The Killzone is a word for the brain which was adopted after the Flare started infecting the people of the world. It is slowly eaten away at by the disease, turning the infected, known as Cranks, into madmen. WICKED is trying to use the patterns in the Killzone of those immune to the Flare to develop a cure, so they send a number of immune "subjects" into the Trials to obtain these patterns.
The drug known as the Bliss can limit the Killzone's activity. Since the Flare eats away at the brain more if the brain is working harder, the Bliss slows it down. However, this way that the Flare works turns out to be worse for Thomas' friend, Newt, who is not immune. Because of all the stress caused by the Trials, the Flare has eaten away at his Killzone much faster.