Jen was only wearing a bikini on the boat because it's January, and she lives in Massachusettes. Jack is scared that his one and only friend will die of hypothermia so he jumps into the water to save her. When he jumps, the boat capsizes. Jack ignores the capsizing so he can save a drowining Jen. He finds her and puts her head onto the bottom of the boat which is now the top. Jen isn't breathing. He tries to give her mouth-to-mouth, but can't stand the taste of women. Then he tries harder and ends up just kissing her instead of breathing air into her. She's dead. Jack begins to cry and sing "My Heart Will Go On" and he dies of hypothermia before that really cute guy on the shore comes and saves him. The cute guy gives Jack mouth-to-mouth, but it is too late for Jack to realize either his sexuality or his life.
To fill the gap left by Jen and Jack's departure, Ben Savage and Danielle Fischel (Corey and Topanga) of Boy Meets World come on the show. Corey and Topanga decide to go on their second honeymoon, but when they arrive in Capeside, they discover that even though they are really sophomores in college that they are only juniors in high school. Because they are only in high school, their marriage is nullified, and they enter immediate custody of the state of Massachusettes. Grams sees Topanga and is touched by this beautiful girl who is so much like Jen that she adopts Jen. Mitch thinks that Corey is the son he never had, in that Corey is a man, and adopts him. Dawson, Joey, Pacey, Andy, Topanga, and Corey are now a tight-knit group of friends. Corey catches one sight of Joey and instantly falls in love. He pursues her until she says that she can't be with him, she's in love with another man. Corey doesn't know what to do. He tries to get in touch with Mr. Feeney, but can't. 
Corey decides the only way he can be with Joey is if he kills Dawson. Late one night, Corey sneaks into Dawson's bed room, picks up a knife and does the Scream-thing in that he kills Dawson. The next morning Mitch tells Corey to go wake up Dawson. Corey pretends that nothing has happened until he enters the room and sees Dawson's body. He cries out that Dawson is dead. The police come to investigate. Officer Doug (Pacey's brother) is the first officer on the scene, and as he sees Dawson lying there with a knife in his back, Doug thnks, "Oh, to be that knife in that nubial back." Doug vows that he won't stop until he finds Dawson's murderer. Doug does some investigating and learns about Corey's presence in the Leery household. Doug immediately suspects Corey until he learns that Mitch wanted Corey in the house. Mitch meant to have Corey look like the suspect. Doug also learned that Corey was adopted because Mitch was ashamed of his son. Obviosuly, Mitch did it. He is arrested.
Joey comes over to see how Corey is coping with all of these problems. Joey says how sorry she feels that he had to enter a home like this. Corey responds, "He was just like a brother to me." Joey says, "Yeah, he was like a brother to all of us. I slept in his bed once a week for the past sixteen years and he never once touched me." Corey said, "But you told me that you were in love with Dawson." Joey, "No. I said I was in love with someone. You must have assumed I meant Dawson." Corey, "So, you didn't love Dawson?" Joey, "No. Why? Did you do this so that I would love you?" Corey looks into his hands, "It's not my fault. My world has been turned upside down. I just wanted to be near you. To have your beauty beside me. My love for you transcended this mortal world." Joey, "Corey, you can't do that. It's immoral to kill. I'm touched that you care so much for me and what you've done is the nicest thing that anyone has ever done for me, but I don't ever want to see you again." Joey turns her head away from him. Corey crying says, "But this was the hardest thing I ever did. Don't you understand the repercussions of my love? I had to say goodbye to Topanga?" Joey turns back to Corey, "You killed Topanga too?" Corey, "No. I just told her we could never be lovers again." Joey, "Oh Corey, I could never be mad at you." Corey, "So you love me?" Joey, "No. But isn't friendship enough for now?" Corey, "No, it's not enough. It will never be enough, but if that's all you're offering me than I'll have to accept it, won't I?"
Just then Topanga appears, she starts crying, "Dawson is dead. Corey doesn't love me. Dawson is dead. Corey doesn't love me." Corey rises and puts a finger to her lips, "Shhh. I love you. I'll always love you." Topanaga, "But you just said that you hated me and couldn't stand the sight of me." Corey, "You are the most important thing in my life and I could never be without you." Topanga, "I love you so much." Corey, "I love you so much too."
Well, now these two crazy kids have reentered their semi-marital bliss. But we still haven't resolved all of our plot lines. Pacey gets part-time work at Capeside Funeral Home. He is at the Funeral Home when Jen and Jack's corpses arrives and starts checking out Jen Lindley saying things like, "Lindley, you're looking all kinds of cute." Jen's hand sprouts up and grabs Pacey's you-know-what. Pacey freaks out...she's alive and she wants to renew that sex pact that the two of them had. But no, it's just Jen's hand that reaches up for Pacey's crotch, because even in death, Jen is a horny slut. Pacey is still at the Funeral Home when Dawson's body shows up. Pacey sees Dawson and starts to cry. His best friend in the whole wide world is dead. Pacey doesn't know what to do. He leaves the funeral home and goes home. He calls Tamara who is in Florida, but can't get in touch with her. Finally, he goes over to Dawson's house and sees Mitch getting arrested as Joey cries and cries. Pacey comforts Joey.
He realizes that he has to stay strong and support Joey who is probably much more upset than him, but then Joey sees Pacey and stops crying. She looks up at him and half smiles in that cute grinnish way that Joey Potter half smiles. In the background we hear Sophie Hawkins singing "As I Lay Me (Down to Sleep)." Joey and Pacey look at each other and realize that they're too good for Capeside. The love these two share means more than the deaths of Jack, Jen, and Dawson. The two of them embrace. Forever they will be together. Pacey turns to Joey and says "I knew it was you, it was always you." Joey says "I don't want to wait for my life to be over. I want to know right know what will it be. Will it be yes or will it be sorry?" Pacey says, "With us, we'll never say sorry again." The two then move away from Capeside and back to Philadelphi with Topanga and Corey, and they all return to their normal ages. In just two years, Pacey and Joey marry and have little kids that will never have to visit Capeside.