Maze Runner spoilers. Skip it if you haven't finished the series.

Newt's death was fake.
WICKED knew that he was not immune, so they took him the night Teresa was taken.
Teresa was placed with Group B, whereas Newt stayed in WICKED's compound safely.
In Newt's place was an avatar like the ones Little Pete and the Gaiaphage created because why not?
The Avatar was programmed to look and act as Newt, to respond the way he would respond, while the real Newt was locked inside of a white room in solitude.
The real Newt was never exposed to the sickness. The avatar however was and was killed by Thomas.
Before the Gladers went to the safe haven, Newt was transported there. Most of the Gladers made it there safely with the exception of Teresa and a few others.
Newt met up with Thomas and Minho and was astonished that Thomas had a new bloody girlfriend. Not as astonished as Thomas was to look at his living friend.
The Gladers lived happily together in the Safe Haven.
THE END!
DONT ANYONE QUESTION IT
If anyone mentions page 250 again I will kindly show them this and point out how wrong they are.
Now clap.
Thank you.