Flood

Were you looking for the novel Halo: The Flood, or The Flood, the ninth level in Halo Wars?

The Flood, designated as LF.Xx.3273 by the Forerunners, (Latin Inferi redivivus meaning "the dead reincarnated" ), referred as the Parasite by the Covenant, are a species of highly virulent parasitic organisms that reproduce and grow by consuming sentient life forms of sufficient biomass and cognitive capability. The Flood was responsible for consuming most of the sentient life in the galaxy, including the Forerunners, during the 300-year-long Forerunner-Flood war. The Flood presents the most variable faction in the trilogy, as it can infect and mutate humans and Covenant species, such as Sangheili, and Jiralhanae, into combat forms. They are widely considered to be the greatest threat to the existence of life, or, more accurately, biodiversity, in the Milky Way galaxy.

Background
Originating from an unknown point outside the Milky Way galaxy, the Flood is an extremely adaptable, prolific and dangerous parasitic life form. The species reproduces and spreads by infecting other organisms, hijacking their bodies and nervous systems in order to transform them into one of many specialized Flood forms. Through infecting a wide range of life-forms, especially those possessing sentience, the Flood assimilates their memories and intelligence, and the species becomes collectively more intelligent as a result. Because of their frighteningly rapid growth rate, as long as enough hosts of sufficient biomass and intelligence are available, the Flood is effectively unstoppable.

They are the cause of the Forerunner-Flood war, which lasted approximately three-hundred years. They were the reason that the Halo Array was constructed, as a last final effort by the Forerunners to halt the Flood infestation and preserve biodiversity in the galaxy. After exhausting every other strategic option, the Halo Array was fired, resulting in the death of almost every sentient being in the Galaxy, save for those that were placed on the Ark and the Shield Worlds by the Forerunners. The Flood themselves starved to death, except for specimens kept in stasis on the Halo rings and other facilities.

Without the presence of a Gravemind, the Flood possess only basic coordination; they are incapable of forming complex strategies and focus solely on attacking and infecting nearby sentient organisms. This stage of a Flood outbreak is known as the Feral Stage. At this lower level, the Flood seek to create an assembly of biomass, calcium, and nervous system reserves, which leads to the creation of a Flood hive and the beginnings of a Proto-Gravemind.

Once a Gravemind is established and the Coordinated Stage is initiated, the Flood become far more numerous, sophisticated, and dangerous. The Gravemind is the guiding intelligence of the Flood, capable of controlling all Flood forms within a galaxy. This Flood entity is composed of the assimilated intelligence and memories of all hosts consumed by a Flood infestation, reassembled into a collective consciousness which coordinates the Flood in an organized manner.

If a Flood form is somehow fully isolated from the Gravemind that controlled it, it will revert to the Feral Stage. If it comes under the influence of another Gravemind, however, it will once again become part of a collective. Any distinction between any of the individual Gravemind forms would be impossible to detect, since each one is functionally identical and is striving for a single goal: the assimilation of all life.

The nature of the Flood's collective consciousness has been likened to that of a socialist utopia, due to the fact that the Flood act as a unified entity, with no individuality that would be present in other, more traditional species. Each component of Flood meta-organism works tirelessly for the advancement of their species.

Origins
The earliest known Flood were in the form of the Precursors, a race of advanced Graveminds. Millions of years before the Human-Covenant War, the Precursors created various species, including the Forerunners and humans. Eventually the Forerunners rose up against the Precursors and nearly drove the species to extinction.

The Flood are believed to have arrived in the Milky Way galaxy from one of the Magellanic Clouds, two small satellite galaxies near the Milky Way, circa 110,000 BCE. Whether this is the true origin point of the Flood remains unknown. They were first discovered by ancient humans near the edges of the Milky Way, aboard automated vessels of unknown origin. It remains unknown who built the cargo ships that carried the Flood into this galaxy. These vessels, which were found crashed on both inhabited and deserted planets, contained millions of glass cylinders filled with a fine dessicated powder, which were inert, relatively simple short-chain organic molecules of unknown purpose.

Humanity studied the material and deemed it to be harmless, but noted that it had psychotropic effects on lower animals. Small dosages were administered to Pheru, popular domestic animals among humans and San'Shyuum, and resulted in more docile behavior. Unbeknownst to the humans or San'Shyuum at the time, the powder was altering the genetic code of the Pheru, manifesting as improved behavior while slowly changing other aspects of their genome.

After several centuries, more disturbing changes appeared. Pheru treated with the powder began exhibiting furry growths and fleshy protrusions, which other Pheru were compelled to consume. Shortly afterward, the Pheru began suffering widespread abortions and genetic deformities, and many were euthanized or released into the wild. Soon afterward, the Humans and San'Shyuum who had been in the presence of the altered Pheru began to exhibit some of the symptoms of the powder-induced "disease."

Affected on a psychological level by the strange illness, infected victims began to consume the sick Pheru, and parts that were discarded also became vectors for the disease. The afflicted then moved onto cannibalism and sacrifice of the uninfected. The infected Humans and San'Shyuum proceeded to spread the disease into other systems, which furthered the scope of the Flood outbreak.

At this point, the Flood infestation, which had previously been predominantly a mind and behavior-altering affliction with only relatively minor physical changes, began to reshape its victims into a variety of forms designed to gather victims, engage in combat, and to rapidly consume useful biomass and other resources. The growing outbreak quickly led to a conflict between humans and the Flood.

It was during this time that the humans discovered a cure for the Flood, and managed to wipe it out while the infection was still comparatively minor. The remaining Flood-carrying ships escaped the galaxy, and the Flood was never to be seen again until the incident at G617 g1. During the interim, humanity (who was then at war with the Forerunners) destroyed all of the original carrier vessels that they had discovered. In addition, no trace of the Flood remained among the Pheru, humans or San'Shyuum.

Because of the lack of evidence, most Forerunners were unaware of the existence or true nature of the Flood, and many dismissed it as a simple excuse for humanity's aggressive expansion. However, several high-ranking Forerunners were fully informed of the threat, and in secret began developing countermeasures should the Flood ever return.

Forerunner-Flood war
"It fed on intelligent life and in doing so, became ever more intelligent itself. The Flood was unique; it used their very strength against them."

- Cortana on the Forerunner-Flood War.

The Flood reappeared as a viable threat in the galaxy when they were first encountered by the Forerunners on the planet G617 g1. Initially, the Forerunners severely underestimated the potential threat this new life form posed, and used tactics more suited to disease outbreak than actual warfare. By the time the infection had begun to spread, the Flood had become a much deadlier and more intelligent foe. The Flood used unarmed civilian assets to penetrate planetary defense groups, first striking at the Forerunner planet of LP 656-38 e, bypassing the Forerunner orbital fleet, and infesting the planet below. They soon moved to similarly infest the planet DM-3-1123b. The sheer numbers of Flood forms on the planets overcame Forerunner ground forces.

While at first the Flood demonstrated a lack of even rudimentary strategic ability, they had numerical superiority: billions of forms were dedicated to planetary assaults, and every member of the Forerunner population was a potential Flood host. In desperation, the Forerunner armada was ordered to commence full planetary bombardment on infested worlds, although at a great cost - many Forerunners were unable to be evacuated before bombardment commenced, leaving the Forerunner military with shallow victories against the Flood. In events where the naval garrisons were unable to commence bombardment, major Forerunner population centers were seen to activate localized weapons of mass destruction, effectively committing mass suicide, but stopping the growing infestation.

Thereafter, the Forerunners realized that ordinary naval tactics were unable to stem the growing tide of the Flood, and decided to pin their hopes of defeating the Flood on extreme measures. While the Forerunners initially deployed the Sentinel robotic drones to fight against and contain the Flood, almost immediately afterwards, the Forerunner Fleet Command contemplated "Premature stellar collapse": using naval battle groups to destroy planetary star systems' primary stars in supernova that would engulf the planetary systems and prevent any possibility of Flood infection.

While the Flood were exponentially growing, spreading from system to system with the intent to infect the Forerunner population, not to wage war with Forerunner battle groups, the tide was turning: the Flood had reached sufficient proportions to create a Gravemind form, a creature that embodied a collective sentient intelligence for the Flood species, and one that could coordinate the Flood swarms in intelligent attacks against the Forerunner fleets. The Forerunners were aware of this, and constructed the Contender class artificial intelligence Mendicant Bias in an effort to destroy this centralized Gravemind and disorganize the Flood. This too failed, with Mendicant Bias intentionally going rampant, joining the Flood cause, and returning from its mission bent on the destruction of its former masters.

The Forerunners began a "Conservation Measure", researching the Flood while constructing an artifact to generate a slipspace portal leading to the Ark on Earth and possibly other uninfected home worlds of Tier 7 races they considered "worthy", such as the various species that would make up the Covenant.

The Forerunners employed many, many measures, including intricate naval tactics in an attempt to contain the Flood, which ultimately failed. Finally, the Forerunners were forced to a Pyrrhic solution, using an array of ring-shaped megastructures, known as "Fortress Worlds" or Halos, built in ages past as superweapons. Because the Flood were parasitic, and their survival was directly linked to the presence of potential hosts, the Forerunners reasoned that eliminating all potential Flood hosts (that is, all sentient life forms in the galaxy) would render the parasite unable to grow and spread, and eventually cause it to starve to death. After all countermeasures failed, the Forerunners activated the Halos around 100,000 BCE, annihilating all sentient life throughout the entire galaxy. However, the human race and many other species throughout the galaxy survived the firing of the Halos because they were safely spared on the Ark, which was out of range of the Halo Array, or because they were protected by Shield Worlds, which were also out of range.

The Flood was contained, unable to reproduce and grow due to lack of hosts, and eventually died out. The only surviving specimens were contained in state-of-the-art, high-security Forerunner research facilities, such as the Halo Installations and the Threshold gas mine.

Battle of Shield 0459
Thousands of years after the end of the Forerunner-Flood war, the human ship Spirit of Fire jumped from Arcadia to follow the signal of Professor Anders, who had been captured by the Covenant. They were led to an unknown planet, which happened to be a Forerunner shield world. Containment measures on this planet had failed catastrophically, and the entire surface of the megastructure was choked with Flood biomass. Ground forces were deployed to investigate the presence of unknown hostiles sighted by the ship's radar. After fighting their way through Covenant forces, Sergeant Forge and several Marine squads were attacked by the Flood.

After a series of skirmishes with the Flood on the surface of the shield world, the UNSC forces discovered that the Flood was creating a proto-Gravemind, and that it may have been jamming the tracking signal that Anders was giving out. On their way to the soon-to-be Gravemind, they encountered several Flood colony forms, and found that by destroying them, the Proto-Gravemind would become weakened. Once they destroyed the proto-Gravemind, Serina found a signal, which was believed to be Anders'.

Captain Cutter then ordered all UNSC personnel on the planet to return to the Spirit of Fire. These orders were impeded by the Flood, which attempted to prevent the humans' retreat, but the Flood were eventually held back long enough for the UNSC forces to return to the Spirit. The Flood attacked the Spirit as it entered the interior of the shield world, but was cleared off by the ship's crew, Sentinels, and a series of "cleansing rings" lining the interior passage. All the Flood forms on the shield world were destroyed when Sergeant Forge used the Spirit of Fire's Shaw-Fujikawa Translight Engine to destroy the Shield World's internal sun, obliterating all Covenant and Flood forces on the shield world. The Spirit of Fire narrowly escaped by performing a hastily-calculated slingshot maneuver around the exploding sun in order to shoot off into space. Without the Spirit's slipspace engine, however, the ship was lost in space, with humanity's only knowledge of the Flood lost with it.

Release
"The only way to stop the Flood is to starve them to death."

- Cortana to John 117 and 343 Guilty Spark.

Although the first firing of the Halo Array starved the Flood that were at large in the galaxy, samples of Flood specimens were kept alive (perhaps in stasis) on various Forerunner outposts for research and scientific study. One such research site was located on Installation 04. This proved to be a grave mistake, as both Humanity and the Covenant stumbled upon the abandoned ring thousands of years after the firing of the Array. Cortana, aboard the, made what was presumed to be a "blind" jump through Slipspace (although it was later revealed that she used translated co-ordinates from a Forerunner artifact found on Sigma Octanus IV) to evade Covenant pursuers. This led both groups to Installation 04, and in turn, the Flood that were kept there. After the crash of the Pillar of Autumn on the Halo Ring, the surviving crewmembers dug in for what they believed would be a long and brutal guerrilla campaign against the Covenant forces on Halo.

Meanwhile, the pursuing Covenant cruisers (among them the Truth and Reconciliation) amassed their ground forces on the surface, who soon discovered an underground Forerunner flood containment facility in the swamps of Halo. Due to the secure nature of the facility, the Covenant came to use it as a fortified base of operations and an area for storing weaponry, oblivious to its true nature. At some point, either through a malfunction in containment equipment or a blunder on the part of the Covenant, the captive flood forms within the facility were released and attacked the Covenant forces inside. Knowing full well what the Flood were capable of, the Covenant forces promptly locked the facility down and evacuated all personnel who survived the Flood's escape.

Keyes and his team were unaware of these events, however, and proceeded to delve deeper into the facility, ultimately coming across one of the unopened Flood Containment Chambers. Believing it was a weapons cache of some sort, they unlocked the door, and were promptly attacked and assimilated by the Flood inside. With a large supply of "edible" sentient life now occupying the ring, the Flood began to multiply and infest most of Halo. Soon, the infestation proved too great even for Halo's automated military force, the Sentinels, to handle, and the ring's commanding AI, 343 Guilty Spark, was forced to call upon a "Reclaimer" (First Staff Sergeant Marvin Mobuto, then Master Chief Petty Officer John-117) to activate the array once more. Hearing of the above events, John-117 was deployed to the area on the drop ship Echo 419, proceeding into the facility, only to find out that most of the Marines he had been assigned to rescue had succumbed to the Flood.

These events brought the knowledge of the Flood to the UNSC. In a war of losses, this was another grim revelation for humanity.

Assault


After the Flood's escape, the Covenant forces across Installation 04 were overwhelmed by the Flood's assault. While the Covenant were occasionally able to hold the line by using vehicular and air support, most of the weaker Covenant soldiers such as Unggoy and Kig-yar succumbed easily to the Flood, and the few Sangheili who remained were outnumbered and infected. The UNSC, having a much smaller presence on the installation, found out about the Flood's might a short while later, when an ODST force engaged with the Covenant near Alpha Base, was ambushed by the Flood and suffered heavy casualties. However, one of the attacking combat forms, PFC Wallace A. Jenkins, who was one of the Marines in the original expeditionary mission to the supposed arms cache, was infected by a weak and elderly infection form whose powers of infection had been dulled by centuries of hibernation, making Jenkins' transformation into a combat form incomplete. Jenkins was still able to resist the pervasive Flood entity in his mind, and although incapable of articulate speech and with a physiologically devastated body, Jenkins was still able to betray the Flood through hand gestures during an interrogation with Major Antonio Silva, informing the UNSC Marine battalion that the Flood planned to assault the UNSC base from a series of underground catacombs underneath their base. In response to this intelligence, the UNSC moved to secure them, and prevented the Flood from staging another attack.

During these developments, the ring's Sentinels failed to effectively contain the Flood, and the Covenant and UNSC sustained heavy losses. The Flood occupied areas of the ring formerly held by the Covenant, although Covenant and Flood forces continued to wage war on the massive ice plains of the ring. Although the Covenant had the benefit of Shade stationary plasma turrets and vehicular/aerial support, the Flood had captured both UNSC and Covenant weapons, most notably M41 rocket launchers and had significant numerical superiority.

One of the UNSC personnel captured by the Flood was Captain Jacob Keyes, a brilliant naval strategist of the UNSC Navy. When he was infected, the Flood sensed that he held knowledge that would be especially useful to the Flood. Keyes knew the location of Earth, the birthplace and major planet of the human race, a planet with tremendous possible assimilation opportunities for the Flood. Instead of becoming a combat form, he was merged with at least four other victims into a massive, engorged Proto-Gravemind aboard the CCS-class battlecruiser, Truth and Reconciliation, a Covenant warship that the Flood had taken over. While he was in the brain form state, the Flood intelligence began to dig through his mind, searching his memories for the location of Earth. Captain Keyes successfully withheld information about Earth by constantly accessing information available on his command neural interface such as his name, rank, and serial number, until John-117 arrived. However, his arrival was too late, for Keyes was already dead. It was at that time the John-117 punched a hole in Keyes' skull to get the Captain's CNI.

The Truth and Reconciliation was a major point of contention between the Covenant Special Operations units and the Flood. The Flood had decimated most of the Covenant crew and garrison on board, leaving only isolated pockets of resistance, mostly small numbers of terrified Unggoy and a few Sangheili aboard the vessel. However, below the Truth and Reconciliation, in a series of rocky canyons, the Covenant were much stronger in force, with large numbers of Sangheili augmented by Unggoy, Kig-yar, and Mgalekgolo, fighting off the Flood. The Covenant Council of Masters in charge of operations on Installation 04, however, were terrified by the Flood presence. Because the CCS-class battlecruiser had been damaged in a previous space battle with the, it had been grounded, awaiting repairs for at least two days. After The Flood were discovered to be aboard the battle cruiser, the Covenant military leadership sent a Special Operations strike force to the Truth and Reconciliation to commence immediate emergency repairs, prepare it for lift-off into space and neutralize The Flood. These efforts, however, failed, with the Flood eventually retaking the vessel. Later, the remaining UNSC Marine forces on the ring staged an assault on the Flood-held Truth and Reconciliation, and managed to neutralize most Flood forms on the cruiser in a swift assault, and prepared the battle cruiser for take-off with emergency repairs to escape from the ring to Earth. However, there was tremendous risk if the Flood-infected vessel traveled to Earth, if there was even one Flood carrier form aboard, "Earth could fall," according to UNSC AI Wellsley, because of the Flood's exponential parasitic potential. Against orders, Marine officer McKay destroyed the warship with whatever Flood forms were still aboard, killing hundreds of UNSC personnel, including an infected Jenkins, but saving Earth and possibly billions of lives from the Flood.

Defeat
The Flood appeared to be interested in seizing space-capable vessels, in the hope of spreading itself away from the Installation and into the stars: they attacked the Pillar of Autumn and CCS Truth and Reconciliation, for this reason. After the UNSC cruiser's crash-landing onto the ring, and after engaging over fifteen enemy warships, it had been taken by the Covenant, although a UNSC raid had managed to temporarily retake the hull. On the third and final day of the Battle of Installation 04, however, the Covenant were in control of the crashed warship when a Covenant patrol was ambushed by the Flood and infected; when it returned into the vessel, the Covenant garrison was attacked by Elite combat forms. The combat forms were able to scatter before they could all be destroyed, and a steady trickle of Flood continued to enter the Pillar of Autumn through vents and openings in the hull, waging a tedious guerrilla battle against the Covenant security force on board.

Eventually, a force of Sentinels came on board, overwhelming the dwindling Covenant forces as the Flood began to attack the warship in full force, in the end almost completely obliterating the Covenant presence, and severely limiting the Sentinels on board. Despite their best efforts and enormous numbers, the Flood, Covenant, and Sentinels were unable to stop John-117 from detonating the wrecked warship's reactors, and escaping in a Longsword interceptor. The resulting thermonuclear detonation severed the ring world, destroying it and its capability to annihilate all sentient life, and simultaneously killed all remaining Flood on Installation 04, along with any other life forms that were on the ring.

Skirmish
After the destruction of Installation 04, on October, 2552, a human prison ship, the Mona Lisa, arrived in the Soell system and managed to retrieve surviving specimens of the Flood for study from the remains of Installation 04. They began to test the parasite on both human and Covenant prisoners, unaware of its lethality. Soon, the infection broke quarantine and the ship was infested by the Flood. The Flood absorbed the the crew and prisoners, then began to build a proto-Gravemind in its engineering section. The infestation ended when Sergeant Zhao Heng Lopez and her marines from the were sent to investigate the ship after retrieving a survivor from the ship. The Flood absorbed many of her marines, leaving her and a single Sangheili to fight for a single-occupant escape pod. The outbreak was most likely contained when the Red Horse destroyed the Mona Lisa using a Shiva-class nuclear missile.

Threshold gas mine
The Flood were also kept in a Forerunner-constructed gas mining facility suspended over Threshold, within at least one of the three arms of the station. A small Covenant special forces strike team, led by Special Operations Commander Rtas 'Vadumee and the Arbiter Thel 'Vadamee, were dispatched by the High Prophets to silence Sesa 'Refumee, the leader of a heretic faction, who was stationed within the mine. The heretics released the dormant Flood within the station in an attempt to halt the progress of the Spec-Ops team through the station.



The heretics' plan backfired, as the Flood killed and infected many of their forces while failing to stop the Arbiter and his team. The Flood broke out of the station's arm and spread to the central core of the station, where they overwhelmed the heretics stationed there. Eventually, even the station's Sentinel forces were completely obliterated as the Flood spread to the upper levels of the station. The Flood were unable to escape the station, however, as the Arbiter managed to sever the cable attaching it to the Forerunner support structure far above, sending the gas mine plummeting to Threshold's solid nitrogen core.

Battle of Installation 05


On Installation 05, the Flood had been in a continual battle with the Sentinels since the firing of the Halos 100,000 years prior. While the infestation had been contained to a quarantine zone established outside the Installation's Library, and presumably was severely weakened due to a lack of fresh host bodies, the Flood had managed to keep a Gravemind form alive deep within the cavernous tunnels of the ring. With the arrival of the Covenant and pursuing UNSC forces, the Flood was able to grow its forces considerably and redouble its assault on the Installation's security forces.

The Flood, despite a significant vehicular and infantry presence in the Quarantine Zone surrounding the Library, were unable to deny access to the Covenant and the UNSC. Miranda Keyes managed to slip the In Amber Clad through the Forerunner Enforcer patrols, while the Covenant launched a ground attack, led by Thel 'Vadamee and involving a small team of Spec Ops Elites, using a gondola to get to the index while attempting to control the gondola and keep it from slipping into Flood or Sentinel hands. Later, the In Amber Clad was captured by the Flood.

Attack on High Charity
Spartan-117, who had arrived with Keyes and Johnson, met Thel 'Vadamee in the clutches of the Gravemind, the central controlling intelligence of the Flood hive, created from the combined intellect of tens of thousands of assimilated corpses. Gravemind attempted to convince Thel 'Vadamee, against his own beliefs, and through the use of the captured Monitor, 2401 Penitent Tangent, and the semi-revived Prophet of Regret to not activate the ring. Still unswayed, although in question of his religion, Thel 'Vadamee prompted the Gravemind to show him, by "Stopping the key from turning.", transporting Spartan-117 to High Charity, and Thel 'Vadamee to Delta Halo's Control Room.

Taking advantage of the distraction that Spartan-117's presence caused, as well as the ensuing Great Schism, Gravemind took the opportunity to deliver himself, as well as a multitude of Flood underlings, onto In Amber Clad and then jumped the UNSC ship inside High Charity, whereupon it immediately crashed into the city's superstructure to deliver its infectious cargo, while a wave of Flood-controlled Pelican Dropships delivered Flood all over the city. The ill-equipped and distracted populace was no match for the Flood onslaught, and the Covenant Holy City was quickly overrun, with even the Prophet of Mercy falling victim to an infection form.

The Flood soon spread to every district, and Flood spores began to infiltrate and overload the ventilation systems; the whole city was becoming Terra-formed into a massive Flood Hive. The Gravemind regularly rebutted the words of comfort the Prophet of Truth delivered to the city’s population over the comm system, to sadistically instill more panic and unease. Spartan-117, having successfully stayed in front of the wave of Flood running rampant in the streets, stowed away on the Forerunner Dreadnought that was leading the Prophet of Truth's fleet to Earth. Cortana, who had to stay behind to manage the situation should Installation 05 be fired, was left in the clutches of the Gravemind, who could potentially learn all possible Human knowledge from her.

Earth, The Ark, and the Flood's defeat


At the conclusion of the Battle of Voi, with the Prophet of Truth activating the Portal and the Jiralhanae fleet escaping to the Ark, a Flood-infested Covenant cruiser appeared out of Slipspace, having penetrated the Elite's blockade of High Charity and crash landed into the city of Voi in an effort to spread. In order to prevent the Flood from escaping and infecting the entire planet, Miranda Keyes ordered John-117 to detonate the cruiser's reactors and search the ship for Cortana, causing the city of Voi to be destroyed and the Flood there eliminated. As John-117 and Thel 'Vadam fought their way to the ship, the Separatist Carrier Shadow of Intent under the command of Rtas 'Vadumee arrived and deployed Sangheili task force to aid UNSC marines. SPARTAN-117, with the help of the Sangheili, was able to battle through the Flood forces, including the newly encountered Flood Pure Forms to reach the crashed cruiser where he found a message from Cortana. Upon this discovery, 343 Guilty Spark arrived pledging his assistance to the Reclaimers. With the Flood spreading, SPARTAN-117 boarded a Phantom while the Sangheili went on to glass the infected areas. The remaining Sangheili forces, fulfilling their mission of removing the Flood from Earth, retreated back to the Sangheili carrier, the Shadow of Intent, along with Cortana's message and Guilty Spark.

With the assistance of 343 Guilty Spark, Cortana's message was repaired, revealing a solution to the Flood menace on the Ark. To Lord Hood's disapproval, Miranda Keyes led UNSC forces allied with Thel 'Vadam's and Rtas 'Vadum's Sangheili's through the Portal.

On the Ark, while the Sangheili and human forces were attempting to lower the shield surrounding the Ark's citadel, the infested High Charity made a Slipspace jump and smashed into the Ark, releasing the Flood inside the structure and causing an infestation on the newly built replacement for the destroyed Installation 04. The Gravemind made a brief alliance with the Master Chief and the Arbiter in order to stop the Prophet of Truth from activating the Halo Array. Once Truth was dead, however, the Gravemind promptly ordered the Flood to turn against the two heroes. The Chief and the Arbiter escaped, however, with some assistance from the Sentinels, who were able to help subdue the flood with ease.

After retrieving Cortana from the derelict High Charity, SPARTAN-117 was able to kill all Flood present on the Ark and the replacement Installation 04 by first destroying High Charity's reactors, causing a massive explosion and the destruction of the wrecked city, then activating the unfinished Halo using the Index Cortana retained from the first Halo. The ring's activation also presumably killed the Flood along with the Gravemind.

Aftermath
With the Gravemind destroyed, and all the Flood on the Ark gone, it is probable that the Flood still exist on the other Halo rings, excluding Installation 05 (which was sterilized by Sangheili forces) or any other remaining Forerunner Installations. The fact that the Flood are not originally from this galaxy further complicates the issue, and how and where they originate from leads to more possibilities. It may explain why the Forerunners preserved some Flood for research on the Halo rings instead of destroying them all, since the Flood would return sooner or later, and it would be better to fight a researched enemy rather than a foreign one. At least for the moment, the Flood are seemingly defeated.

Biology


The Flood is an anomaly in all known biology; their mode of growth and reproduction would make them incompatible with any natural ecosystem. They are extremely adaptive, and transform hosts to suit the species' current needs.

Capable of surviving extreme environments ranging from -75 to +53 degrees Celsius and even underwater (in early stages of life), the Flood can withstand the varied environments of all known colonized planets. However, the Flood seem to thrive the most in moist and humid areas, and it is thought that the extremely cold weather patterns near certain important areas of the Halo Array are intended to hinder the Flood. In order to give themselves ideal living conditions, the Flood will alter the environment to better suit their needs.

All Flood biomatter is made of a unique, undifferentiated "Super-Cell", which relays information and coordinates the cellular assembly like conventional neural cells. It is also capable of flexing and moving like muscles, and can be arranged to mimic any bodily organ that is required for the Flood's use. This combination of traits has earned it the analogy of "thinking muscle", due to its versatile nature.

The Flood Super-Cell physically resembles both neuron and glial cells in structure, with a central cell body and many tendril-like, branching structures.

Infection
In order to reproduce and grow in biomass, the Flood needs to infect and assimilate other life-forms. While capable of infecting nearly any organism, the Flood shows a strong preference for sentient life forms, as assimilating them allows the Flood itself to increase its overall intelligence.

Flood infection is typically carried out by specialized Infection Forms, which are the most complex forms that can be generated from Flood biomass during the Feral stage. Upon sighting a host, an infection form will leap for the most accessible area of the victim's torso; if the target is an armed human or other bipedal species, this is typically the left side of the chest below the neck, as most combatants will expose this area while shouldering their weapon. Upon contact, the Infection Form will rasp away at clothing and flesh until it has burrowed into the chest cavity. At this point, the Infection form extends tentacles that tap into the victim's spinal cord or other nerve center, paralyzing the victim and forcing a "match" with the nerve signals produced by the Flood form.

To begin the physiological conversion of a host, the Infection Form injects encapsulated Flood Super Cells into the victim. As it does so, the form analyzes the entire genetic code of its host, allowing the Flood to determine the most effective use of the victim. Simultaneously, the inserted Flood cells capture and break down the host's cells into organic raw material, which is then absorbed and assimilated into the attacking Flood cells.

The Flood infection then uses the absorbed biomass to create new masses of Flood Super Cells. As the flood continues to use the resources of the host body, particularly its calcium reserves, the parasite's own cells build upon and augment the framework of the host to produce one of a variety of Feral-Stage Flood Forms.

The infection process is not limited to living hosts; deceased organisms are also susceptible to infection. As long as the host has not decomposed to the point where the body and nervous system have completely deteriorated, the Infection Form can infect and convert the host.

The Flood infection utilizes the host's biological content as the fuel for its work, which is consumed and employed at prodigious speeds. From the beginning until the end of this complex, multi-step process, the Infection Form keeps the body alive by chemically isolating the host's brain, which is an essential part of the parasite's mission of consuming and converting the host organism.

Despite primarily relying on Infection Forms for acquiring host life forms, the Flood can infect hosts through other means. Flood spores, if inhaled in significant quantities, can transform a host into a combat form. Even the most basic form of Flood genetic material is virulent; once inserted into a host, it will mutate the host's DNA over the course of generations until it is capable of forming its own Flood super cells. . When infected by these secondary mechanisms, host organisms tend to mutate at a more restrained level that maintains the structure and form of the infected life form, albeit with a significant number of haphazardly placed tendrils, claws, and minor organs, such as sensory stalks.

Neurological
Infection forms selectively target other species that possess sentient intelligence and are of sufficient biomass, and can infest living or lightly wounded dead bodies. Infection forms have tendrils that pierce the skin of the host and find their way to the spinal cord. They then synchronize with the host's nervous system and gain control of their body, replacing its consciousness with the ravenous and voracious psyche of the Flood. Any useful information present within the host's brain, such as battle strategies and technical knowledge, is retaineed for use by the Flood. Despite this lingering of certain memories, no trace of the original mind's personality remains; only a simplistic and primal urge to assimilate other species drives the organism after infection.

In isolated cases, such as when the Flood seek very specific information from an individual's mind, they utilize an alternate, undescribed method of infestation that does not kill the host immediately; this allows the Flood to "burrow" into the host's mind, eventually giving them access to the entire scope of the host's memories. This has only been specifically seen when the Flood sought information from Captain Jacob Keyes, such as the location of Earth or a starship that would free them from Installation 04. In addition, if the Infection Form that initiates assimilation is extremely aged or damaged somehow, the host may remain alive and conscious; Private Wallace Jenkins suffered such a fate, remaining alive and fully aware of his situation despite the mutation of his form, even exhibiting limited control over his body at times when the Flood instincts were dormant.

If the Flood have amassed enough sentient hosts to form a Gravemind then their behavior becomes far more coordinated, and the Flood collective becomes much more deadly as a result. The Gravemind may also speak directly through combat forms and pure forms under its control.

Physiological
While baseline neurological assimilation is the same regardless of host species, Flood infection includes physiological transformations, which are species-specific.

Higher-level species capable of combat, such as Humans, Jiralhanae, or Sangheili are selectively infected to become Combat Forms. Combat Forms retain the overall profile of their original species, although they are significantly altered. Organ-based systems' physiology are corrupted, organ-specific functions are decentralized, and body cavities are decayed, making hitbox-selective incapacitation impossible; organ functions are decentralized, thus, decapitation does not down a combat form.

Furthermore, highly area-specific munitions, such as sniper rifle projectiles, are completely ineffective, as picking off selective areas of a combat form leads to no wide-scale physiological impediments, and the projectile will punch through the decayed flesh rapidly, exiting through the other side of the combat form without consequence.

Combat forms also generate tentacles very quickly without regard for the skeletal structure of the host, with tentacles protruding from the combat form at odd locations, typically localized to the chest axial regions, such as the neck, armpits, or torso. A single arm is oftentimes transformed into a claw-like or tentacle-like structure with multiple offshoots, with the remains of the host's manipulators, such as a hand, still attached, albeit pushed aside.

The majority of the host's musculature is replaced with FSCs' acting as muscles, which are connected to the remains of the original cardiovascular system. This bestows prodigious levels of physical strength to the new Flood form, which enable it to strike with devastating force, move with tremendous speed and agility, and jump to tremendous heights. The newly-developed forms are highly capable climbers, able to to move up and down and across most surfaces with tremendous ease.

The price for all of these formidable abilities are that the required metabolism is so rapid and extreme, that the host organism is rapidly broken down by the parasite as the infection continues to make use of its host. This is dramatically demonstrated by the rapid decomposition and disintegration of an infected life form, which will eventually become a stunted, bloated, mobile generator and incubator for more Infection Forms, which is commonly known as a carrier form.

The Flood sense their surroundings using specialized tentacles, which are tipped with red ganglia and usually protrude from the chest area of the Flood form (or head, in the case of Pure Forms). Exactly how these organs work is unknown; they may provide visual or chemical information, or perhaps a combination of both.

Countermeasures


There has only been one confirmed way to effectively stop a Flood infection without causing mass extinction, or after an infection form attacks a host. However, two possible exceptions are known. One of which is to contract the disease "Boren's Syndrome", a neurological condition where radiological exposure causes electrical anomalies in the host nervous system, similar to some of the effects caused by several biologically enhancing drugs used in the ORION Project, the precursor to the SPARTAN Program. In the case of both neural frequencies of the host are scrambled, apparently without major negative manifestations to the host. However, it has been suggested that during Flood infection, the infection form is unable to tap into the host's nervous system to kill and consequently infect them; therefore unable to proceed to a large-scale physiological mutation, although Flood DNA is sliced into host's DNA, apparently imparting the host with increased regenerative capabilities, although this has not been independently verified. Avery J. Johnson, having Boren's Syndrome, escaped the containment facility where The Flood attacked two squads of UNSC Marines. However the Boren's Syndrome was a story invented to cover his past in the ORION Project and the side-effects of his (experimental) enhancements, so the validity of each as a countermeasure against Flood infection is questionable. In the novel Halo: The Flood, Cortana uses an electrical charge which she generates from Master Chief's suit to destroy an infection form that was attempting to infect him.

While Boren's syndrome left untreated may leave the victim immune to the Flood, leaving it untreated usually equates to death within a couple of years. There is said to be a one in a billion chance that research, from someone so inflicted with Boren's syndrome in a way that they cannot be infected, could be carried on to produce a cure.

Since the Flood is a parasitic life form, they depend on other organisms for survival. Thus, the most effective way to stop a large-scale infestation is to take away their food sources. The Forerunners attempted this by bombing large population centers, but this was seen as one of their last resorts and as such was performed too late in the war to make much difference. The last resort was the use of the Halo installations, which destroyed all sentient life in the galaxy and starved the Flood into extinction. However, the Forerunners' plan included some measures to preserve sentient life and return them to their home planets, allowing the Flood's "food source" to persist. Unfortunately, at the same time, specimens of Flood spore cells were kept for analysis on the Halo Installations, possibly in accordance to the Mantle, allowing the threat of the Flood to be merely forestalled, not eradicated.

Environmental stimuli seem to have an effect on Flood metabolism. Halo installations typically artificially incorporate low temperature into environments suffering Flood outbreak and to create natural obstacles to Flood progress, regarded as Quarantine zones. At least one Flood Research Facility used low temperatures to keep its specimens inactive and dormant as it studied them. This may be the reasoning behind keeping Installation Control Rooms in low degree weather, impeding their occupation by the Flood. The Flood are also vulnerable to temperatures on the other end of the spectrum. Plasma weapons will burn through them, as well as Sentinel Beams, which were specially designed to counter the Flood, indicating that the Forerunners had determined energy weapons to be the best 'basic countermeasure' available to fight the Flood. It may be a side-effect of the Flood's conversion of the body into biomass, breaking down cellular integrity and increasing flammability. But even still, there has only been one method to defeat the Flood on a large scale effectively and with minimal losses.

The cure
During the Human-Forerunner wars, humanity (who at the time was a technologically advanced, spacefaring race) discovered another way to defeat the Flood. Using genetic engineering, a third of the human population was altered to carry a set of specially designed genes. This group of humans was then allowed to become infected by the Flood. Once the genes were exposed to Flood DNA, they triggered a cascade of cell destruction that spread throughout all Flood biomatter. The majority of the Flood died off as a result, although they would return in full force ten thousand years later. This cure was destroyed by the humans, considered as a final act of revenge against the Forerunners, leaving them unprepared for the second Flood strike.

Developmental stages
The Flood go through four distinct developmental changes.
 * 1) During the Feral stage, the Flood are at their simplest form: they communicate via pheromones and have the instinct to harvest enough calcium to establish a viable Gravemind.
 * 2) The Flood become truly dangerous during the Coordinated stage: at this point, they are controlled by the Gravemind that was created in the first stage.
 * 3) In the Interstellar stage, the Flood take control of space-faring technology which they use to consume the local star system. Subsequently, they spread throughout the galaxy to infect more hosts.
 * 4) The Intergalactic is the last known stage the Flood enters, theoretically, in which it utilizes all captured technology to depart to uninfected galaxies to further replicate. It is assumed that the Flood that had arrived in the Milky Way had descended from Intergalactic-level Flood.

Flood forms
The Flood is composed of a variety of specialized forms, each filling a different role in combat. The most basic Flood form is the infection form, which infects hosts by hijacking their bodies and nervous systems. Infected hosts then undergo a rapid series of transformations, becoming lethal combat forms. Combat forms are used to subdue and secure additional hosts for infection, and once they have outlived their usefulness as warriors, they transform into carrier forms, spreading the Flood by spreading more infection forms.

Once the Flood has amassed enough bodies to create a Gravemind, it is capable of generating "Pure" forms, which are created solely from assimilated nutrients and biomass. Pure forms can spontaneously mutate between three configurations: Stalker, Tank and Ranged forms.

The Flood at this point relegate the combat forms to defensive purposes or as additions to the biomass, calcium, and nervous system reserves of the Flood hive, and rely increasingly on the pure forms as their primary instrument of infantry force. However, in order for the pure forms to fully replace the combat forms, the pure Flood population must be large enough and in a state of equilibrium, which is in a constant state of flux depending on Flood gains and losses. Because of this, it is common for the combat forms to serve alongside the pure forms, in addition to the Infection and carrier forms, as the acquisition of hosts and technology would likely outstrip the speed in which the Flood can generate pure forms.

Combat behavior
While possessing an unusual sentient intelligence, with Combat Forms still retaining extremely high-level cognitive functions such as vehicular operation, traits such as dexterity and complex battlefield tactics are notably lacking in the Flood, especially in their psychological and combat behavior. While the Gravemind coordinates Flood strategy on a galactic scale, small encounters are not coordinated between individual Flood warriors.

The Flood's combat strategy is simple: they throw themselves at potential hosts in huge numbers and with any and all weapons available. Flood tactics are based primarily on asymmetrical warfare: the Flood uses all types of its different forms to kill the enemies that it sees. Infection forms swarm across the battlefield in waves, reanimating any corpses they can find, while Combat forms attack and kill any hosts in sight. Pure forms, if present, provide support to Combat forms in a number of ways: Stalker forms move to strategic positions and mutate into either Tank or Ranged forms, which can destroy enemy vehicles or fortifications or provide suppressing fire from afar.

The Flood have a strong preference for close-range combat: combat forms possess extremely powerful melee capabilities due to their specialized claws and tentacles, and are capable of dropping a SPARTAN-II MJOLNIR armor’s shields in half with a single hit. Carrier forms cause tremendous devastation at close ranges, and their explosions are extremely devastating to friends and foes alike at close range, with the added benefit of disseminating infection forms in the immediate vicinity of enemies. Infection forms are capable of attacking only at point-blank ranges, exploding in damaging bursts when meeting an opponent's personal energy shields or instantly grabbing hold of an unshielded enemy organism and infecting it. Combat forms can also use firearms, and have been seen clutching them in one of their hands (regardless of whether it is one-handed or two-handed). However, combat forms are extremely poor warriors at range with ranged weaponry: it is believed that the neurological ramifications of Flood infection significantly decrease accuracy, as well as weapon recoil if held in only one hand.

However, as mentioned previously, the Flood demonstrates a curious higher intelligence despite their poor combat aptitude and coordination. The Flood collectively learn any general information a species possess, even if only one member of that species is assimilated. For example, during the ill-fated raid on the Infinite Succor, after even one Sangheili was assimilated, all the Flood could open any doors and access any system on the ship immediately afterward, demonstrating that the Flood can share collective knowledge across their species. Furthermore, when the Flood assimilated the Prophet legate, the Minister of Etiology, the Flood reflected the high-level knowledge of the Legate through its individual organisms to Special Operations Commander Rtas 'Vadumee, mocking him with the words, "the Forerunner could not defeat us...what chance you?". The Flood, however, reflect unusual knowledge in the individual psychologies of its individual species in processes facilitating increased infestation: The Flood were sighted gathering bodies in the corners of the Covenant ship Truth and Reconciliation, perhaps making it easier for Infection Forms to find hosts to reanimate. The Flood were also gathering body parts for a new Brain Form aboard the Infinite Succor.

Flood Combat forms have been sighted crudely operating Ghosts, Warthogs, Wraiths, and Scorpions in ground operations, although with slow deliberation and clumsy driving and accuracy. The assimilated crewmen of the UNSC Frigate In Amber Clad were also able to initiate a Slipspace micro-jump for the frigate and perform rudimentary maneuvering of the In Amber Clad, navigating the frigate from the atmosphere of Delta Halo to High Charity and then crashing the vessel into a tower, releasing Pelican dropships to rain down upon the capital.

Notable victims

 * Minister of Etiology
 * Private Wallace A. Jenkins
 * Private Riley
 * Captain Jacob Keyes
 * Sub-Commander Bero 'Kusovai
 * Private Manuel Mendoza
 * Lance Corporal Eugene Yate


 * Prophet of Mercy
 * Prophet of Regret
 * Prophet of Truth
 * Bok

Changes from Halo: Combat Evolved to Halo 2

 * In addition to making low growls, the Flood make screeches and roars, which were not present in the first game.
 * Their skin is more textured, giving the Flood a more realistic and necrotic look. The faces of the human forms are also more readily recognizable.
 * If a combat form has both arms shot off, it will walk slowly then explode, releasing an infection form. This eliminated the Flood Buddy glitch.
 * Rather than having to "gather bodies," the Flood can seemingly infect hosts over the course of a few minutes or even a few seconds.
 * Rather than corpses reanimating themselves, an infection form will enter the body, then reanimate it.
 * If the player is attacked by an infection form while their shields are down, the character will die instantly. In Halo: Combat Evolved, it would simply take a bar of health away.
 * Some combat forms derived from Elites still have functional energy shields. However, they never possess active camouflage.
 * Flood combat forms can use vehicles, albeit clumsily and are also able to board the player's vehicle; they will then proceed to melee the player character.
 * Melee attacks do little to no damage against the Flood in Halo: Combat Evolved. They deal a bit more damage in Halo 2.
 * The Flood prefer to stay back and fire on the player rather than rush him. This could be because of the presence of the Gravemind, though, from a gameplay perspective, it is due to improved artificial intelligence.
 * In Halo: Combat Evolved a combat form would walk slowly when shooting at the player. When losing the arm that shoots, it would charge the player character. In Halo 2, combat forms either use a melee attack or shoot at the player in these situations.
 * If a player is wielding an energy sword or shotgun, a combat form may retreat. They will not do this if a player is wielding other weapons.
 * Unlike in Halo: Combat Evolved, shooting one infection form will not result in the rest of the swarm exploding with it. However, infection forms are encountered in proportionally smaller numbers in comparison to Halo: Combat Evolved.
 * Infection Forms appear noticeably less textured and detailed than in Halo: Combat Evolved.

Changes from Halo 2 to Halo 3

 * Brutes may now be infected and transformed into combat forms.
 * Melee attacks and plasma weapons were nearly useless against the Flood in Halo: Combat Evolved and Halo 2, but now can be used effectively against the Flood. The Flood are much more vulnerable to ballistic weapons, as well.
 * Infection forms can mutate humans and unshielded Elites and Brutes into combat forms within seconds.
 * Pure forms are introduced.
 * Combat forms wield weapons far less frequently than in Halo: Combat Evolved and Halo 2.
 * Carrier forms release significantly more infection forms when they explode. The explosion does not push the player away much as in Halo: Combat Evolved and Halo 2. In addition, carrier forms are significantly more difficult to kill with projectile weapons, but they are easily destroyed by plasma weapons.
 * Running over infection forms while driving a vehicle can result loss of steering and possibly overturning of the vehicle. Any infection forms that are hit by the vehicle will not pop.
 * Flood combat forms can no longer commandeer vehicles, like they could in Halo 2.

Changes from Halo 3 to Halo Wars

 * Infection forms no longer push back the heads of their Elite victims; it appears as though the Flood actually use the hosts' heads. In addition, combat forms have more tentacles than before; they resemble spikes rather than flexible appendages.
 * Grunts and Jackals can be converted to combat forms.
 * Infection forms do not explode when they are shot in the cinematics.
 * Several new forms created from creatures indigenous to Shield 0459 are introduced.
 * Carrier forms do not always explode upon death.

Miscellaneous

 * The Flood's AI routines in Halo: Combat Evolved was originally intended to be "every bit as complicated as the Covenant", but full implementation was prevented by time constraints. The final, simplified behavioral responses were later explained as part of the Flood's overall coordinated strategy.
 * Part of the Flood's Binomial nomenclature, Inferi, is Latin for "The Dead", and could be a reference to Roman mythology, as this was their name for the Netherworld and its inhabitants. Inferi means 'The Dead' and Redivivus means 'renovated, reconstructed, rebuilt or recycled' so literally Inferi redivivus means 'The Dead Reconstructed'.
 * In Halo: The Flood, John-117 was attacked by an Infection form while his shields were low. The Infection form had slit the under parts of his armor, exposing his neck, and almost tapped his spinal cord. If not for the quick use of an electrical shock by Cortana to kill the form, John would have been infected like many billions before him.
 * In Origins, during the scenes in which the Flood attacks the Forerunner planet, there appear to be many types of Flood, from very large, near-Gravemind-like ones that could level buildings, to flying versions of Infection forms. In addition, some of the variations seen in Origins are based on concept art for the original game. One explanation for this may be that the Flood had acquired many species. Another explanation may be that the Flood had grown so much, and the Gravemind was so powerful, that it could create Pure Forms for whatever purposes he needed.
 * There is a species of fungi that is frighteningly similar to the Flood, the Cordyceps unilateralis. They attack carpenter ants and take over their neural system in order to make the ants go to high places. By the time it gets there, it's been rotted from the inside out like a Flood host and it releases spores from that vantage point.
 * The Flood seems to be the reason for the "Gore" label on the ESRB rating. All three games of the Halo trilogy are rated for "Blood and Gore"; But Halo 3: ODST, which uses the exact same engine as Halo 3, is only labeled for "Blood", as the Flood are one of the only absent enemies. Halo: Reach is also rated for "Blood", as the Flood were absent.
 * In a PC World article, the Flood was voted as #31 of the top 47 "most diabolical video game villains of all time."
 * The Flood was named #45 on IGN's Top 100 Videogame Villains list.
 * The Flood was named #77 on Wizard Magazine's list of the Top 100 Greatest Villains of All Time.

List of appearances

 * Halo: Combat Evolved
 * Halo: Combat Evolved Anniversary
 * Halo 2
 * Halo 3
 * Halo Wars
 * Halo Legends
 * Origins
 * Iris
 * Halo: The Flood
 * Halo: First Strike
 * Halo: Ghosts of Onyx
 * Halo: Contact Harvest
 * Halo: Glasslands


 * Halo: Evolutions - Essential Tales of the Halo Universe
 * The Mona Lisa
 * Human Weakness
 * Soma the Painter
 * Wages of Sin
 * The Forerunner Saga
 * Halo: Cryptum
 * Halo: Primordium
 * Halo Graphic Novel
 * The Last Voyage of the Infinite Succor
 * Breaking Quarantine
 * Halo: Blood Line