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.

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.

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.

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.