, and Pacey is nowhere to be found. After many false alarms, Gail throws a baby name shower to try and think for a name for the baby, and the baby is born. While Dawson awaits the arrival of his new sibling, Dawson and Gretchen wonder what their future holds when Gretchen considers an out-of-town job... Meanwhile, Jack faces an unexpected situation when he learns that Tobey falls victim to a vicious crime.

As everyone gets ready for this year's senior prom, some bad news causes Gretchen to reflect on her life, and Joey worries about Pacey's odd behavior. Meanwhile, Jen and Jack meddle in each others' lives... resulting in some interesting prom dates. At the prom Joey and Pacey confront once unspoken issues, and the festivities cause conflict for Gretchen, as she questions her relationship with Dawson, while an unhappy Jen is rescued by an unlikely individual after she and Jack arrange dates for each other. Jen decides to drown her sorrows.

As the school year draws to a close, changes abound for the class of 2001. While Joey and Dawson deal with their respective break-ups, Jen makes a startling decision about her future. In his own way, Jack helps Jen to rethink it. Meanwhile, Dawson has his own decision to make with regards to Gretchen when an unusual opportunity comes their way. And when Mr. Kubelik from Worthington asks Joey to bring Pacey with her to a party for incoming freshman, which fills the pair with hope that they might be able to have a future together after all. Joey and Pacey come to terms with the end of their romance.

As graduation approaches, Joey has a tough time preparing her speech, and Dawson helps her find some bittersweet inspiration. Joey gets an unexpected surprise gift from her late mother. Pacey wonders if he's going to graduate at all, and he worries that his last final will be the toughest one. He walks out of it after the teacher makes a comment on him, costing him his diploma. Meanwhile, Andie McPhee returns home for the cap and gown ceremony, and is surprised to meet Jack's new boyfriend, Tobey, and a devious Drue, who has just moved to Jen's after being kicked out of his home by his mother after a fight, convinces Jen to help him pull a hilarious senior prank. Pacey tells Andie he has decided to take the job offer on a boat for the summer.

Accepted early to USC, Dawson finds his last night in Capeside has arrived much sooner than everyone had originally anticipated. While Dawson looks forward to spending the evening with Joey, Jack and Jen, Mitch has other ideas. Meanwhile, Dawson's not the only goodbye Jen has in store for her, as she bids farewell to the house she's been sharing with Grams. Finally, Joey says goodbye to Dawson in her own way.