Fantastic Beasts 2 Ending And Twist EXPLAINED
5. Newt Picked A Side
At the end of the film and in the immediate aftermath of Leta's death, Newt tells his heart-broken brother Theseus that he's now chosen a side. For the rest of the film, despite working for Dumbledore on the side of good, Newt clearly thought himself to be sitting on the fence. Despite the fact that everyone could see that Grindelwald was a monstrous magic-Hitler. Quite why he refused to pick a side at any other point remains to be seen, but now that he has he'll presumably be actively working against Grindelwald and his followers.
Newt now presumably works for the Ministry, having initially refused based on his childhood fears of being stuck working behind a desk. The reality is that that as an Auror, he'd never sit behind a desk, so he needn't be scared. Plus, the Ministry needs him and his fantastic beasts so much that he'll probably be given the freedom to do what he wants in his new position.
Curiously, the Ministry seem surprisingly willing to allow someone who was expelled from Hogwarts without finishing his exams to take up the office of Auror, but it's not like it would end up being the last time.