After her father leaves to answer a phone call, Rory suddenly sees Jess, and discovers he has moved back to Stars Hollow. Only a complete idiot would fail to realise it was to see Rory again, and Rory isn’t an idiot. She kisses Jess, warning him not to tell anyone what happened, then runs back to her boyfriend Dean with a cheery, “Welcome home!”.
Yep, falling in love with a Gilmore girl isn’t any picnic. Just ask Dean.
The kiss with Jess in this season finale is a counterpart to the kiss Rory had with Dean in the finale of Season 1 as they reunited after breaking up. The first kiss had Dean looming over Rory and grabbing her almost roughly, as if taking possession of her (Jared Padalecki’s height partly explains this). The kiss with Jess, another reunion, is far more gentle and intimate, much more romantic. It feels more like Rory giving herself to Jess, rather than allowing herself to be taken.
Alexis Bledel and Milo Ventimiglia were a real life couple during the filming of the show, which is one reason why it appears far more convincing. They are almost too comfortable together for a first kiss.
The Annotated Gilmore Girls 
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