Wow some of you really aren't trying to understand the story and just claiming it's bad Storytelling.
I'll break it down so it's easy to understand. (there will probably be spoilers.)
The Libarian and Didact are both Prometheans which are High class Forerunners, some of the prometheans are also Human but most looked like the Forerunners you see in halo 4 due to being mutated. The Foreunners you see attacking (bigger, hunched over ones) you are highly trained Warrior-Servants they are mutated humans just like The DIdact once was. But Prometheans are both Forerunners and Humans it's just most of the Forerunners are mutated humans that weigh 800 lbs and can crush a human skull with their bare hands)
The Forerunners felt they should take care of the balance of the milky way galaxy making sure that all species keep from exinction or too much power, they did this by following the "Mantle" which is their bible and holds all the rules and regulations to balanceing the galaxy.
The Humans in 110,000 BC had developed technology that rivaled the Forerunners but then they came across "The Flood" a Viral species that consumes sentinal beings and makes them their own to prevent their own extinction they teamed up with the Covenent (San 'Shyumu) to take them down which worked and they found a way to neutralize the threat of the flood. The Forerunners caught wind of this and being the "custodians" they thought that their choice to neutralize the flood violates the rules of the mantle and so they waged war on them and defeated them, broke their alliance, de-evolved humans as punishment to a more primitive stage, and lost the cure for the flood. Soon the flood began attacking the forerunners and it nearly whipped them out so they created the halo rings to destroy the flood before they were whipped out completely. The Forerunners where lead by the Didact who was killed by another commander of the forerunners but inhereted someone elses body at somepoint. The forerunners did not want to use the halo array because it violates the mantle despite being whipped out by the flood. But in the end the DIdact did and later he did not want humans to be their succsesor because he did not trust them so he created an artifact that could turn humans into Forerunners instead but it just disinitgrated them this is "The composer."
since the other forerunners strongly opposed this act they imprisoned the didact in the Cryptum (the red ball)
The Libarian was married to the Didact and had kids with him but all those kids died at war against the humans and San 'Shyumu.
The Libarian believed in the Humans to be their succsessor like the other forerunner but unlike her husband, she was afraid of her husband using the the composer to wipe out humanity so she tweaked human DNA and eventually come up the immunity to the composer which she intended to give to Master chief. She set up the de-evolved humans to be the succsesor to the forerunners in their last dying moments even cortana and all the technology the humans aquiired. THe humans even have access to the halo rings just in case the flood returned. The covanent had a misconception about the halo rings they thought they would unlock "The Great Journey" and when they found out they couldn't control it they got jealous and angry and attempted to whip out the humans. They even unleash the flood again (some what accidently) at one point on the humans (but they end up consuming both) In halo 3 despite a breif truce to get ahold of the flood they covenant prohet betrays their alliance and is even willing to sacrifice his own people to destroy humans so Master Chief kicks his ass but doesn't beat them.
The story is complex i'm sure I might of missed something but that's the nutshell.
