Season three of "The Following" starts with Joe Carroll on death row and Ryan, Max and Mike working to stop another string of murders. By the end of the season Ryan is on a search for Theo and a member of the Federal Bureau of Investigations suffers an attack.
In the first few episodes of season three, Mark and his followers capture an FBI agent and Ryan seeks an old enemy for help. Ryan, Weston and Max suffer a loss and must work together to find those responsible. Meanwhile, Mark, Kyle and Daisy plan an attack on Ryan, forcing him to turn to another enemy for help.
Near the middle of the season, an important trial goes awry and the FBI must look for a missing person. Ryan and Mike end up tracking their target to a small town and begin to concentrate on a new threat. Also, Max rejoins the team. Approaching the end, Ryan and the new killer are led to Joe for different reasons while Mark reaches a decision.
A hostage situation develops that Ryan must deal with on his own. Theo and Penny find a means to disappear and then Ryan begins a search for Theo. In the end, Mark and Daisy gain information that gets them closer to the FBI and alliances are shaken as the search for Theo continues.