The Other Experiment
On the way back to Bureau, Tris, Amar, George, and the others find an body of an young boy with blonde hair, who has an bullet wound in his head, but, he's alive.
They were lied to. It wasn't an war that caused the experiments, it was the sun, and then then an deadly virus.
The difference is, they wanted to test what makes them Immune, Wicked tested them for the cure. The genetically cured is the immune.
The Flare never reached Illinois, making it safe for the non immunes, but that doesn't mean that there aren't cranks.
When Newt wakes up in the Bureau, he's confused, why would these people save him? Why was he alive, and where are the gladers?