DEAN: I don’t know, Rory. Maybe . . . maybe, um . . . is there a way we could be friends? … If you want to.
RORY: Oh, I want to. I really want to. But –
DEAN: Don’t ask me how I’m gonna deal with him. I have no idea.
Although Rory was initially reluctant to have coffee with Dean, and refused to eat anything, by the end of this scene they are chatting easily, and she is smiling and sharing his custard pie. When Dean asks if they can be friends, she says she really wants to, with Jess being relegated to a “But – “.
Rory was friends with Jess, which gradually damaged her relationship with Dean until they broke up (again). Now she agrees to be friends with Dean while going out with Jess – what could go wrong? Of course, Dean is very much wanting it to go wrong, in order to cause Jess the same sort of problems he believes Jess caused him.
It does feel typically unfair that just as Rory is starting to feel more relaxed and confident with Jess, Dean worms his way back into the picture. Because drama.
The Annotated Gilmore Girls 