It had happened before. Many times. Now, the cycle is once again coming to pass. It had nearly been broken for good, leaving the universe an echoing, empty place, devoid of life. The Parasite starved, and those that ignited the flame, those that activated the Halo's, were all that was left. Only a few, they began to rebuild.
Much later. Human civilization has extended from Earth to colonize different planets. The UNSC, the humans main Military strength, have encountered foreign beings in the universe. There was no greeting, no negotiations, no chance. They meant ill, and soon, Humans were facing total eradication at the hands of a far superior race.
Their technology was more advanced, their weapons devastating, and all attempts at communication were ignored. One by one, the colonies were glassed, the planets very surface scorched by the enemies fleets. They took no prisoners, showed no mercy, and the only victories that the UNSC could muster in ship to ship combat was when they outnumbered the enemy 3 to 1. Even then, victory was not certain.
The Covenant, they called themselves. An affiliation of alien races, brought together under the religious council of The Prophets. The Forerunners, as their Gods were called, were the ancient race that activated the Halo's. The Prophets preached that the Forerunners will was the total eradication of the humans, and that the activation of the Halo's would ascend them all to salvation.
Blindly, The Covenant followed, reaping world after world, pushing the humans back. And then... the truth was known. When the Covenant learned of the Halo's horrifying effects, and the true identity of the humans, the Forerunners direct descendants, there was a civil war, tearing the Covenant in two.
Those who remained with the Prophets warred with Earth, where a mysterious 'Ark' was said to be the remote activation for all the Halo's.
Those that broke away joined the humans, assisting them to survive where before they had blindly sought their extinction. An alliance was formed, and the combined might of the two ended the Prophets quest.
Now, in the afterglow of the war, the end to the long years of bloodshed, a new, terrifying foe would rise, as it has done countless times before.
The Flood had returned, and now this alliance must hold, for they face a genocide that will consume every planet in the universe. No one will be spared.
Now, only the initial attacks have begun. UNSC and their new allies must mobilize to exterminate this enemy, and finally break the cycle.
[Some aspects of the original plot and time line have been altered]