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 was a galactic conflict that occurred between the Forerunners and the Flood parasite. It was started on G617 g1 around 100,300 BCE, 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 millions of 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.

While powerful, the Forerunners were not the only major civilization in the galaxy. Other races had also developed interstellar empires, including prehistoric spacefaring humanity, who had allied with the early San 'Shyuum. Around 110,000 BCE, the Flood entered the galaxy from one of the Magellanic Clouds and caught the humans and San 'Shyuum by surprise, infecting their populations and taking their worlds at a steady rate. Eventually, the Flood receded from the galaxy due to its own long-term strategy, though this retreat was widely believed to be the result of a cure created by humanity. When the Forerunners dismantled human civilization in the aftermath of the human-Forerunner wars, this secret was supposedly lost.

The threat of the Flood would shape Forerunner politics for millennia to come, with different rates having differing views on how to best prepare against their return. A series of devastating superweapons, known as the Halo Array, was created by the Builders while the Warrior-Servant Prometheans, led by the Didact, devised a more strategic defense solution consisting of numerous military installations known as Shield Worlds. However, the Prometheans lost to the Builders and were forced into exile, and an array of Halo rings was constructed. This also secured the Master Builder Faber's position in the Ecumene Council's favor for over a thousand years.

Aware of the inevitability of the return of the Flood threat, the Lifeworkers led by the Librarian began indexing and protecting species across the galaxy, cataloging them at an extragalactic installation known as the Ark, as a method of countering the total elimination of all sentient species in the galaxy. Due to its colossal scale, this "Conservation Measure" would last all the way until the end of the conflict with the Flood.

After over nine thousand years, the Flood returned, 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.

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.

After ten thousand years of absence, the Flood reappeared on the planet G617 g1, a lightly inhabited world harboring a small commune of Forerunners. The Flood 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
"Know that a thousand other plans were tried and failed. Millions of brave and honored souls died trying to avert this terrible, desperate situation."

- A Forerunner log describing the situation the Forerunners found themselves in.

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. As the Flood continued to spread, 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. Among these failed plans was the use of the Composer, a highly sophisticated Forerunner machine designed to convert organic beings into digital intelligences. It was hoped that this device would save the population of the galaxy from the Flood by converting them into non-organic forms, in the process uplifting them into a transcendent state of immortality. However, the process was flawed, and a satisfactory transition of the consciousness into digital form remained outside the Forerunners' reach.

Over the course of the war, the Flood grew in number and formed a centralized intelligence to coordinate their efforts; a Gravemind, which proceeded to evolve into a Key Mind as whole planetary ecosystem fell to the Flood parasite. The raw computing power of these enormous collective intelligences began to overrun the most formidable Forerunner naval countermeasures, which consisted of using Keyships and drawing the Flood into pricey naval engagements. 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. While galaxy-wide sterilization using the Halo rings existed as an option, the Forerunners would not resort to the Halos until the very end.

While there was a defensive barrier known as the Maginot Sphere where the Forerunners managed to hold the Flood at bay before the very end of the war, the Forerunner Librarian journeyed beyond this line at great personal risk, continuing her millennial mission of indexing and documenting sentient species across the galaxy, 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. During this stalemate, the Flood was exponentially growing and readying for an attack.

Crisis
"I kill you all and I enjoy it. I destroy you in your indolent billions - in your gluttony, in your self-righteousness, in your arrogance. I pound your cities into dust; turn back the clock on your civilization's progress. What has taken you millennia to achieve I erase in seconds. Welcome back to the [Stone Age], vermin. Welcome home."

- An excerpt of Mendicant Bias' hate-fueled diatribe against the Forerunners after the AI's defection to the Flood.

The Forerunners had created a powerful Contender-class artificial intelligence known as Mendicant Bias, and tasked it with leading all of their defensive efforts. Mendicant had deployed major fragments of itself on numerous warships as well as all of the twelve installations of the original Halo Array. Around 100,043 BCE, Mendicant Bias was charged with the first test-firing of a Halo, Installation 07, near the former Precursor world of Charum Hakkor. As a result of this small-scale activation, an ancient entity imprisoned on Charum Hakkor, known as the Primordial, was released and subsequently transported to Installation 07 for study. Master Builder Faber tasked Mendicant Bias with interrogating the Primordial before having Installation 07 moved to a hidden locale to conduct his own unsanctioned experiments in secret. During its 43-year long discourse with the Primordial, Mendicant Bias was convinced by the entity, actually a Gravemind, to turn against its Forerunner masters.

Around 100,000 BCE, Faber used Installation 07 to suppress a San 'Shyuum insurrection, practically wiping out the species aside from samples indexed by the Librarian. The Ecumene Council deemed this a severe violation against the Mantle, the Forerunners' pledge to preserve all life in the galaxy. The remaining Halo rings were to be brought to the Capital and were slated to be decommissioned, as they were deemed too destructive. This turned out to be a miscalculation on the Forerunners' part, as the rampant Mendicant Bias would arrive aboard Installation 07 and take control of many of the Halo rings over the capital. Despite heavy resistance from the Forerunner fleets, Mendicant Bias successfully fired Installation 07 in the Capital system, delivering a catastrophic blow to the Forerunner leadership for a time.

Up until this point, the Forerunner government had downplayed the Flood threat, even keeping it hidden from the general populace of their core systems. However, they were eventually forced to take more drastic measures in order to survive. The Forerunner government remained in disarray after Mendicant Bias' attack. The Ur-Didact had only recently returned from a millennium of exile, but the Master Builder, before being removed from power, had managed to capture the Didact and abandon him in a Flood-infested region of the galaxy. However, the Didact had duplicated his essence to another body, creating a secondary incarnation of himself, known as the IsoDidact. This copy assumed the role of the original Didact and reassumed command of the Forerunner military. Hoping to defeat the Flood via conventional strategy, the IsoDidact reactivated his shield worlds and the defense plan he had engineered thousands of years earlier. The Forerunners scored a temporary victory as the IsoDidact's forces reclaimed Installation 07 and captured the rampant Mendicant Bias. The Ecumene Council, which had been crippled by Mendicant Bias' attack, was reinstated shortly afterward as the "New Council".

Final years
The Forerunners' victory was short-lived. Undeterred the Flood continued to spread, with the Forerunner defenses unable to stop the Flood's advance, over 500,000 star systems were infected by the Flood. The Flood now controlled two thirds of the ecumene; these areas were referred to as "Burns". Although Mendicant Bias had been disassembled and scattered across the ecumene, the facilities in which the disparate parts of the metarch were held were eventually overrun by the Flood and Mendicant was soon reconstituted as the commander of the Flood's fleets. Furthermore, as the Flood gained more biomass, it continued to develop into more potent and dangerous forms; massive compound mind nodes known as Key Minds were formed as entire planets were assimilated.

In this late stage of the war, the Flood became powerful enough to use neural physics-based technology, allowing them to take control of the numerous Precursor artifacts, such as star roads, that had lain dormant across the galaxy for millions of years. The Forerunners did not possess any formidable defense against the sheer power and destructive capability of the Precursor constructs, which were capable of effortlessly dealing widespread devastation on entire Forerunner fleets and worlds, as well as manipulating space-time to become unsuitable for Forerunner slipspace travel and leaving entire fleets stranded or lost in anomalous slipspace transit.

Endgame
With the defenses of the Capital and the entire Orion complex failing and the Forerunner fleets across the galaxy being steadily ravaged by the Flood, strategic command of the ecumene was placed in the greater Ark, which eventually held the last remnants of the ecumene aside from minor pockets of survivors across the galaxy. The Librarian's biological specimens - including her core human population - once held on the Ark's surface were moved to the nearby Omega Halo, which, along with Installation 07, was the last of the Master Builder's original Halos.

The remaining Forerunner leadership eventually gathered at the greater Ark, including the Ur-Didact, who had been recovered from deep within the Burn by the Master Builder. Soon after their arrival, the Ark came under siege by Mendicant Bias and its fleet of Flood-controlled ships and star roads. The Master Builder was restored to command, as he claimed to be able to recalibrate the Halo Array to be able to target neural structures--in other words, the Flood and their Precursor "allies". While this was true, it was too little, too late, and he knew this better than anyone: he revealed the location of the lesser Ark to the IsoDidact and ordered him there.

The penultimate battle of the Forerunners was bitterly short: Omega Halo's primary weapon, having never been upgraded, could only fire in one direction and it was able to fire only once, tearing a hole in the approaching Flood wave and striking Path Kethona; while seemingly devastating, the Flood paused only momentarily to restore their line. Further delayed only slightly by the desperate defense offered by Offensive Bias, Mendicant Bias and the Flood fleet destroyed Omega Halo and the greater Ark, along with most of the Forerunner fleet.

In the chaos just before the battle was joined, the Ur-Didact - who had been driven mad by the Gravemind - used a Composer to harvest the essences of the entire human population of Omega Halo, to the horror of the Librarian who had placed all of her hope in humanity. The Didact planned to use the essences of both the humans and his own Prometheans to build an army of war machines which he delusionally believed could fight an extended campaign against the Flood. This was a grave transgression in the eyes of the Librarian, who had already laid plans for humanity as the successors to the Forerunners. In order to stop the Ur-Didact, the Librarian forcibly incapacitated him and imprisoned him within the shield world Requiem.

Firing of Halo
"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."

- The Librarian to the IsoDidact.

The IsoDidact (rescued from the destruction of Omega Halo by Monitor Chakas), Offensive Bias, and the remaining Forerunners headed to the lesser Ark, along with the surviving biological specimens from the greater Ark. This formerly secret installation contained the Forerunners' final weapon: the newer Halo Array, which would purge the galaxy of sentient life, depriving the Flood of all biomass that they could consume, thus halting them. The seven rings were deployed in their designated locations across the galaxy, and while the firing preparations were being conducted, Mendicant Bias and the Flood prepared to assault the Ark. In order to give the IsoDidact time to fire the rings, the Librarian journeyed to Earth, broadcasting a feint message to draw the Flood there. Ignoring the IsoDidact's pleas to return to the Ark, the Librarian calmly embraced her inevitable demise in the savanna near Mount Kilimanjaro, overlooking the construction of the Portal to the Ark.

To ensure enough time for the Halo Array to fire, the IsoDidact ordered Offensive Bias and all that remained of the Forerunner fleets to delay Mendicant Bias and its Flood fleet. While the IsoDidact initiated the Halo Array's activation sequence, the Flood fleet engaged the last Forerunner fleet in a massive naval battle. Feigning incompetence and using delaying tactics, Offensive Bias and his fleet held off the Flood as the Halos activated, exterminating all sentient life in the Milky Way galaxy. With the previously Flood-controlled ships now adrift, Offensive Bias annihilated Mendicant's remaining fleet within minutes. Offensive then proceeded to extract the last remaining shard of Mendicant Bias from one of its core ships and return it to the lesser Ark.

Aftermath
The Halo effect purged the galaxy of all sentient life, eliminating the threat of the Flood as it was deprived of available biomass and its centralized consciousness. All Precursor artifacts and structures, composed of neural energy, were likewise destroyed.

The surviving Forerunners on the Ark, under the leadership of the IsoDidact, imprisoned what was thought to be the last component of Mendicant Bias deep within Installation 00. The lifeforms sheltered on the Ark were eventually returned to their homeworlds and reintroduced them to their native ecosystems, now free of the Flood, by the remaining Forerunners and their automatons; this process was led by the new Lifeshaper, Chant-to-Green. After this re-seeding effort was finished, the surviving Forerunners left the galaxy.

List of appearances

 * Halo: Combat Evolved Anniversary
 * Terminals
 * Halo 2
 * Halo 3
 * Terminals
 * Halo Legends
 * Origins
 * Halo: Cryptum
 * Halo: Primordium
 * Halo 4
 * Terminals
 * Halo: Silentium