Imagine if The Didact decided to join our side 100,000 years ago in an effort to stop the Flood instead of attacking us and de-evolving us, leaving them alone to fight the parasite. I also think the Forerunners were afraid of others species surpassing them, therefore de-evolving species and taking away their tech (so much for following the Mantle you -Yoinks!-).
Flood would be destroyed, Humans and Forerunner become BFF’s, and no Halo games.