The Wookiee Is the Father
In one of Rory's lowest moments, she sleeps with a Wookiee. That is to say, she sleeps with a human dressed as a Wookiee who she meets while researching her (doomed) piece on people who wait in long lines for things. The timeline doesn't exactly work out; if she sleeps with the Wookiee at the end of Spring, she would be six months pregnant at the end of Fall, when Lorelai and Luke get married and the series concludes. Rory is wearing baggy clothes, but even an oversize sweater probably wouldn't hide a six-month baby bump. Plus, Rory wouldn't keep something like that from her mother for six whole months.