The book is about several characters and how their lives intertwine, but mainly it's about a girl named Cassie. Cassie's life is turned upside down when a series of "waves" of an alien invasion begin. The 1st Wave is a huge electromagnetic pulse that renders all electronics - including cars - useless. This is followed by four more waves of increasing atrocity, including a violent plague, which wipes out Cassie's mother. Cassie finds herself alone, determined to find her little brother, Sammy, whom she was separated from at a refugee camp. She comes into contact with the mysterious Evan Walker along the way; she is torn between trusting him and letting him help her, or assuming the worst...that he's part of the invasion. Throughout the novel, things are never really what they seem, you can never tell who's lying, and people are brainwashed to believe something that isn't real.
There were several parts of the book that really confused me - like what exactly the "aliens" were. It never really made sense to me. Evan tried to explain it to Cassie once, but it still seemed sketchy to me. I found myself skipping pages sometimes, too, trying to get to the good parts.