Pacey, enlightened by getting good grades, decides to take a sail on his boat and takes Jen with him for company. Meanwhile, Andie has an interview with Drue's mother for a college acceptance. But her medical records get in her way in which the egotistical and snobbish Mrs. Valentine worries about Andie's mental stability and outright denies her the spot. Everyone's plans change when a big storm rolls into Capeside, trapping Pacey and Jen at sea where Dawson and Joey steal a motorboat, owned by a cranky old resident, A.I. Brooks, to rescue them while Andie takes control of the situation at the Yacht club to wait out the storm. At sea, Jen and Pacey 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.

When Bessie takes a weekend getaway, Joey's hoping to get some studying done. But between her responsibilities at the B&B and Pacey's affections, Joey's hard pressed to find a moment alone to study for an English exam, and as if that wasn't enough, she's trying to cope with her feelings about having seen Dawson kiss Gretchen the other night at the Christmas party. Pacey's got his own issues with that 'kiss' and he's convinced Dawson and Joey need closure, once and for all. Meanwhile, Dawson's collaboration with A.I. Brooks on a documentary on his life story begins, which rejuvenates Dawson's filmmaking spirit and learns more about Mr. Brooks, whom never got over his best friend stealing away his girlfriend. Also, Jen takes Jack to a "Gay-Straight Coalition" meeting in the hopes that he'll meet some gay friends. But Jen seems to fit in with the crowd more than Jack does, who meets the militant founder Tobey.

While the rest of the school goes to the snowy mountains of Vermont for a ski weekend, Dawson stays behind to help Grams keep a bedside vigil at the hospital for the near-death Mr. Brooks. But things become complicated when Dawson learns that Mr. Brooks had earlier asked him to sign a medical clause which leads him to be forced to make an impossibly hard decision to decide whether or not to cut off Brooks' life support systems. Meanwhile, the ski trip evening takes an unexpectedly romantic turn when Jen sprains her ankle, she breaks into her room's mini-bar, gets drunk and nearly sleeps with Jack. At the same time, Drue and Anna Evans sneak into the events pretending to be another couple since Drue has been banned from the ski trip and Anna does not go to school at Capeside. Also, Pacey and Joey find their own ways to keep warm on the cold night by taking their relationship to the next level.

Unusual episode about four separate plots told in chronological order rather than concurrently as in previous episodes. "About Last Night": Left behind at the ski lodge, Pacey and Joey are forced to go home by bus where they talk about their sordid night before where he is insecure about his performance and she brings up her own insecurity. "The Big Picture": In Capeside, Dawson is forced to face Mr. Brooks' death by going through his belongings with Gretchen. But soon, Dawson gets surprised to find out that he is Mr. Brooks' will and finds himself with a lot of money in his hands, and no idea of what to do with it. "Excess Baggage": As punishment for breaking into her hotel mini-bar and getting drunk during the class ski trip, Jen is forced to see a psychologist where she can discuss her "inner teen issues." But Jen finds the psychologist, Dr. Tom Frost, to know more about Jen than she does about herself. "Seems Like Old Times": Joey's path with Dawson's collide when they spend an evening catching up on the past weekend and its many happenings. Dawson thinks Joey is different in some way. Here, he asks her the big question: did she or did she not have sex with Pacey during the ski trip? Torn between hurting her best friend by being honest, or lying to him, Joey outright lies and says she didn't sleep with Pacey.

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.