Flood

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The Flood (sometimes called The Parasite by The Covenant) is a species of virulent, parasitic organisms that thrive by consuming other sentient life of sufficient biomass.

Infection Form
It exists on multiple levels of organisms, the highest the Flood can conjure is the Infection Form without using other bio-mass. This form, while harmless from a distance and on its own, is dangerous in large numbers and can therefore compensate for its fragility with numbers and overwhelm larger creature[s]. They are able to infect any large (and smart enough) organism by latching onto it and penetrating down to its nervous system with tendrils and releasing spores. The Flood forces a match with the host's brain levels and can begin to control its bodily functions. The Infection form then deflates it self and nestles within the relative safety of a host's body cavity. Their spores begin to alter the host, using its calcium stores to conjure additional flood super-cell biomass, and change the genetic structure of the host's anatomy, mutating and growing tentacles and whatever else is of use.

Combat Form
Taking control of the host body, the victim becomes a Combat Form of the Flood. Usually only strong host bodies are taken over. A weakened Combat Form may be used as an incubator for additional spores and more Infection Forms. Weaker races may also be used for Incubators - namely Grunts.

In Halo 1, a Flood Combat Form could be incapacitated by shooting off both arms, then killed with a headshot. In Halo 2, however, shooting off a Combat Form's arms resulted in the Infection Form coming out of the Combat Form's chest, then attacking you; making it extremely difficult to pacify a Combat Form for study. This does, however, get rid of the Combat Form. In Halo 2 you can instantly kill a Combat Form by shooting at it's chest, where the tendrils come out. You will know that you have a perfect shot when the crosshairs turn solid bright red and a small red dot appears in the center. This destroys the Infection form, leaving only an empty shell of a corpse. You may have to do this multiple times, though, even though it may appear like you have a perfect shot. This also can be done with Sniper Rifles or Beam Rifles, but it is very hard to do so. Shotguns do not work, since they kill it anyway. This is best done on Sacred Icon (Level) with a Battle Rifle.

Carrier Form
When an Infection Form takes over a body that is unsuitable for combat, or once a infected form is damaged beyond usefulness, it becomes a Carrier Form. Eventually when a Combat Form has lived long enough, it too will mutate into a carrier, regardless of damage taken. Carrier Forms perpetuate the Flood species by acting as incubators for new Infection Forms and keeping them safe until they're fully developed. Once the Infection Forms are ready, the carrier simply explodes spontaneously, sending the new Infection Forms flying into the air. As soon as they are released, they begin searching for new hosts.

Brain Form
The Brain Form is an uncommon Flood type. The Brain Form is a type of Flood unlike all the others in that it lacks any sort of mobility. While the Infection, Combat, and Carrier Forms are dangerous and always hostile, the Brain Form is passive in a tactical sense. When the Flood attempt to control a starship or interface with a computer system, the Brain Form is used.

It is suspected that the observed Prophet Forms and Gravemind are types of Brain Form.

History
Next to nothing is known about their origin. Some have suggested that the Flood were a weapon of mass destruction that grew beyond their masters' ability to control (Note this has recently been disproved by Joseph Staten [cinematic lead of halo & halo 2]). Others think that they are some kind of primitive life form accidentally discovered by the ancient Forerunner race. Many also think that they were a Forerunner attempt at cloning or resurrection. Others believe it was an early attempt at creating a super weapon. However, their destructive ability is not to be doubted.

The Flood were kept by the Forerunners for scientific study on the Halos. Although the intention was to wipe out the Flood by destroying everything of significant bio-mass, therefore starving the Flood, the fact that they still exist indicates that the Forerunner's plan may have failed.

Assimilation
Flood take over the bodies of hosts and assimilate them into Flood. This is done by the Flood Infection Forms. Infection Forms have a long tendrils that pierce the skin of the host and find their way to the spine. They synchronize with the host taking over the brain functions to prevent resistance or cries for help. After this time, the original mind is erased memory by memory, till nothing is left but a "hungry" flood form. Separate tendrils release aggressive Flood DNA into the host, causing the body to mutate into a Combat Form or a Carrier Form.

They use the Combat Form for the most obvious reasons, to have a "military" to attack and later capture more able bodies. The only known way to effectively stop a Flood infection is to have Boren's Syndrome, the radiation-caused disease that Sergeant Major Avery J. Johnson has. Boren's does not completely deny the infection, however, which is proven by the fact that Johnson has an increased, but still limited, regeneration ability.

Of the many species in Halo, only two are known to produce fully matured Combat Forms; the Humans and the Elites. The Grunts are believed to be mutated into Carrier Forms because they are too small and weak to be effective as Combat Forms. While there has been no evidence as to why the Flood have not shown assimilation of other species, many theories abound. Jackals are believed to have a too porous, bird-like bone structure. Brutes are believed to lack sufficient neural function. Drones are also supposedly ignored for their deficiency of calcium. Some believe that the Flood have certain "tastes", similar to those of Humans. Hunters cannot be successfully assimilated by the Flood due to their bodily makeup consisting of multiple, possibly hundreds of invertebrate entities. It is speculated that other, larger races, such as Drinol become larger Flood organisms, such as Flood Juggernauts, but neither of these creatures has been encountered by humans yet. It is also possible that the Flood has, in fact, assimilated these species, but has yet to exhibit their respective "Forms". The lack of any corpses of any kind after a Flood attack adds even more suspicion as to the real abilities of their assimilation process.

Halo: Combat Evolved and Halo 2
Though the Flood can survive in environments that are suitable to both Covenant and Humans, they prefer to alter it to their own preferences. This happens when the Flood release deadly spores that only they can breathe. Only someone wearing a gas mask or other protective garment can survive through the change. The Flood can alter the atmosphere and thus the planet transforming it so non-Flood life forms cannot survive and thus they become easy prey for the Flood. After the Flood was released on Halo they began to change it, but thankfully they did not succeed.

The Flood are a very intelligent race. They gain the knowledge of the hosts they infect. In addition, they are under the control of the Flood "puppet master" Gravemind (this is revealed in the Halo 3 plot summary on bungie.net). The UNSC, tends to use firepower rather than numbers, preferring a tactic of using a few strong, well trained units, with a lot of firepower, to achieve their goals. The Covenant, tend to outnumber and overrun their enemies, relying more on the bravery and courage of their loyal soldiers rather than pure firepower. The Flood on the other hand have no obvious strategy. They fight without fear of death or injuries, as a lone Combat Form will sometimes sacrifice itself for the further case of the whole. They attack by finding a group of enemies and send everything they have with whatever weapon they have, sometimes no weapon at all. They seem to prefer close combat. Their poor weapons skills make them poor shots. But they have powerful whipping tentacles that cause great damage at close range. They also have been known to kill their own by accident. They can do this and not worry, as disabled Flood bodies can be reanimated by Infection forms. Dead Flood can only be permanently disabled by being completely destroyed. Methods of destruction can be high-powered explosions, the form taking too much damage, high-speed collisions with vehicles, sharp objects like the Sword, extreme heat, decomposition, or, once it is dead, shooting off both of its arms to prevent reanimation.

Halo Graphic Novel
It should be noted that the Flood assimilation and behavior in HGN was somewhat different from the games. It is stated by the Legate that the Flood is mentioned in the holy texts of the Forerunner and they are one of the tests before the Great Journey. He also stated that the Flood were gathering bodies and body parts,giving them to the larger organism which demonstrated some form of intelligence and the general consumption of animal matter. This is similar to the events in Halo 1 where the Master Chief boards a Covenant ship to find Captain Keyes. Cortana notes the Flood are gathering bodies and it is most likely for the Brain Form that was found on the bridge.

Also, the rate of infection in the Covenant forces was extremely fast. Within minutes of contact, many Elites and Grunts were mutated quickly into Flood forms. The mutations occurred randomly and were not uniform in any way. Sometimes the Elites were transformed into larger forms than the Combat Form. Other times they developed a Flood-like carapace and on many occasions on the Infinite Succor, the Flood used tentacles as their primary weapon similar to the Gravemind. However, when Rtas 'Vadumee battled his comrade Kusovai, Kusovai over the duration of the battle continued to mutate, suggesting the possibility that over time any infected host can mutate further and further.

In addition, the Flood can instantly absorb knowledge from an infected host into their collective mind. When Rtas's teammates were assimilated, the Flood could open any doors and access any system on the ship right after the teammates were assimilated. When the Flood then assimilated the Legate, the Flood reflected the knowledge of him to Rtas while he was in engineering, mocking him and stating that that "The Forerunner not defeat us...what chance you?" It would appear that the threat of the Flood is far greater that previously assumed.

Trivia

 * Another form of Flood dubbed the "Flood Juggernaut" was intended for Halo 2 but cut out at the last minute. The Juggernaut's attack and movement profiles are still in the game, as is the model.
 * The first known Human to be infected by the Flood was a UNSC Marine named Private Riley.
 * An error in the flood animations in both Halo and Halo 2 is that Combat forms are always seen wielding two-handed weapons, such as the Shotgun, with one hand, and never seem to need to reload them. Just like other AI, the Flood never run out of ammo.