Forerunner-Flood war

"A hundred thousand years ago, a great civilization existed in this Universe. Like all great civilizations, they faced a sudden and dire turn of events. A threat to their primacy from outside. Something they never expected, never prepared for, a deeply alien threat they called simply The Flood."

- Cortana

The Forerunner-Flood War, also known as The First Flood Outbreak was a galactic event that occurred between the Forerunners and the Flood parasite. It was started on G617 g1 some 100,000 years prior to the present, and lasted approximately three centuries.

Background
The Forerunners originally 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 superluminal vessels, create sophisticated artificial intelligence and set up massive superweapon networks. They measured their advancements in Technological Achievement Tiers.

At some point during their development, the Flood were discovered to have entered the galaxy from an undetermined extragalactic point of origin, contesting the Forerunners for control of the entire 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 super-weaponry, specifically the Halo Array. As a method of countering the total elimination of all sentient species outside the Forerunner's shielded planets (the result of triggering the Halos), the Forerunners began indexing and protecting them from Flood assimilation out of emotional, habitual, and ideologically-motivated actions driven by their Mantle religion to defend all sentient or pre-sentient galactic life.

Beginning
"It devoured everything it touched. At first, their technology, their courage seemed like it might prevail. But they waited too long to see the threat, to join the fight. The Flood had spread too far and too wide."

- Cortana on the Forerunner-Flood War.

The Flood entered the Milky Way galaxy some time before the war, lying dormant on the uncharted world designated G617 g1, 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 a few years. Eventually, Forerunner fleets were forced to commence orbital bombardment on Flood-infested worlds to prevent the Flood's spread to other planets.

Stalemate
Following the 300 years of devastating warfare between the Flood and the Forerunners, the highest levels and tiers of the Forerunner Fleet Command began to realize that Forerunner species extinction was plausible at the Flood's discretion as so many Forerunners had fallen victim 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 large 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, depriving the Flood of all biomass that they could consume, thus halting them. However, Didact, a high-ranking military leader, adamantly refused to activate the Halos, saying that it would overturn the Forerunners' 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. At least three installations, the Ark, Onyx Shield World and an unnamed Shield World, were constructed by the Forerunners for shelters for themselves when the Halos fired.

While there was the Maginot Sphere 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 and San 'Shyuum, filling every vessel possible with documented species for transit to the Ark for safety in the 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. It's coming for you."

- Librarian to the Didact

During the stalemate, the Flood was exponentially growing and readying for an attack, and eventually they assaulted the Forerunner core systems with thousands of Flood-filled super luminary vessels. While three Forerunner naval groups, the Emergency Circumstance Fleet, Security Fleet, and Suppression Fleet, were recalled to defend against the Flood attack, Mendicant Bias became rampant 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 its 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 them, as well as the galaxy's various other species, protecting them with the Ark.

The Didact sent a rescue party for the Librarian, in an effort to send it to the Ark before it would be forced to activate the Halos and kill all sentient beings, but Mendicant Bias destroyed the rescue party, leaving the Librarian stranded on Earth away from the Ark. The 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 loyal Forerunner 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 as it formed a spherical defensive formation while the Array activated. Using feint tactics, the Forerunner fleet held off the Flood as the Halos activated, annihilating all sentient life in the Milky Way galaxy. Those saved were sheltered on the Ark. The surviving Forerunners left the galaxy, and the Flood were halted, and the centralized Gravemind form eventually died.Then, Keyships began escorting various alien life forms back to their homeworlds, so that life could finally return to normal, with no threat of the Flood.