Forerunner-Flood war

"Every vessel we can fill, we send to the Ark. I dare not cease the mission. Not now, not until I've done all I can. Each one of these souls is finite and precious. And I'm close. Close to saving them all."

- Forerunner Librarian to Didact

The Forerunner-Flood War was a galactic war between the Forerunners and the Flood believed to have started in 98,379 BC and definitively ended at 97,448 BC.

Introduction
The Forerunners are originally believed to have evolved in and colonized the Milky Way galaxy, organizing themselves over a large number of terrestrial planets and colonizing multiple worlds as well as forming a structured military which included both naval elements and ground forces. The Forerunners were of sufficient technological capability to construct create supraluminal vessels, to create sophisticated artificial intelligences and to create massive superweapon projects. At some point during their development, the Flood were discovered and to have entered the galaxy from an an undetermined extragalactic point of origin, contesting the Forerunners for control of the galaxy. While the Flood sought to assimilate all sentient life, the Forerunners attempted to defend against the Flood threat using several measures to both directly combat them as well as carry out research in regards to their capabilities. As time progressed, they also began to develop and create superweaponry, specifically the Halo Array. As a method of countering the total elimination of all sentient species (the result of triggering the Halos), they began indexing and protecting them from Flood assimilation out of the noble ends to defend all sentient or presentient galactic life.

Beginning
The Flood entered the Milky Way galaxy at approximately 98,379 BC, and initially caught the Forerunner military by surprise, using captured non-military vessels to penetrate local Forerunner naval blockades to descend and land upon Forerunner-colonized worlds, overrunning local defenses and converting billions of Forerunners per world with hundreds of millions of Flood forms within days. Forerunner fleets were forced to bombard Flood-infested worlds to prevent the Flood's spread. The Forerunners grouped together under one centralized government.

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 a lot of 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, depleting the Flood of all biomass that they could consume thus halting them. However the Didact, the apparent 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 centralized sentient intelligence to coordinate their efforts; Gravemind, and their "raw computing power" began to overrun the last Forerunner naval countermeasures, which consisted of using Keyship vessels and drawing the Flood into pricey naval engagements which lasted for approximately 300 years. However, even Forerunner commanders realized that their naval tactics were being overcome, and a new 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 sentient species across the galaxy, including the Sangheili (Elites) and San 'Shyuum (Prophets), filling 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. 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 Gravemind, turned against the Forerunners for the Flood cause.

With naval strategies failing, the Forerunners turned to their Halo project; securing other species 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 Forerunners saw a unique potential in the human species, creating a "Conservation Measure" for the protection of the human species, shielding them with the Cartographer Building.

The Didact sent a rescue party for the Librarian, in an effort to retrieve him/her for the Ark before he/she would be forced to activate the Halos and kill all unshielded sentient beings, but Mendicant Bias destroyed the rescue party, leaving the Librarian stranded on Earth apart from the Ark. Forerunner military collapse forced the Didact to activate the Halos. Mendicant Bias attempted to prevent the Didact from doing as so, but was stopped by a Forerunner-loyal artificial intelligence, Offensive Bias.

While the Didact began the activation sequence for the Array, the Flood fleet attacked, and the remnants of the Forerunner fleet formed a spherical defensive formation while the Array activated, using feint tactics to hold off the Flood fleet as the Halos activated, annihilating all sentient life in the Milky Way galaxy save those sheltered in the Ark and Shield World or on Earth protected by the Portal. The Forerunners were believed to be extinguished from the galaxy, and the Flood were halted, and the centralized Gravemind form was destroyed.