Forerunner-Flood war

The Forerunner-Flood War was a galactic war between the Forerunners and the Flood.

Beginning
The Flood entered the Milky Way galaxy at least at 98,379 BC, and initially caught the Forerunner military by surprise, using captured non-military vessels to penetrate local Forerunner naval fleets and descend and land upon Forerunner-colonized worlds, overrunning local defenses and billions of Forerunners per world with billions of Flood forms within days. Forerunner fleets were forced to bombard Flood-infested Forerunner worlds to prevent Flood spread. The Forerunners grouped together under two centralized governments: first the Mantle and afterwards, the Guardianship, and bombarded dozens of Flood-infested former Forerunner planets.

Stalemate
After 300 years of devastating warfare between the Flood and the Forerunners, the highest levels of Forerunner Fleet Command began to realize that Forerunner species extinction was possible, as so many Forerunners had fallen to the Flood. After Flood spreading continued, planetary self-bombardment after Flood infestation turned into complete system-wide destruction by detonating planetary system stars after even minimal Flood presence was detected in a Forerunner system. Forerunner military forces were ordered to don heavy armor and other personnel were ordered into protective stasis. Flood were taken into M-type Forerunner installations and studied in an effort to find yet another countermeasure. Hundreds of other unsuccessful methods were attempted by the Forerunners to overcome the Flood, and all possibilities were exhausted as a final countermeasure came into mind for the Forerunners: activation of the Halo Array and destruction of all sentient life in the galaxy, and depleting the Flood of all biomass that they could consume, thus halting them. However, the Didact, the appearant commander of the Forerunner military, adamantly refused to activate the Halos, saying that it would overturn the Forerunner pledge to preserve all life in the galaxy.

However, the Flood were growing in number, and were forming a number of centralized sentient intelligences to coordinate their efforts: Gravemind forms, and their "raw computing power" began to overrun the last Forerunner naval countermeasures, which consisted of using Keyship vessels and drawing the Flood into pricy naval engagements, which lasted for approximately 300 years. However, even Forerunner commanders realized that their naval tactics were being overcome, and a final solution was necessary if the Forerunners were to pull of out this "stalemate": a Contender-class artificial intelligence, Mendicant Bias, was crafted by the Forerunners to directly attack the Gravemind forms and any surrounding Flood biomass in an effort to decapitate Flood consciousness. Two installations: the Ark and the Shield World, were constructed by the Forerunners for shelters for themselves when the Halos fired.

While there was a "Maginot line" where the Forerunners held the Flood at bay, the Forerunner Librarian journeyed beyond this line at great personal risk, indexing and documenting entient species across the galaxy, including the Sangheili (Elites) and San 'Shyuum (Prophets), and filled every vessel possible with documented species for transit to the Ark for safety in the Forerunner campaign to save all species possible from the advancing Flood.

Endgame
"Something is wrong...at night I can see it--flitting shadows--black against the stars. Thousands of ships! Not spiraling outward, but heading for the line! This is the tipping point, Didact. It's no longer feeding."

- Forerunner Librarian to the Didact

While during the stalemate the Flood was exponentially growing and readying for an attack, eventually, they assaulted the Forerunner core systems with thousands of Flood-filled supraluminal vessels. The systems under attack were promptly evacuated by Forerunner fleets while three Forerunner naval groups: the Emergency Circumstance Fleet, Security Fleet, and Suppression Fleet were recalled to defend against the Flood counterattack. Mendicant Bias fell to rampancy and instead of attacking the Graveminds, turned against the Forerunners for the Flood cause.

With naval strategies failing, the Forerunners turned to their Halo project: securing other species along with remaining Forerunners into the Ark while readying the Halo array for firing. Upon this, two Forerunner units beyond the failing defense line, the Primary Pioneer Group and Advance Survey Team-Alpha, came across Earth at the edge of the Milky Way galaxy. The Librarian journeyed there in his quest for categorization, finding the human species and also creating a portal on Earth that would lead to the Ark.

The Didact sent a rescue party for his son, the Librarian, in an effort to retrieve him for the Ark, but Mendicant Bias destroyed the party, leaving the Librarian stranded on Earth apart from the Ark. Forerunner collapse forced the Didact to activate the Halos. Mendicant Bias attempted to prevent the Didact from doing as so, but was stopped by Offensive Bias.