The Forerunner Sect is the left over builders, life-workers and miners which are lead by Iso-Didact/Librarian or their descendants. The Flood that I am talking about return from Path Kethona, they are the over cumbersome biomass that has many keyminds, hundreds of graveminds and proto-graveminds; the scary first-born flood.
So heres how it would pan out.
Flood Defeat
The forerunners remnant would most likely be lead by the Iso-Didact and Librarian or their descendants. They are intellectual, cultured and responsible; and having survived the first Forerunner-Flood War they would know that to win they must unite.
The Humans and Covenant have had similar experience with the Flood of late and so would know the same way to win against the flood is to unite.
The bond between this alliance (Human-Forerunner-Covenant) would be strengthen by the fact that the Covenant believed the Forerunners as gods; and that the Librarian and Iso-Didact value Humanity. Thus being the glue of the alliance.
Once the flood is decimated, I believe the Forerunners being the most advanced and wise, would try to eradicate the battle lines between the Human and Covenant. They would form a treaty and unite into a cohesive Empire which upholds the mantle, thus sharing the role.
The races would live peacefully for decades, but Humanity would act yet again in war, and try to either take over as singular tyranical leadership of the Empire or split away. This would cause an uproar and so war would once again be waged.
The Forerunner-Covenant Empire would either revolt or rise against the tyranny or protect their species from being destroyed by the colossal force that is Humanity.
Humanity Defeated
Humanity growing arrogant in their power would thus be obliterated by the Forerunner-Covenant Fleet. The Covenant and Forerunners would live together in peace, trying to recover from a thousand-year old war.
Forerunner-Covenant Empire Defeated
As the dust starts to settle in the peaceful galaxy, more sentient species emerge, The Covenant and Forerunner Empire offer them spots in the alliance, yet they use it only for personal gain, stealing technology and waging war. This time the Forerunner-Covenant alliance has grown weak and thus is killed.
Sentients Defeated
The new sentient species dominates all life until the precursors return. The Precursors destroy this pitiful race and start creating life yet again as they did millenium ago. A echo is heard in the wind “They will never learn, War always arises.”
Seems history will always repeat itself.