I believe that with the way Halo Wars 2: Awakening the Nightmare ended, it is possible that we will see the Flood a lot more. Personally, I believe that Cortana will be the cause for this.
My theory is that Cortana most likely does have the Logic Plague, her current form is made of all the Rampant fragments formed over the years since the Gravemind had her and during her time on the Forward Unto Dawn. Obtaining the Domain and upholding the Mantle of Responsibility allows her to have complete control over the guardians, to have a forced unity of all life. However, this is also something the Flood aims to accomplish.
In Halo 5, Cortana states that “AIs can assume the Forerunners’ Mantle of Responsibility. And once there is peace, they can focus on poverty, hunger, illness.”
The Flood also believes in such a concept.
According to the Bestarium from Halo 3, the Flood resembles a “Utopian socialist ideal as there is no wealth, no poverty, no want, no crime, and no disease; every individual works for the advancement of the Flood as a whole.” If this is the case and Cortana does actually have the Logic Plague, she will be able to use the Guardians to disarm all life in the Galaxy, allowing the Flood to rebuild their colony, and assimilate all life with ease. This also means that Cortana may not originally be the antagonist to begin with.