Once again, the show opens with Joey and Dawson discuss their lives and the movies.
Jen tries to get Dawson to do something with her but he tells her has plans with Joey. Joey walks up to he and Jen in the hall telling them about her opportunity to go to France. Jen is excited for her and encourages her to go while a flustered Dawson is speechless.
Joey tells Bessie about the trip and Bessie congratulates telling her if she decides not to go it's an honor to just be asked. Bessie then reminds Joey it's her turn to visit their dad the next day in prison. Joey tries to tell Bessie she doesn't want to go but Bessie reminds her that it's his birthday and she went last year so it's Joey's turn to go.
Doug sees Pacey riding his bike and stops him to tell him their dad is looking for him. He continues to berate him then leaves.
Joey thanks Dawson for going with her to see her dad. He asks her if she's made a decision about going to Paris and she tells him she has not. She asks him what he would do if he left and he grins and tells her suicide then he admits if France would make her happy then he would be happy for her.
Once at the prison, they find out visiting hours are over and they will have to come back the next day. Joey isn't thrilled about riding the bus back so Dawson suggests they spend the night. Once at the hotel they discuss what side of the bed they are sleeping on and decided it sleep on their normal sides. Once they are settled in bed, Dawson tells her he would really miss her if she went to France. He tells her he wants to figure out where they are and what is between them. She asks him how do they do that but he doesn't know. She asks him what he is scared of. At first he doesn't answer but finally he replies, "I don't know."
At the hospital Grams tells Jen that Gramps is recovering. She tells her God healed him and they argue a few minutes about God.
At the prison Dawson tries to leave to give Joey and her dad a chance to be alone. She tells him not to leave. Mr. Potter comes in and greets the two. He tells her she is beautiful and that he's glad she's there. He tells her he misses her family and Joey asks him if she misses her mom. He tells her he does and she tells him she is going to France and that the family he misses is no longer in existence. Joey leaves the room and Mr. Potter asks Dawson to tell him about Joey. Dawson rambles on about Joey and finally he starts rambling about how if she goes away he doesn't know what he'll do, that's she's not just his best friend, she's his everything.
Back home Dawson and Joey walk on the dock and talk about what Dawson and Mr. Potter talked about. She tells him she hates her dad and Dawson tells her sooner or later she has to deal with those feelings. She asks him if she has to deal with them in France and asks him to give her a reason why she should stay but Dawson says nothing. Joey nods her head telling him that's what she thought then she gets in her boat and heads for home.
At the hospital Jen sees Grams crying and Grams tells her Gramps had another stroke. Jen asks what happened and Grams explains prayer is important at that time. Jen questions her faith but Grams stands firm.
Pacey walks into the Icehouse and asks if he can eat there. At first she tells him the kitchen is closed but he tries to talk her into letting him eat there because he doesn't want to eat at home. Pacey tells Joey about an incident in his childhood and she suggests he tell his dad how he hurt her. He asks her if she did that and she admits she did not but that she is leaving right that minute to go. She talks Pacey into taking her to see her dad.
Jen talks to her Gramps at his bedside. She talks to him for a while and eventually tells him she feels helpless and that she wants to help him get out of the bed.
Once again, like before, Joey arrives at the prison after visiting hours are over. Pacey pulls the guard to the side and after moment the guard leads Joey in.
As Dawson is sitting in his room Jen climbs in the window. Jen tells him she misses him and he tells her he's there. She asks if she can spend the night, like friends, like Joey does and he tells her ok. They lay down on the bed and she puts her head on his chest and cries about her grandfather. He strokes her hair and tells her it will be ok.
Joey meets her dad outside the prison fence and tells him he messed up but not because of the things he did but because he doesn't know her. She tells him she's all right. She asks him if he loves her and he tells her he loves her more than she'll ever know. They talk and her dad tells her Dawson loves her even if he's never told her and that he knows she loves him too and tells Joey that she must tell him and not make the mistake he did. Joey steps up to the fence, touches her dads hand and tells him she loves him. She tells him goodbye and leaves.
Joey rows over to Dawson's the next morning to tell him how she feels and climbs in the window to see Jen kiss Dawson. Dawson jumps up to run after her while Jen tells him it will be ok. Dawson tells Jen he's got to stop Joey to tell her she has the wrong idea about them. Jen asks if Joey really does have the wrong idea about them and Dawson lets her know she does. He runs down to the dock but Joey is already gone.
Jen goes home to find Grams sitting on the front porch. She asks how Gramps is only to find his condition hasn't changed. Grams looks at Jen then asks her if she's ok and Jen tells her it's nothing. Grams tries to get Jen to attend church with her but Jen walks away.
Next there is a montage: Joey rowing home; Dawson goes her to her house looking for her; she sits at the dock in town as Dawson looks for her at the Ice House; Joey wanders through town as Dawson looks all over for her.
During the time that Dawson is looking for Joey, Jen gets a call that her gramps has died.
Later Jen finds Grams sitting in the church praying. She goes in and sits down next to her. Grams continues to pray asking God to keep her husband safe for her and Jen adds, for me too. Grams breaks down and cries.
Dawson finally finds Joey hiding in his closet. He tells her there is nothing between he and Jen and she tells him it doesn't matter because they are just friends. She tells him she went to his house to tell him she's tired of the drama in her life and leaving town makes the most sense to her. Dawson begs her not to leave telling her they can grow up together. She tells him she wants to be honest with him and he tells her he wants to be honest with her too. She asks him if he's sure he wants to be honest because it's a big responsibility. He looks at her and says nothing. She nods and tells him she'll see him later and turns away. He calls her name, grabs her arm and kisses her. The season ends with them locked in a passionate kiss.