Warning: The following contains SPOILERS for Fantastic Beasts: The Crimes of Grindelwald!
The end of Fantastic Beasts and Where to Find Them teased the continuation of Jacob and Queenie's relationship, hinting that love will conquer the magic and law that separated them. This happy ending is a far cry from the where the two stand at the end of Fantastic Beasts: The Crimes of Grindelwald after Queenie leaves Jacob to join Gellert Grindelwald. Actor Dan Fogler has revealed what Jacob is thinking at the end of the film now that Queenie is gone, saying:
So after all that happened between them, after Queenie used a love potion spell on him and dragged him to Paris to get married, after his love wasn't enough and she left his side to stand with Grindelwald, Jacob still loves Queenie and longs for her to come back to him. He has no doubt that he would forgive her if she did.
This sentiment rings true for Dan Fogler's character, as Jacob Kowalski has always been deeply earnest and loving, and the kind of person who would forgive the people he cares about. It was because of his love and concern for her that their troubles began in the first place, when he didn't want to get married for fear of the potential consequences she would suffer.
Throughout Fantastic Beasts: The Crimes of Grindelwald, the thing that is driving Jacob is to be with Queenie again and make their relationship work, and even after she walked away from him, he loves her and he can't give up on her completely.
As Dan Fogler told The Knockturnal, you see Jacob in this state of longing at the end of the film after the calamitous events at Grindelwald's rally. Jacob is standing with an unlikely group of good guys at the entrance to Hogwarts awaiting Jude Law's Dumbledore. You can see Jacob with his attention elsewhere in the image below.
Jacob is clearly heartbroken here, displaying the very personal cost of this strife. There is so much going on at the end of the film, as lines have been drawn, sides have been chosen and the Wizarding World is on the brink of civil war. But amidst the rising tensions in this still foreign world, Jacob Kowalski's concerns are extremely personal.
Jacob is not thinking of revenge against Grindelwald or what happens next, he is simply thinking about Queenie. I imagine he may have some guilt as well, for not going along with her marriage ideas and for calling her crazy out loud at the rally. I expect Jacob's desire to get Queenie back to be a big part of his story in Fantastic Beasts 3, and that may lead him to recklessness and danger.