JESS: Well, whatever else happens between us, at least we know that part works.
Rory and Jess leave the diner separately, Jess claiming that he has to pick up a part for his car, while Rory needs to get home and study. As Lorelai knew immediately, that meant they were planning to meet somewhere.
When Rory catches up with Jess, they kiss. It’s not their first kiss – that happened at Sookie’s wedding about six months previously. But it is their first kiss as a couple (closely followed by their second kiss as a couple).
It is two weeks since Rory and Dean broke up, so they haven’t rushed into kissing, probably because Luke walked in on them when they tried before. Jess’ comment makes it clear that the physical attraction between them is not going to be a problem, whatever else might be.
The viewer might note from Jess’ comment that he is expecting other types of problems to come between them, which is remarkably foresighted for a teenage boy, or unusually cynical.
The Annotated Gilmore Girls 
later in the seasons luke and lorelai also do the same thing of lying to meet outside away from everyone. cute
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