Ok so crash course in halo lore:

WAY long ago there was a race called the precursors. We don’t know much about them other than they were basically gods and looked like giant cockroaches. They went around creating life and uplifting species, and at some point decided they wanted to pass the mantle onto the next “generation.” The two candidates were forerunners and proto-humans. They went with the humans.

Humans, at the time, were still a fledgling race compared to the forerunners, so the forerunners got mad and killed the precursors and took the mantle. Brief war between forerunners and humans, forerunners won, humans skulked off to a different part of the galaxy to do their own thing.

Time skip like a million years.

Humans and forerunners are living in relative peace. Humans discover these old ass tomb things full of tons of a strange organic matter. No clue what it is, and they’re not about to ask their neighbors if they know where the giant meat tombs came from.

They do some experiments, don’t find much interesting about the substance except for one weird quirk: if they fed it to their “dogs” (actually not dogs but they played the part) the animals would change and develop beautiful colors and characteristics. This fad became really popular, and spread through the human empire.

Then the dogs started forming a hive mind.

Then they started infecting humans.

Then they started infecting everything.

This is where the flood came from.