I've only played the games and read fall of reach, also googling halo timeline (wiki search), and finding the terminals in the game would help.This is my theory to the plot regarding halo4. Here goes:
Precursors create all sentient life in the galaxy, including forerunners, humans, and flood. Forerunners have war with Precursors to claim the mantle(protectors of the galaxy) and drive precursors out of the galaxy.
Precursors unleash flood in the galaxy as a test to humans and revenge to Forerunners. Humans decide to take it upon themselves to try and destroy the flood but in doing so destroy forerunner colonies. Didact, leader of the military caste presumes humans are too violent and want to claim the mantle for themselves. So begins human/forerunner war. Humans lose and as a result are genetically altered to Neanderthals and put on a halo installation.
Forerunners are now facing a war with the flood and are losing and as a last resort before firing the rings, Didact composes most humans on halo installation blaming them for bringing the flood and turning them into promethians to combat the flood which still fails. As a result he is accused of his actions by the librarian (his wife) and locked away on requiem. Rest of humans are put on earth(I think) by the mantle and librarian.
Forerunners have no choice but to activate the halos and eradicate all sentient life in the galaxy, but not before the librarian stores all said sentient life DNA into seed ships in requiem and repopulate the galaxy once again after rings fired. Time of forerunners passes.
Fast forward to halo saga. Humans halt flood infestation. Have a cease fire with Covenant even though theres still factions out there that are still delusional(storm for example), and must claim the mantle of responsibility and find a way to have a cure/eradicate the flood which was the librarians(and precursors) plan all this time. While didact still wants to compose humans as a form of eradication but also obedience(promethians).
Whoof, please don't troll. This is just my theory.
Basically didact wants to do things things his way and thinks humans are too aggressive to have responsibility over the galaxy, while the librarian and precursors know humans are next in line to be the caretakers of the galaxy, and the only way It's going to get proven is by once and for all destroying the flood and bringing peace to the galaxy.
Master chief being genetically enhanced plays a big role along with Cortana being almost human and no mention of the Arbiter or Halfjaw putting a stop to storm. Which leads me to believe that will all be fleshed out for the sequels along with introduction of next gen flood.