The Second Ship (The Rho Agenda Book 1) by Richard Phillips. In 1948, an alien starship fell from the New Mexico sky—and immediately vanished behind the walls of the Los Alamos Laboratory. Since that day the US military has endeavored to reverse engineer the ship’s alien technology through top-secret research known only as the Rho Project. Now, decades after the crash, the government is prepared tell all.
In 2035 after ecological disasters nearly destroy the Earth, 26 survivors are trapped by an alien race in a sterile enclosure known as the Shell. Fifteen-year-old Pete is one of the six children who were born and raised in the Shell. As the survivors grow sick and die, Pete and the six struggle to rebuild the earth using brief time-portals into the past where they bring back children. In 2013, mathematician Julie Kahn works with the FBI to solve a series of inexplicable kidnappings.