Prinz Eugn
Member
I don't think Chief is going to be compelled to run. His reception post Halo 4 as shown in the comics is warm and he's still on active duty. It's pretty clear the brass is on Chief's side—after all they sacked Del Rio for leaving him behind. ONI might have its own reasons for hunting him down, but I think it's more likely Chief goes AWOL of his own volition.
Yeah, I think they've set up a Chief firmly disillusioned with the growing power of ONI.
I just assumed Halo 5 would be about Chief hunting down Halsey to resurrect/fix Cortana while Locke hunts down Chief because of that Librarian genesong stuff.
EDIT: Perhaps Chief bails when he finds a message Cortana left him pointing to some space magicky thing that might fix her/save the universe, and that's where we get the desert War Sphinx.