In the Maze Runner film series, what is the origin of the virus?
How does the virus affect a human?
Does it create a reptile inside the body, like in The Strain (2014) tv show?
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The origin of the Flare has not been shown in the film completely yet. Bits and pieces of the story have been shown, but not a definitive answer yet. It will be revealed in Maze Runner: The Death Cure in 2017.
Spoilers ahead: In the books:
The Flare virus was created as a means of population control by the World Government following a geological disaster (solar flares/sun issues) that results in widespread geological damage (entire sections of the Earth have been turned into deserts due to extreme heat, including Chicago that the Scorch Trials revolves around), but the virus got out of control. The world government blamed the Solar Flares for the virus and rage zombies, hence the disease was called "The Flare".
As to what it does:
The Flare eats away at the Killzone area of the brain. This results in Cranks, the rage zombies that we see in Scorch Trials. It damages the body, and the mind, driving people to become insane cannibals. The immune, most of the kids we see in The Maze Runner and Scorch Trials, produce an enzyme in the Killzone area of the brain that kills the virus. This is why they are being studied, pushed, and (in the movie, harvested for that blue liquid)/(In the books, they are looking to find the most immune kid, and cut open the brain to study how it works to find out how to duplicate the cure).
No, there are no lizards or parasites involved. Especially not Vampire Parasites like The Strain. Teen Dystopia series, not Teen Vampire/Mythological Horror.
I agree with N.Teen, The Flare virus was engineered by the founder of World In Catastrophe Kill-zone Experiment Department (WICKED) in an attempt to control the human population because there was so many people dying, the founder says that the virus was supposed to wear off after a while but the virus got out of control and now only the immunes can stop it before the virus kills all of the human species. Nothing mentions on how the immunes were suddenly 'immune' to the virus, and the number of them is massive, it is like as if it is an experiment to see who is strong enough to withstand the heat, this basically indicates that if they can survive the Flare virus, they can survive the heat, but that got out of control so they are now killing and experimenting on the immunes. Why this happens is not explained, but this is my interpretation of the origin of the Flare Virus.