Claire Matthews has died from wounds inflicted by Molly's stabbing. During the attack, Ryan Hardy twists Molly's neck and kills her. A year later, Ryan has moved to New York City where he lives on his own and is teaching. On the first anniversary of Joe Carroll's death, a group of remaining cult members attack several passengers on a subway car. The FBI brings Ryan and Mike Weston back on board to assist in gaining information on the identity and motives of the attackers. Ryan dismisses the FBI's request for his help and appears to want nothing to do with the situation. However, back in his home, he continues his secret interest in Joe and the case along with his niece, Max Hardy, a New York City detective. New followers of Joe are also revealed including twins, Mark and Luke, while Joe himself is revealed to be alive with a new appearance.
Joe is living with a former admirer of his, a prostitute, Judy, and her daughter, Mandy, under the alias "Uncle Daryl", Judy's supposed brother who just returned home from war in Afghanistan. One of the men Judy sleeps with, a local reverend, comes by her house looking for Judy but finds she isn't home yet. After realizing Joe's true identity from a television news report, the reverend is killed by Joe with Mandy's help. The twins, Mark and Luke, break into the home of a couple with a young child. Ryan is led to the house by Max's tracking of the twins' phone during a call. The twins continue to draw Ryan's attention by having him show up at a benefit event where the only survivor of the subway murders and new interest of Ryan, Lily Gray, is speaking. After an attempted attack, Ryan helps Lily go unharmed and shoots Luke in the arm, with the only other injury being to Lily's assistant, David. The twins escape as Luke tends to his injury. Meanwhile, Emma is currently living with other remaining cult members with an entirely new look. She becomes interested in finding out the identity of the murderers making the news and eventually finds a way to call them, leading to the realization that Joe may not actually be dead.
Joe reveals to Judy and Mandy his plans to leave their home at night as Judy expresses her resentment for Joe murdering the reverend. She pulls a gun on Joe but he had previously taken out all of the bullets. He attempts to choke her to death but stops when Mandy begs for him to. Joe ties Judy up, setting up a crime scene implicating the reverend for when the police discover the home. Joe looks for his knife, but Mandy finds it and proceeds to stab her mother to death. Joe sets the home on fire before departing with Mandy. Meanwhile, Agent Mendez and other investigators find Emma's home and raid it, killing all of the followers inside but one, who is taken into custody. At the time, Emma was out meeting with Mark, as the two exchange information about their respective groups of Joe's followers. He brings her back to his room where she meets Luke, Gisele, and Carlos, though Luke soon-after stabs Carlos, killing him. Ryan continues to visit and talk to Lily against orders banning interaction between the two. He soon discovers her in a lie and with the help of Weston's subway video footage realizes that Lily is involved with the cult. Lily escapes and taunts Ryan over the phone. She meets up with Luke, who drives away after calling her "mother."
Joe and Mandy sneak into the house of a young mother with two children. The mother, Jana, is revealed to be a friend of Joe and provides him with a fake ID and cash. She tells Joe she has not been able to find his son, Joey. The FBI finds out that Lily was adopted by a billionaire and inherited his money. There are no records of her giving birth but a former housekeeper gave birth to twin boys before her death. When Luke and Lily arrive at a large country estate, they are greeted by Mark as well as a diverse group of three who refer to Lily as their mother. Emma is also at the house and remains uncomfortable despite Lily's attempts at warming up to her. When Joe calls, Emma hesitantly tells him that it is safe for him to come there. Joe arrives and upon embracing Emma, she bursts into hysterical tears before he moves on to meet the rest of the group. Meanwhile, Ryan continues to track Agent Mendez and the FBI's work on the case, despite their unsuccessful surveillance of him. Max helps Ryan find David's (Lily's lawyer) residence where, upon arrival, he finds him dead on the floor. His murderer, Gisele, gets away before Ryan realizes who she is. Ryan is arrested by Agent Mendez but is released soon-after. Weston, who still doesn't believe Joe could be alive, visits Max at her office and advises her to back off from helping Ryan. She insists she has no involvement. After a chase through city streets and two physical fights between Gisele and Max, and then Ryan, Gisele gets on a train just before it pulls out of the station. Ryan calls Max and she reveals she is on the train, looking at Gisele. Agent Mendez makes a phone call to her significant other, informing her that she will working late and will be unable to pick up the kids. Her partner is revealed to be Joe's friend, Jana. She complains that she had to give up becoming an FBI agent in order to care for their kids.
Lily introduces Joe to everyone in the house. Emma expresses her bitter feelings towards Joe abandoning her; he apologizes repeatedly and asks for another chance. Luke and Jamel, one of Lily's "sons", go to meet up with Gisele. Max and Ryan catch up with Gisele and bring her to a local motel where they handcuff and question her. Gisele gives up the supposed location of Joe, which is really the warehouse she was supposed to meet Luke and Jamel. Ryan heads there and is confronted by Luke and Jamel. Ryan shoots Jamel dead and is shot in the stomach in return. Gisele breaks her thumb to escape the handcuffs while Max is distracted and runs away to meet up with Luke. The two follow Ryan's trail to a local house where Ryan attempts to clean up his wound despite the homeowner showing up and panicking. Ryan stabs Gisele with her own knife upon her entering the house and falsely telling him that she killed Max. Luke runs into the house and holds Gisele as she dies, and Ryan runs off. Back at the house, Lily requests that Mark distract Emma for a bit. Mark locks himself and Emma in Lily's art room to allow Emma to draw, an old passion of hers. Emma leans in to kiss him as he reveals he cannot handle body contact unless he initiates it himself. Meanwhile, Lily has locked a young school girl in a cage and drugged her, presenting her to Joe as a gift for him to kill. Joe angrily refuses at first, thinking Lily is attempting to control him, but later goes through with the murder. Weston, Mendez, and the FBI discover an image of Joe and Mandy from a surveillance camera, but fail to actually identify the man in the picture as Joe. Ryan returns to the motel and embraces Max upon seeing her alive.
After spending the night together, Joe and Lily discuss Lily's idea of moving everyone to Lily's house in Venezuela. Joe hesitantly agrees. Ryan invites Weston to bring the FBI to Connecticut, where he and Max have been tracking Lily's group. Weston comes alone and along with Ryan and Max, capture Luke at a field near Lily's house. Ryan proposes a trade with Lily, offering Luke in exchange for Joe. Lily drugs Joe to keep him asleep while Mark, Lily, and a hostage of hers meet up with Max and Luke for the exchange. Max lets Luke go in exchange for Lily's captive being released, unharmed. Lily, Mark, and Luke run off as Weston and Max chase after them. At Lily's house, Ryan encounters one of her other sons, proceeding to stab and kill him. Inside, Emma and Mandy discover an unconscious Joe and manage to wake him up. They escape the house after killing Lily's daughter who attempts to stop them. Before driving away, Joe stares down Ryan, who has made it into the house and sees the trio leaving from a window. Weston catches up with Luke and shoots him, though Luke has a bulletproof vest on. Lily and Mark drive off believing it to be too late to save Luke. Weston repeatedly punches Luke, leaving him bloody and unconscious. The FBI blocks an airplane from departing, believed to have Joe inside. The pilot reveals the trio left the plane after the man got a phone call. Ryan tells Mendez he saw Joe alive and he was the man in the plane, which Mendez claims she will handle on her own, also revealing that Max and Weston have now lost their jobs for their involvement. Ryan, Max, and Weston conclude that somebody from the FBI must be compromised and feeding Joe information. Emma gets a call from Lily, which Joe answers and expresses his contempt with Lily's news of Luke's supposed death, causing Lily to have an emotional breakdown.
Joe, Emma, and Mandy arrive at a cult compound. Two authority figures, Robert and Julia, have them blindfolded and handcuffed before entering the trucks. Ryan meets with Agent Mendez about who in the FBI may be giving Joe information; Ryan leaves, unsure if he can trust her. Weston leaves the FBI building to go home because he feels mentally unstable after assaulting Luke. Max asks Ryan to give up with Joe, but Ryan admits he's formed an obsession and must kill him. Max is captured by a man hired by Lily, as the man's son records the capture on video. The man ties her up and hangs her by her hands from the ceiling of a basement. Weston returns to help find Max. Joe meets with Micah, the cult's leader, and offers his help with the cult in exchange for a place to stay. After Ryan receives the video of Max on his phone, he questions Luke, who remains in custody at a hospital. Luke reveals the man's name: Kurt (Bowlen), known as "The Huntsman" - a known serial killer. The FBI find Kurt's home; Ryan and Weston handcuff his son until he reveals where his father is. Max escapes into the woods, with Kurt chasing her. FBI police dogs track them down and Weston finds Max right before Kurt is shot dead by Ryan. Julia gives Joe a lie detector test to ensure his intentions are genuine. He, Emma, and Mandy are taken to a ceremony, which Micah reveals is to take the blood from a cult member to wash away all of their sins and bring them a step closer to "going home." Emma is selected and strapped to a post where Micah slits her wrists and eventually drinks her blood. She faints, but survives. Ryan receives a video text message from Lily and puts it on screen in the FBI's office. Weston recognizes Lily is at his father's house, as the video turns to his father strapped in a chair. Mark slits his throat and kills him. As Weston runs out of the room crying hysterically, Lily teases Ryan that she has more surprises in store for him. Ryan catches Weston weeping outside and holds him.
The funeral for Weston's father takes place, with Ryan and Max attending. Afterwards, a journalist, Carrie Cooke, with an apparent history with Ryan shows up and unsuccessfully tries to get him to comment on Joe. Inside, Director Franklin of the FBI tells Ryan that he wants him working on the case and will supply him with whatever he needs to work off the books. Back at Micah's cult, Emma insists to Joe that they leave, though Micah soon-after officially initiates them and Mandy into the group. In private, Micah tells Joe of his interest in killing people and having Joe write a book about him. Max and Ryan turn their focus to Joe's college professor, Dr. Arthur Strauss, who lives an hour away from the lighthouse where the events took place. Ryan goes to Strauss' home and questions him about Joe while planting a microphone in his living room. He leaves after Strauss insists he has no involvement. Carrie comes to Strauss' home for interview questions but is captured upon entering the house, which Ryan hears over the audio receiver and rushes back to the house. One of Strauss' students, Cole, sprays a chemical into Ryan's face, causing him to temporarily faint. He wakes up tied to a wheelchair, across from Carrie who is strapped to an operating table. He has a flashback to a few months prior, waking up to Carrie telling him they slept together, though he doesn't remember after a night of heavy drinking. Strauss has a flashback as well of Joe showing up after the lighthouse events injured and needing help. Weston finds Cole as Cole was looking for tools and shoots him. Ryan frees himself and then Carrie. Ryan and Weston tie Strauss to the table and whip his hand until he reveals that Joe had a connection to a female in the FBI. Joe and Micah discuss taking the cult to the next level, despite Julia being against the idea. Micah suggests throwing Joe a celebration, but Julia expresses her concern about having Joe around causing too much attention to their cult. At a party, Micah passes out tablets to some of the cult members, including a new friend of Mandy's, Erik. The tablets eventually cause them to foam at the mouth and kill them as Micah leads the group to chant "send them home with shouts and praise," suggesting those killed are moving on to the coveted after-life. While having them buried, Micah has Julia taken away after she begins acting out in frustration. Emma and Joe reconnect back in their room where Joe says their next move is to tell the world that he's alive.
Micah tells Joe of his desire to "make a splash." Max and Weston narrow their list of possible moles in the FBI, a list including Agent Mendez. Ryan doesn't believe she's guilty, but questions her outside of her apartment. Micah sends Robert and Emma on a mission as his "messengers" along with an ex-killer cult member, Lance. Ryan and Weston track Mendez as she travels to Jana's house. Jana brings Mendez into the garage to talk, where Jana stabs her. Jana's friend lets Mike and Ryan in. They find Mendez and have an ambulance called before cornering Jana and questioning her about where Joe is. Jana proceeds to shoot herself in the head. Mendez is taken away, alive, in an ambulance. Micah asks Joe for advice about how to handle Julia and the tension between the two. Joe and Micah later kill her after she attempts to shoot him but fails due to the gun not being loaded. Robert, Emma, and Lance show up at a book store where Carrie is having a book signing and they begin killing at random before Emma hands Carrie a video clip, instructing her to share it with the world or else they'd come back for her. Robert and Emma escape, but Lance purposely stays behind and is eventually shot dead after holding a knife to a police offer. Carrie plays the clip on her news report, which Joe watches along with Micah, Emma, and Robert. While watching, Joe hands out drinks to the group. Micah realizes the video they're watching is not his. It's instead a video of Joe announcing to the world that he's still alive and nobody is to feel safe. Micah proceeds to fall to the floor and foam at the mouth, having been drugged and killed by the drink. Robert later gathers the cult and proclaims Joe as their new leader. Back at Ryan's apartment, Weston walks Max out and ends up getting into a car with unknown men. Carrie shows up and has dinner with Ryan, who eventually kisses her as she's on her way out. Weston is transferred to another car and blindfolded on the way to a location where he meets up with Agent Philips. Philips brings him to a room where he comes face-to-face with Claire Matthews.
A flashback shows Claire in the hospital, with Weston and Turner telling her the plan to put her into witness protection and not tell anyone that she is alive, including Ryan. In present day, Weston catches Claire up on everything and she expresses interest in helping find Joe instead of letting witness protection move her, but Weston insists she stays safe. At Corbin, Robert introduces Joe to a group (Mallory, Lucas, Patrick, and Tilda) who have volunteered to be the next messengers. Tilda picks out her choice of first victim and Lucas kills the man. They later kill another innocent family. At both murders, they leave behind a note saying "no redemption without blood." With the help of Carrie, Ryan gets the message out to Joe that the FBI has captured Dr. Strauss and he is cooperating. This leads Joe to call Jana, but Ryan answers her phone as the FBI unsuccessfully tries to track down Joe's location. Flashbacks show a younger Joe as he was first mentored by Dr. Strauss, where Strauss revealed more about Joe's past: Joe was sent to America by his uncle after his parents both died. Back at Corbin, Emma and Mandy argue after Mandy walked out of a gathering with Joe and other Corbin members. Mallory and Patrick later go to a restaurant that Mallory was previously fired from to make their next murder. FBI shows up after Max tips Ryan off about Mallory. Ryan tries to get information about where Joe is out of Mallory, but Patrick slits her throat before being shot dead. Joe anoints Tilda and Lucas once they return from their mission. Carrie and Ryan fool around again after Carrie tries to convince Ryan that he's making progress, professionally and personally. Claire tells Turner that she refuses to go to Arizona, and instead wants to see Ryan.
Joe gathers a group of Corbin followers and has a volunteer stab another Corbin member, Carla, to kill her, thus "sending her home." Robert confronts Joe about his reason for choosing Carla, as she was close to Robert. Joe calms him down and asks Emma to follow him and ensure she's able to keep him close enough to stop worrying. Joe and Emma also discuss Mandy's lack of progress at Corbin, with Emma feeling like she's a lost cause. Later, she looks up Mark's number online, and calls him after packing a bag and leaving Corbin. Meanwhile, Ryan and Mike continue researching information on Lily Gray and cults that believe in blood sacrifice. Two men cause chaos after stabbing a group of people at a bakery, sending them all to the hospital. At the hospital, two of Lily's helpers, Serena and Decklan, and a few others follow a plan put together by Lily to rescue Luke and send him home to Lily and Mark. Luke escapes the hospital after being chased down by Ryan, though Serena and Decklan are killed by Mike and Ryan, respectively. Carrie goes on air to report the news of the attack, which Joe and Emma angrily watch. Claire again requests to see Ryan, feeling she can help him. She's given permission, provided her son and mother are moved to another location which Claire will not be given information on unless she returns to witness protection. She later shows up at Ryan's apartment as Mike panics and tells Ryan that he can explain everything.