Rory walks through Chilton’s front gates with Paris, Paris doing all the talking. As Paris heads to her locker, Rory looks around apprehensively, then walks back through the gates. She’s not only skipping school but also missing out on a meeting of the school paper which she told Lorelai she had after school, meaning she wouldn’t be at the graduation ceremony until 6 pm. This doesn’t seem like something a really keen journalist would do. Perhaps Rory hopes to make it back to school in time for the meeting.
Skipping school for no reason, especially at this crucial point of the school year, seems like something Chilton wouldn’t be very impressed about (let alone Paris). However, we never see Rory face any consequences for it. Perhaps she made up the work she missed, or Lorelai wrote the school a note or something to explain her absence.
Note that even while approaching the school with Paris, Rory is already looking away as if wishing she was somewhere else, or looking for an escape route.
The Annotated Gilmore Girls 
It’s also the only scene I recall where she wears a gray sweater as part of her Chilton uniform. Perhaps that is also a clue to her behavior that day?
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You have me at an disadvantage, because I only speak American as a second language – to me, she’s wearing a cardigan. I thought a sweater was the same as a jumper? What’s it called when you have a woollen pullover without any buttons, then???
This isn’t the first scene where Rory wears the grey cardigan, she wears it at the start of the episode, but you’re right that it seems to be the first episode she does so. Previously she wore a navy blue sleeveless jumper (a vest???) in spring or autumn, when it wasn’t cold enough to wear a blazer.
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