Flood

Spoiler warning: Plot and/or ending details follow.

The Flood is the collective term for a species of parasite (or more accurately, an omniparasite - as they can infect any species of sufficient biomass) that was discovered on Installation 04 (Halo) and are now known to inhabit Installation 05 (Delta Halo), as well as the Covenant City of High Charity, and Covenant gas mining installations around the gas giant Threshold, and Threshold's satellite Basis.

The Flood first appear in the level entitled 343 Guilty Spark of Halo: Combat Evolved. This level begins in a swamp which was the last known location of Captain Jacob Keyes. In fact, that's who Master Chief is trying to locate, at the behest of Cortana who tapped into Halo's control system and discovered that Keyes was about to stumble upon something vicious and uncontrollable.

Well Enough Alone
As the Master Chief begins his trek through this swamp he runs across a crashed human ship, and very nearby a crashed Covenant drop ship. You also run into a few straggling Covenant Grunts and Jackals who are panic-stricken and running from... something.

Being naturally curious, the Chief goes in the direction from which these Covenant are running. After all, "the enemy of my enemy is my friend," right?

Wrong.

Master Chief locates a structural entrance into some sort of base which delves pretty deeply into the crust of Halo, and after a few elevator trips downward, you start to notice that it's gotten very quiet. Too quiet. There is almost no human or Covenant presence, but plenty of human and Covenant viscera. Master Chief (MC) locates a sole human, who is quite obviously suffering from the effects of post traumatic stress disorder, and he begins to shoot at MC, and utters the cryptic phrase:

"Stay back! You're not turning me into one of those... things!"

Unfortunately, the Master Chief had to eliminate this unknown screaming marine. As he continued deeper, he discovered PFC Jenkins, who fell into the his arms and immediately died. We are then introduced to The Flood by way of Jenkins' helmet recorder, which provides a video detailing the final moments of Jenkins' life.

The Flood
It is at this point that the game of Halo irrevocably changes. The Covenant are still your primary enemy - but with the introduction of the Flood, they are often distracted, as they are also battling the Flood. Also the orderly combat formations in which you've thus far been engaging (One or more Elites commanding packs of Jackals and Grunts) become chaotic and frenzied.

The Flood appear as alien zombies. They are, in actuality, parasites (not unlike the Head-Crabs of Half-Life), which worm their way into their hosts' nervous systems, and spawn whip-like appendages, which are used as weapons. They are incredibly agile and they lack the capacity for pain, and are completely negligent towards the integrity of their host bodies. This makes them incredibly strong, fierce and reckless.

What makes the Flood so disturbing is that they are not evil, nor are they fueled by zealotry or conquest - as are the Covenant. Their only desire is to feed and reproduce. They are parasites, nothing more.

However, midway through Halo 2, they appear to be evolving into something more: they appear to be displaying heretofore unseen intelligence, displaying knowledge of vehicle and tactical aircraft operation. Of course, they are remarkably careless and haphazard in their control of vehicles - they will grab any vehicle that moves, direct it toward a potential host, and jump out of the vehicle at the host, leaving the vehicle to careen wherever it will. This includes flying vehicles as well.

The Flood are not typically known to be careful or orderly in anything they do.

Flood Varieties
There are several flavors of the Flood:

Infection Form
Presumably, this is the Flood at its basest form. They appear as little scurrying pods. They are very vulnerable to physical attack (one shot from a simple pistol is enough to wipe out several, or you can simply squash them by running over them), but they compensate with sheer numbers and speed. When attacking en masse, they look like a wave of pods bearing down on you... thus the name The Flood. These are the creatures that actually infiltrate a Human or Covenant body and turn them into a Warrior or Carrier.

Infection forms can regenerate fallen warrior forms. This doesn't happen in Halo 1, but in Halo 2 you can sometimes watch infection pods slip into fallen warriors to get the corpses back into the melee.

Warrior Form
The Warrior form are the most dangerous. They were once humans and Covenant Elites who have been killed and overtaken by the Flood. Their heads lie limply and uselessly to the side and the arms are used only to heft weapons. Their primary appendages are whip-like branches which poke out from the host body, as do the sensor stalks, which the flood use to "see" their enemies. These whip-like appendages are also used as weapons to slap any Covenant or human that dares interfere with it. The Flood in this form are capable of superhuman (and supercovenant) strength. They can jump unbelievable distances, they are extremely fast, and they pack heat. The upside is, they do not notice when you throw grenades at them. They are not terribly bright, and they do not work cooperatively with other Flood. A shotgun blast is enough to drop one. But be careful, they oftentimes get back up after you think you've killed them, and they whip you from behind.

Carrier Form
Waddling meatballs that explode. Jackals and Grunts do not impress the Flood. Therefore, they don't use these creatures as combat units. Instead the Flood use them (and also humans who are too damanged or weak to be combat effective) as spore/infection dispersal units. They appear as huge waddling sacs. When they are damaged or when they get close to a potential host, they drop and explode, sending Flood Infection and gray-green liquid everywhere. The explosion is as effective as a grenade blast, should you be unfortunate enough to be near one that blows up. This is apparently the Flood's primary method of reproduction.

Pilot Form
Only one of these appear in detail throughout the games - At the end of the level entitled "Keyes" in Halo 1. However, near the end of Halo 2, though, you see this form attached to bulkheads in ships and all over High Charity near the Forerunner ship. This flood is different in that it not mobile. It doesn't even appear to be sentient. But these flood absorb some knowledge from their host-minds, allowing them to learn how to pilot aircraft.

Master Chief's first encounter with this form of Flood was during the rescue operation of Captain Keyes. Unfortunately, Keyes is beyond rescuing. When MC locates Keyes in the steerage of the Covenant Ship, The Truth and Reconciliation, Cortana notes that there are "No human lifesigns present. The captain, he's one of them!" He appeared to be a massive pulsating Carrier with a human(ish) face poking out of the front, and attached to the helm. Unfortunately Keyes had tactical data implants in his head (presumably this is why he was saved as a Pilot, and not turned into a Warrior, Carrier or left to rot where he fell), and they could not fall into enemy hands. So the Master Chief did what he had to do, and removed the implants through Keyes face.

Gravemind
A seemingly unique form of flood, the Gravemind is an enormous Venus Fly Trap looking creature that speaks with a loud resounding guttural voice, and forces the Master Chief and The Arbiter into an alliance. He's also taken The Prophet of Regret hostage as well as 2401 Penitent Tangent (Monitor of Installation 05, which is 343 Guilty Spark's counterpart). The Gravemind does not look like or act like any other flood - and the only reason we know that he is Flood is because The Arbiter refers to him as such: "Kill me or release me, Parasite, but do not waste my time with talk!" (The Convenant refer to the Flood collectively as "The Parasite") The Gravemind's true nature is currently something of a mystery, but my theory is that he's some sort of "central" flood mind, like the Borg-Queen. However, the Flood act like individuals who are unaware of other individuals. They do not cooperate with each other, nor do they act as a unit. So a hive-mentality would definitely be a contradiction to what we know of the flood so far.

Perhaps the reason the Flood are dangerous enough that the Forerunner would actually build the galaxy-destroying Halos is because these Gravemind creatures unify the flood into unstoppable juggernauts.

Further bulletins as events warrant
Some Covenant were not soon as infested in Halo 2. These were two new species revealed to be in the Covenant forces: Drones and Brutes. Drones are insectile creatures which can fly and wield weapons, and Brutes are incredibly strong.

However this can be explained, easily enough: The Brutes are simply too strong for the Flood to kill, and their hides are possibly too thick to penetrate even after death. There is one cut-scene where the Flood launch an attack on the Covenant Hierarchs only to be destroyed by the Brutes.

In the case of the Drones, other than their ability to fly, there's not much too them. They are extremely weak and vulnerable. The only value they could provide to the Flood would be "air superiority", but given the Flood's lack of fine motor control within their hosts, they probably couldn't operate the wings adeptly enough for lift-off.