A origem do Flare ainda não foi mostrada no filme. Bits e pedaços da história foram mostrados, mas não uma resposta definitiva ainda. Será revelado em Maze Runner: The Death Cure em 2017.
Spoilers ahead: Nos livros:
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".
Quanto ao que faz:
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).
Não, não há lagartos ou parasitas envolvidos. Especialmente não Vampire Parasites como The Strain . Série de Distopia Adolescente, não Adolescente Vampiro / Horror Mitológico.