In the final book of the Maze Runner trilogy, we find Thomas once again held by WICKED. They tell him that not all of the Gladers are immune to the Flare. Thomas and his friends leave WICKED and go to Denver to try to find a way to take down WICKED and also get their mind control chips removed. They find out that WICKED initially created the Flare as some sort of crowd control virus once the sun flares wreaked havoc on the planet. They believed that there weren’t enough resources to sustain all of the life on Earth, so they created the flare to kill off a portion of the population. They believed that the flare would spread quickly and kill quickly but that it would also die off leaving no lasting repercussions. The flare lasted much longer than they initially anticipated and that is why they have been looking for a cure.
In the end, they realize that there will never be a cure, so the immunes all leave and start a new world away from WICKED.
It was a great trilogy but ended on a sour note. The entire time we are hoping that they finally get a cure to the flare so that they can cure everyone that is infected. We are left with there being no cure, everyone that is infected is doomed and they need to start over.