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: the Mantle.

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 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 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. 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. Prior to the firing, 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. Of particular interest was a region devoid of any fauna, presumably somewhere in modern day Africa. The Librarian journeyed there in his quest for categorization, finding a planet empty of sentient life. After the Librarian had indexed all life on Earth, he/she had built a hidden portal to the Ark, at New Mombasa in Africa. After planting a garden "Eden", the Librarian spent the remainder of his/her life on Kilimonjaro.

In the meantime, the Flood, along with the aid of rampant Mendicant Bias, attacked the Maginot Sphere from multiple vectors. Sensing that any defense was futile as long as the Flood had more resources to consume, Didact knew that the only chance to stop the Flood was to activate the Array. Didact sent a final message to the Librarian as the trigger was pulled, dreading the fate they wrought through 300 years of war. All sentient life in the Milky Way galaxy were annihilated by the Halo Array. The Forerunners were believed to be extinguished from the galaxy, and the Flood were halted, and the centralized Gravemind form was destroyed.

As all sentient life died, all that remained were the crew-less fleets. The battle, then, fell between the artificial AIs Offensive Bias and Mendicant Bias. With all infected lifeforms dead and no new lifeforms to infect, Offensive Bias was able to use the remaining Forerunner fleet to destroy the Flood fleet. Defeated, Mendicant Bias was captured and stored at the Ark for study, where it remains to this day.

Epilogue
The firing of the Halo Array was successful in that it halted all Flood, save those preserved for research, by killing all sentient life in the Milky Way. However, the Forerunner race was reconstituted on Earth as Humans. It is believed that Human life started in Africa, presumably in the garden of "Eden" that the Librarian planted. While the exact process in this which humans populated Earth is unknown, all the Forerunner culture and technology is left for Humans to rediscover. Hence, Reclaimers.

Trivia/Speculation
A clue as to how Forerunners were reconstituted as Humans may be in the Librarian's remarks about how "special" Earth was. The reference to "Eden" is also a giveaway. In addition, the report by the Primary Pioneer Group and Advance Survey Team-Alpha groups identified Earth as a "promising" planet.

Although just speculation at this point, it is possible that the Librarian could have somehow "planted" human life in Eden. Presumably, the reason why the Librarian found it "well worth the effort it took to build one final gateway even at this late hour" was so that Forerunner would reconstitute on Earth, find the portal, travel to the Ark, and reclaim the technology.

The advance of Human culture and civilization and their lack of Forerunner technology/knowledge is explained by the Librarian's work at hiding the portal to the Ark. Humans were therefore trapped on Earth with no access to knowledge or technology save what they discovered themselves and later space exploration.

Even though all sentient life was destroyed with the firing of the Halo Array, Flood specimens were saved for research. This may be due to the origin of the Flood. Even if all Flood were destroyed in the Milky Way, it may be possible that more would come from other galaxies. Hence, the necessity to preserve specimens for research in case there is a future incursion.

Contradiction to Cradle of Life Comic
The story presented in the Terminals and the rest of the Halo trilogy is contradictory to the Halo 3: The Cradle of Life comic, where humans are shown to be existing on the planet when Forerunners arrived to build the portal to the Ark. This is likely an error on the part of the ad campaign that featured the comic.

Further evidence of contradictions: In the Halo 3 level Cortana, Gravemind proclaims the following to Master Chief: "Child of my enemy, why have you come? I offer no forgiveness, for the sins of the father are passed to the son". From Guilty Spark: "You may be Forerunner, but this is my ring." Further evidence is provided by the Prophet of Truth, in his need for human hands to activate Forerunner technology and in what he says. In addition, Halo 1 and 2 both have significant clues as to the relationship, particularly in the comments made by Guilty Spark.

It is possible that Humans were are a different species that was somehow reconstituted after the firing of the Halo Array, but the evidence in the games suggest otherwise. While the Terminals do show the Librarian remarking the Earth was special because of "them", the use of the term is ambiguous. In addition, the report by the Primary Pioneer Group and Advance Survey Team-Alpha show they found "a planet capable of supporting life located within the near border region of the [galactic halo] with no indigenous sentient species." Presumably this is referring to Earth, as it is located near the border of the Milky Way.

It is possible to speculate on re conciliating the differences, such as the humans being created as part of an experiment prior to the firing, but it seems more plausible that the comic is incorrect and plays no role on Halo's story.