There was no shield spell capable of holding an obscurus so when Newt tried separating the one from the Sudanese girl he just hoped he was far enough from civilization that it wouldn't harm anyone before fizzling out of existence. He wasn't counting on it having enough primitive instinct to detect a new host. But it's fine; Newt's dealt with so many wild creatures it shouldn't be too difficult adjusting to having one inside him. And the obscurus takes a likely to it's new obscurial like every other fantastic beast Newt comes across . Sure, it flares up every now and then when Newt becomes overemotional in misguided attempts to get rid of whatever is bothering Newt but otherwise it's well behaved thus so long as he doesn't go into a high stress environment then Newt has everything under control he totally does stop laughing Pickett.

Frank really needs to get home because Newt is developing attachment issues and a boat trip followed by a trek through muggle America shouldn't be too much hassle, right?

tl;dr: In which obscurus latch onto magic people like horcruxes. The one in Sudan latches onto Newt.

Bonus for Graves/Newt and/or my kingdom for Grindelwald/Newt but it is by no means a deal breaker.

Double bonus for Pickett and the obscurus as bros united to keep Pickett's Tree-the Host-Newt safe.