"Gods" and "Demons" reference the Gravemind, maybe the flood aren't gone? Well, technically they're not. Remember before the events of Halo there was the forerunner and Flood war. The forerunner ships hid stowaway cells from spores they were researching. There are still a plethora of forerunner ships, weapons, constructs that would hold the flood. Hell, even the librarian's realm hid samples of the flood in those huge ass light containers, not actual samples, but the dna.
Bottom line is, we'll see the flood sometime in the next game or this game. As for the whole reason Locke is hunting Chief? Well probably because Chief disobeyed Laskey's orders to take a loving break, stole the armor they took off of him, probably commandeered a ship, and flew to another place where he can get answers. Without authorization. That, or Chief is now some sort of advanced human that the UNSC and ONI wanted to research or something along the lines of that, remember the librarian basically boosted his evolution Geno to avoid being digitized by the didact. He probably isn't even human anymore.
