A Red Sun Rises. The New Earth Trilogy, #1

Nine years ago, an unknown poison called the "Red" saturated the atmosphere of the entire planet, killing off everyone except a remnant of immune survivors. Jake is a survivor, but the Red has left its mark on him, changing him in strange ways he does not understand. The answers to his questions, however, will not be found inside the gated confines of his small community. The immune are not the only survivors.
A handful of non-immune scientists and their families also escaped death by retreating inside a giant underground bunker called the Hole. Unable to breathe the outside air, the inhabitants of the Hole search for a way to fix the air. Seventeen-year-old Paige grew up in the Hole. Its concrete hallways and chambers are all she knows. Trained as a medic, she works with her father to find a way to cleanse the atmosphere and restore the balance of nature.
Paige and Jake live in different worlds, each seeking answers that seem impossible to find. Everything changes when their lives collide in a chance encounter. Paige realizes that Jake may hold the key to defeating the Red, and Jake, in turn, realizes that Paige and her people may have the answers about where he came from and why he is what he is. With time running out, the two rush to uncover not only what the Red really is, but also the strange connection growing between them.