Ryan Hardy, Agent Mike Weston and FBI Specialist Debra Parker, who is brought in to lead the investigation into Joe Carroll and his followers, dive deeper into the history of Carroll's psyche. To do so, they enlist the help of Carroll's ex-wife, and Hardy's former love, Claire Matthews. Meanwhile, Emma, Jacob and Paul keep Claire's son Joey at a house in the country as they prepare for their next move

When Claire receives a phone call that may lead her to find her son, the FBI and Ryan Hardy set their next move into motion, causing panic at the farmhouse. Meanwhile, Joe Carroll seeks a lawyer from his past to send a message that has deadly results.

With Joey Matthews still missing and the search for Joe Carroll escalating, the FBI brings in Nick Donovan to run lead on the case, much to Ryan and Parker's dismay. Meanwhile, a follower from the past meets up with Joe Carroll, and their plans have a life-threatening result.

After losing Claire to Joe's followers, Ryan and Parker attempt to recover while the FBI tracks down an undercover location that may have dark ties to Joe's following. Meanwhile, Claire adjusts to life at the follower's mansion and has an unexpected reunion, while Emma and Jacob continue to deal with Emma's betrayal.

In the explosive Season One finale, Ryan races to stop Joe Carroll before his endgame reaches a deadly conclusion. Meanwhile, Joe leads Claire to a special location and the ultimate showdown between good and evil takes place.

Ryan continues his search to find the correlation between the recent tragedies in New York City and Emma and the existing members of the Havenport cult, while the FBI becomes increasingly aware of his undercover agenda. Meanwhile, a shocking event leads Joe to put a new plan in action.