Gilmore Girls Season 6 was a hard season to follow because of the not so happy relationship of Rory and Lorelei that once was. It is a very strained season with everyone involved due to complications in relationships, school and life in general. Times are tough especially between Rory and Lorelei, Lorelei and Luke, and Rory and Logan. One of the amusing moments throughout this season that caused some interesting problems was when Taylor Doose, the town selectmen, decided to change the names of all the streets in Star Hollow back to their historical predecessors. This causes much aggravation for most of the townspeople, especially those that have businesses on those streets that have been named as such.

The season begins by Rory dealing with her yacht theft from the previous season. She is sentenced to three hundred hours of community service working on road crews. Once she starts, she gets into a fight with a girl over something trivial which has an overall bad ending. Once she completes her one hundred and twenty fifth hour of her community service, she decides that she wants to go back to school, and ends up getting a job on campus as the Yale Daily News Editor. Paris, a friend of Rory's from high school, terrorizes everyone at her mother's inn trying to restore the relationship of Lorelei and Rory. Paris also realizes that she is broke and that her tuition is now going to be paid by her because her parents won't do it any longer.

Luke has accepted Lorelei's marriage proposal and buys her an engagement ring. After he has done so, he soon finds out that he has a daughter that he never knew about named April, a very intelligent little girl who does her own DNA test to determine Luke's paternity. Luke doesn't tell Lorelei about April, and she ends up having to find out from someone else in the town. Although she is upset, she is not upset because Luke has a daughter, she is upset because he didn't tell her when he found out. In attempts to show him that, she helps throw a birthday party for April, who gains Lorelei's trust and comes to like her.

In an attempt to salvage Lorelei and Rory's relationship, Sookie decides to make both of them godparents of her two kids, Martha and Davey. They both attend the christening but it is strained and they do not talk to each other.

Then Rory's best friend Lane gets married to her longtime boyfriend which causes an uproar among the whole town because Rory is missing in action and is not there to help plan the wedding, and it is left up to Lorelei. During this time, Rory was with Logan who had been out partying and drinking way too much. Rory was trying to make him see that his actions are only hurting himself. He does finally see this when a drunken accident lands him injured in the hospital and Rory leaves him to the care of Paris, a very abrasive, and abrupt person. Paris tries to teach him a lesson by refusing to care for him and makes him take care of himself.