This tv tie-in-novel begins with the last scene from the last episode of the television series, with Kyle Baldwin giving his government agent father, Tom Baldwin, a shot of promicin, the substance that can give a human extra normal abilities. Kyle himself has a weird intuitive ability that takes the form of a young red-headed woman named Cassie. She's the one who urges him to help Collier and start this new religion around the 4400 and Promicin. Things get disturbing in the novel because he's actually having sexual relations with her, so he's basically screwing himself.
Richard Tyler, who has incredible telekinetic abilities, is broken out of jail by Jordan Collier's followers. It's Jordan, the self-proclaimed leader of the 4400, who is starting a new religion based on a ninety-year old prophecy. Collier's body was almost taken over by "The Marked" in Season Four of the television series. They are from the future who have infused their personality onto "hosts" in the past and try to prevent the 4400 from influencing humanity. They want the "Big Catastrophe" to happen since they benefit from it. Basically, they don't want their timeline changed. So Collier convinces Tyler to be his assassin and go after them, one by one. You see, Tyler can make it look like an accident, such as having one of them choke on his food while eating dinner.
There's also a group that's determined to clone the body of Kyle's cousin, who had died. He had taken the promicin shot and developed the ability to spread Promicin through the air. But since this substance kills 50% of the people exposed to it he was responsible for nearly 9,000 deaths in the Seattle area. This group thinks that if they can clone his body (it's one of the group's abilities to manipulate DNA) they'll be able to reproduce this ability.
A lot happens in this book and it tidies up a lot that was unresolved at the end of the television series. Richard Tyler finally gets what he wants and The Marked are seemingly defeated. Basically, if you're a fan of the show you'll enjoy this quick read.