RORY: I thought we could see a movie or something.
DEAN: You’re not free.
RORY: How do you know?
DEAN: ‘Cause you’ll be working on your application all weekend.
Dean is now experienced enough to know that when Rory says she’s free to spend time with him, that means, unless she has unexpected homework to do. Or a test to study for. Or Paris wants her to do extra work for the newspaper. Or she suddenly discovers she’s got to do volunteer work all summer. He can even anticipate it coming before she can. Instead of fighting with her over it, he’s learned to just accept it.