I haven't read every bit of Halo media but this is what I've gathered. I think it's right for the most part...
So you know, throughout the Halo universe, you learn that Humans aren't the only species. Humanity first encounters the Jackals and quickly afterwards, the entire Covenant. The Covenant, throughout their years, learn of the Forerunners, an ancient species of sentient life forms that created the Halo Array and many various technology far more advanced than anything they'd ever witnessed. However, their ideals and understandings of the Forerunners are flawed and pushed to radical extremities by the Prophets, which result in fanatic beliefs that the Forerunners will lead them to godhood via the Great Journey by use of the Halo Array.
We learn throughout the series that the Halo Array is actually a weapon, built as the last measure against the Flood, the parasitic life forms bent on taking over all sentient life throughout the galaxy.
In the books and various media, we learn that the Forerunners were preceeded by another ancient race of beings called the Precursors, who originally held the Mantle of Responsibility and vast technological wealth and power throughout the galaxy. The Forerunners rose up and overthrew the Precursors in a great war. This led the Precursors to create the Flood parasite as an act of revenge. The Precursors sealed the Flood away in some sort of tube or vial, but it was lost throughout the ages.
Throughout the millenia, the ancient humans eventually came into existence and stumbled upon the Flood in an archaeological excavation. After several generations, the Flood was able to manifest itself in a certain species and rose up to take over anything and everything. This led the ancient humans to flee and struggle for survival, which I think was what the Librarian was referring to when she was telling Chief about the violent uprising of humans. The ancient humans went to war with the Forerunners, with the Forerunners eventually killing most of the humans, not knowing they were running from the Flood. The Flood arrives soon after, and the Forerunners fight a losing battle, weakened after thousands of years fighting the humans. They create the Halo Array and fire it, eliminating every living being in the galaxy, but not before storing their genetic codes.
Chief and humanity, along with every living species in the galaxy are a product of the Forerunners restoring life to the galaxy.
The Didact is a Forerunner, who was punished for killing the humans and imprisoned in a timelock. He tricks Chief into releasing him from imprisonment on Requiem, starting the events of Halo 4.
Diehard Halo fans correct me!