Alright so im just going to throw everything that i believe about halo 4 and the “NEW” evil. So if you guys have been reading the books you Should know that The Master builder killed the UR-Didact, BUT it turns out he actually survived. Source wiki, sorry i dnt have the link on me. Anyways and im sure you guys all ready know that he transferred all his thoughts and personality to Bornstellar which technically makes him the new Didact.
So im guessing its either going to be one of the two, and chief will find the truth by one of them being his ally.
And just for other Fun Halo things. Apparently the flood was a weapon built by the “Precursors” to fight against there children the :Forerunners" during the Precursor - Forerunner war.