Through the Halo games I’ve been working on this theory that pretty much explains who the Forerunner were, why all the characters are the way they are, and what’s going on.
In the beginning, the Forerunner evolved on one of the later covenant planets. The Forerunner were and are, humans. They built massive starships and colonized much of the universe. They eventually built intelligent robots like the monitors that were kept in their position of servitude by a programmed love and respect for their masters.
All was well for the Forerunner, until they began to work with powerful genetic engineering. The Forerunner were able to create completely new plants and animals with robots that could generate a stem cell from scratch. A small group of Forerunner began experimenting with ethics testing, and created different creatures with different programmed concepts of right, wrong, and purpose. They created a creature of an extreme communal drive, and the belief that the universe must be assimilated into one giant unity. This creature would be later known as the flood.
The flood, highly intelligent and using the best of Forerunner technology, spread rapidly, using the knowledge from the lab where they were created to rapidly spread. The Forerunner, caught off guard, began to build robots to fight and contain the flood, but it was of little use. Forerunner scientists, frustrated by the fragility of human soldiers, began to genetically engineer a race of extremely dedicated and fanatical super-soldiers.
They created tactical leaders with swift maneuverability, the Elites. Then they created the Hunters, with powerful arms, and an extreme passion for their mates. And finally, the Brutes were manufactured to act as durable shock troops to disrupt the lines of enemy flood.
But it was of little use. The robots of the Forerunner, seeing the future extermination of their masters, began storing the DNA of multiple creatures from their world. In the reaches of space where there were no Flood, the robots began work on a series of Halos, giant superstructures that would destroy all life on the universe. In the eyes of the robot builders, this would destroy the flood, and enable the robot builders to repopulate the galaxy with all that they saw fit.
When the Forerunner were all but defeated by the flood, the robots asked a Forerunner to fire the Halos for them (since the robots revered the Forerunner), and all life in the universe was, in the blink of an eye, rendered dead.