The disease

The disease, also known as the sickness, is the cause of the disaster. It affects people roughly over the age of fourteen (or sixteen if reading the US version). It is unknown for certain how the sickness works but, it's likely that it is a parasitic infection. Children under sixteen are not infected because they were not born when the parasites were in their "spore" stage and spread across the world.

The Disease
The disease is a parasite that controls its host. Real-life examples of this can be found here on Earth that operate in similar ways. The disease spreads by spores (eggs) in the bloodstream.

History of the disease
Throughout the books, the origins and history of the disease is hinted at in many ways.
 * It is likely the disease originated from space. Diseased characters such as the Green Man refer to themselves as "a fallen star". This makes sense as such a deadly and intelligent disease would surely have been detected already. As well as this, the disease seems to already be highly evolved, despite having little contact with the world. Suggesting it had a long evolutionary history on another planet.
 * The disease made its way up the food chain after it made first contact, infecting fleas, bats and other mammals. It is hinted at that the disease is thousands of years old.
 * The Inmathger were an isolated human tribe in South America. It is presumed that the Inmathger are infected, but do not show symptoms of infection. Or else their tribe would have been destroyed. One possible explanation is that the disease had not evolved to the point it could control humans when it had infected the Inmathger, and they built up an immunity as the disease evolved, which the rest of the world did not have(save for cases of natural immunity).
 * 15 years before the outbreak of the disease, researchers from Promithios Biomedical discovered the Inmathger tribe, the disease spread from the possibly immune Inmathger to the researchers, one of which was Mark Wormwold, The Green Man.
 * Now in a new domain, the disease began spreading from London, all the way across the world, within two years, almost every human on Earth was infected. But the disease was smart, it disguised its cells as human cells to avoid detection from the medical world and from the body immune system. This level of intelligence and adaptability is practically impossible, further suggesting this disease originated off-world.
 * The researchers who were first infected would go on to have the Twisted Kids, theses kids were all mutated. It is suggested that this was an experiment by the disease in merging human cells. The disease warped the minds of the researchers to hide the children away, and thus, keep its existence a secret.
 * After infection, the disease entered a hibernation-like stage and stopped spreading. Fourteen or so years later, the events of The Enemy begin.

Intelligence
The disease has a level of intelligence that is impossible for such a small creature to have, there are some explanations.
 * 1) The parasite uses the human hosts brain as a machine, using its processing power to boost its own learning. This would explain why infected can "hear" the disease and sometimes talk as if they were the disease as a person. This would be the parasite appropriating the brains of infected for itself.
 * 2) The disease operates as a hive mind, using the brain power of every infected individual to create a vast intelligence.
 * 3) Being an alien organism, we do not know how smart the disease is on its own. Given that somehow the parasite can remember its own evolutionary history, and an understanding of how to hide itself and its adaptability, it is likely the disease is quite intelligent on its own.

Events of the Series
Over the course of the seven books, the parasite enters the final stages of its life-cycle.
 * After fourteen years hidden inside its human host, the parasite awakens. Firstly, infected are turned into brain-dead husks of themselves, who crave kids flesh because its the only thing that holds back the infections. It should be noted that the parasite would rather the kids stay alive to be its next host, but it is the blood of children that the infected crave as it brings them temporary relief from the disease.
 * Over the course of the two years of the series. The parasite grows stronger and smarter. It established a subsonic communication network that can be audibly heard if enough sickos are present. All infected can hear it; including Paul, Matt and Wormwood. The Twisted kids can even communicate with the sickos.
 * The events of the book all revolve around the parasite getting ready for a new burst of spores, though the infection can still spread from a bite (this is a plot hole). The parasite chooses two sickos (St. George and an unnamed woman) to lead an army of sickos together to spread. By this point, the parasite has grown from being microscopic to an insect sized creature, suggesting the life cycle goes; Eggs, parasite, insect.
 * St. George's Army is all killed and burned, preventing the disease from spreading or reproducing, Small Sam's blood acts as a cure, ensuring the disease can have no new hosts and will eventually go extinct.

Stages of the disease:

 * 1) Basic fever symptoms such as cough, cold, blemishes, tonsillitis and a mild fever.
 * 2) Blistering, swelling, boils, black nails, yellow eyes and grey skin. Loss of self control also occurs at this stage.
 * 3) Burst eyes, warty tongue and a unrecognisable body. The disease causes necrosis and disfigurement.
 * 4) Rupture of skin and organs, accelerated decomposition and necrosis and ultimately death.

Sunlight
The disease is made worse by sunlight. It is revealed in The Fear, that when an infected adult is exposed to the sunlight for a long period of time, the disease spreads faster and makes the victim explode, also revealed somewhat in The Enemy. Some sickos can gain a resistance to the effects or wear things such as sunglasses to lessen the effects of sunlight. Most likely, the parasites are affected by strong UV radiation having past generations lived previously under a dense canopy in the rain forests.

Flesh
In The Dead, it is described that eating children's flesh can make the sickness spread slower. Greg eats what he describes as "smoked meat", although it is really children's flesh. Drinking children's blood has a similar effect. Sickos have a clearness of mind after eating kids. In later books, Wormwood explains that good blood will drive out bad blood. A few surviving children were born with an immunity to the disease and their resistances are key to making a cure.

Telepathy
In The Sacrifice, it becomes clear that people with the disease can communicate via telepathy or ultrasound. It is possible that the parasites are the cause of this. The frequency that is emitted by sickos is a high whining sound that only the girls could hear in The Sacrifice. In The End, another louder sound is emitted by Paul while communicating with other sickos. Some sickos host stronger parasites and draw crowds of other sickos together with a hive mind. In The End, Fish-Face says that she and her father nearly share a mind and can read each others thoughts.

The Green
The two stronger and more "sane" sickos (Wormwood and St. George) are obsessed by a great green and become convinced that they are angels that have been friends with wildlife. Their confused ramblings give an idea as to the origin of the disease. It may have originated from space as they say they fell from the sky and are fallen angels. The disease then worked its way up from fleas to birds to mammals and humans. (In The Enemy, the monkeys in Reagent's Park are also affected.) They existed in the green, which was the jungle. An important thing to mention is that Wormwood and St. George both have split memories that they confuse. The past lives of the parasites and their own lives often get mixed up. The parasites might therefore have their own sort of self awareness or intelligence.

Unanswered Questions
There still remain a few key unanswered questions about the parasite. Whilst some of these are actual plot holes, other maybe nit picky and unimportant.
 * How does a bite infect someone with the disease if the parasite was said to have stop producing spores?
 * A parasite spreads eggs, not spores.
 * Why do all the sickos need to be together? If it was to kill Small Sam, why do they not all go to him?
 * How do the sickos survive starvation and other diseases?
 * Why is Matt not attacked, is he immune?
 * What about the rest of the world? Did any other grown ups release their spores?
 * The full life cycle, would be seventeen years, not sixteen, including a year of spreading around the globe.