Newt is pretty explicit in the film than he feels humans, in general, to be vicious and that his poor, precious creatures need to be protected from them. So what if we took that to the logical extreme.

Maybe the bad guy (Grindelwald or whoever) was trying to get Newt on their side and the brainwashing went too far. Maybe there were one too many poaching incidents or mistreated animals. Either way, Newt has enough.

He is going to kill everyone.

Bonus
+ The bad guys were in favour of Newts new policy at the start until they realised that Newt really does mean to wipe out the entire human race, not just the ones the bad guy wants rid of
++ Newt is perfectly willing to use creatures to kill as long as it doesn't endanger the creature.
+++ The dragons are really happy that Mummy is back and are happy to burn down anything he wants