Gilmore Girls' finale revealed that Rory is pregnant, but left the father of her unborn baby a mystery. The series, which concluded its initial run back in 2007, was revived by Netflix in 2016 for the limited series Gilmore Girls: A Year in the Life, which picked things up with Lorelai (Lauren Graham) and Rory (Alexis Bledel).
The four new Gilmore Girls episodes - "Winter", "Spring", "Summer", and "Fall" - charted the lives of the titular Gilmore Girls across the course of a year, and included some major plot points and character developments that fans had long been waiting to see, including the marriage of Lorelai and Luke (Scott Patterson). It all built-up to the much-hyped final four words of Gilmore Girls, which turned out to be an exchange between Rory and Lorelai: "Mom?" "Yeah?" "I'm pregnant."
While some fans had predicted that Rory would become pregnant in Gilmore Girls season 8, the reveal nonetheless came as a bit of a shock, not least because it was the ending of the revival and, as it stands, the ending of Gilmore Girls as a whole - with no resolution as to who the father of Rory's baby actually is. Since Amy Sherman-Palladino is now busy with Amazon's The Marvelous Mrs. Maisel, it doesn't appear as though we'll ever get more Gilmore Girls episodes to explain who the father is, and instead have to rely on some speculation.
The most common answer is that it's Rory's ex, Logan (Matt Czuchry), who is the father of Rory's baby. The pair had an affair across Gilmore Girls: A Year in the Life, making him the most logical and likely option for being the father. It'd certainly make sense for it to be Logan than some of the other contenders, if only for the fact that he's a much more well-known character, and it'd be more surprising of the father of Rory's baby was someone audiences weren't too familiar with.
Nevertheless, it is possible that it's someone else, and Netflix has also fuelled speculation about this in the past. In Gilmore Girls season 8, Rory dates a guy named Paul (Jack Carpenter), although the running gag is that she keeps forgetting about him. Although it seems by the Gilmore Girls finale that she hasn't seen him in months, it's still possible that they did sleep together again and we just didn't get to hear about it - which would fit with the recurring joke. Another theory is that it's the unnamed Star Wars fan (the one who wears a Wookiee costume) who Rory sleeps with in "Spring", although again this seems too early, but could be a fudge on behalf of the writers.
It's less likely to be Jess (Milo Ventimiglia), since despite his and Rory's clear chemistry, they don't get back together in Gilmore Girls: A Year in the Life. Logan is the obvious answer to being the father of Rory's baby, and the most logical too. He is to Rory what Christopher is to Lorelai, and the series ending with Rory falling pregnant to him brings the entire story of Gilmore Girls full circle. It then better contextualizes Rory's final scene with Chris, when she speaks about him not being there when Lorelai was pregnant, and if there were more episodes would make the parallel between Luke and Jess even clearer too. We may never know for certain who the father of Rory's baby is in Gilmore Girls, but we can assume it's Logan.