Thomas, and his friends who are still alive, have escaped being WICKED's lab rats. Finally free to roam Earth as they please- since it basically belongs to them now- and start a new civilization of immunes. Gally had joined them, and was still with them after WICKED's lab had been exploded by the Right Arm. Now their real journey began after rough times, and huge sacrifices, practically the whole human race was to die. Every last non-immune would eventually die if they weren't yet, because natural selection just has to rule out, sadly.