Former FBI agent, Ryan Hardy is called out of retirement to track down Joe Carroll after he escapes from prison. Hardy works closely with an FBI team, which includes young, razor-sharp Mike Weston. The investigation also leads Hardy back to Claire Matthews, Carroll's ex-wife and the mother of the criminal's young son, Joey. Hardy soon discovers that Carroll has an ever-growing cult of followers.

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

A new follower is found in Rick, who is on a determined path to follow through on Carroll's orders. Hardy and the FBI attempt to predict Rick's course of revenge, which leads to a surprising outcome. Meanwhile, Paul's jealousy over Emma and Jacob's relationship leads to a breaking point, and the origin of Hardy and Carroll's relationship.

Maggie devises a plot to put an end to Hardy. Meanwhile, tension rises as Paul reveals a secret that Jacob has been keeping from Emma and more information about Hardy and Claire's past relationship is revealed.

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.

Joe Carroll's true intentions are revealed through a new follower, Charlie. As Ryan learns of Joe's plans, he tries to stall Emma, Jacob and Paul by taunting them in hopes of turning them against each other. Meanwhile, Emma makes a shocking decision.

With the help of attorney Olivia Warren, Joe Carroll makes a case against Ryan and the FBI to be transferred to a different facility, but Ryan suspects a larger plan may be at play. Meanwhile, Emma and Joey arrive at a meeting point and come across another one of Roderick's men who has a secret of his own.

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.

With Weston still in the hospital, Ryan and Parker attempt to outsmart their new leader Nick as a way to continue their search. In a surprising move, Joe reaches out to Ryan to demand Claire's location and reveals that he will go to great lengths to lure her out of FBI custody. Meanwhile, followers from the past make a shocking return.

After discovering Claire's location, Joe sends two followers to capture her, but Ryan may be one step ahead. Meanwhile, Jacob struggles with recent decisions causing his reunion with Emma to be less than ideal. Also, a relationship from Ryan's past plays a significant role in his future.

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.

The Havenport Police Department is brought onto the case and Roderick's role as sheriff is called into question, which leads him to make a shocking decision that threatens the safety of Joey. Meanwhile, Ryan goes against the FBI, hoping to gain the trust of one of Joe's followers.

Ryan, Parker and Weston prepare to storm the follower's mansion, but Joe already has an escape plan in action. Meanwhile, disguised followers create a diversion at the town evacuation center, which causes panic among the residents and leads to a dangerous kidnapping of one FBI official.

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.