The Fallen Race Trilogy by Colin Patrick Garvey

Everything in ex-Marine Sean O'Connell's life changes in an instant when an unspeakable evil enters a small and secluded Midwestern cottage town during the 4th of July holiday and snatches his wife and son, along with the other residents of the the town. This mass disappearance occurs under the guise of a terrorist attack on American soil, and Sean, the lone "survivor," finds himself on the run trying to put the pieces of a puzzle together, desperate in his search to find his family. His only allies are a cryptic treatise written nearly 60 years ago by his friend and mentor, Dr. Albert Rosenstein, a beautiful but deadly assassin named Sloan, and his childhood friend, Sergeant Jonathan Kaley, who has his own strange connection to the mass disappearance. The treatise, which suggests the actual capture of extraterrestrials by the American government, ominously forecasts mankind's chance of survival in the event of a global invasion by these superior beings.