Five boys gather on a dock and sing of the sea. Then they grab one of their number, tie him to a brick, and throw him into the water. He sinks beneath the surface as the others sing. A man with a maze tattoo on his arm, Leith Glendower, comes out and tells them that supper is ready. As the boys go back, Leith looks down at the boy in the water but does nothing.
Casey finds an unidentified body on the beach and calls Audrey and Nathan. It’s Leith, and Casey confirms that he’s been dead ten hours. They recognize the maze tattoo and locate a set of car keys on the body. It has a photo of Leith with the woman on it. Casey has also found a handwritten suicide note and Nathan figures the woman can tell them more.
Back at the station, Duke comes in to see Nathan and asks about the dead man. He’s interested in the tattoo but refuses to say how he found out. When Duke looks at the photo, he admits that he doesn’t recognize the man but insists that he has to find out his identity. Audrey identifies the woman as Mary Collins, who runs the soup kitchen at Driscoll’s church. Nathan tells Duke to get out and then goes to the church. Mary identifies the man and admits that he’s been on edge for the last few weeks, but doesn’t believe he’d commit suicide. Nathan asks about the tattoo and Mary says that it’s a family thing with the Glendowers. She suspects that Leith was concerned about money, and that he gave her and her 10-year-old son Daniel money despite the fact they were no longer together. Nathan explains to Audrey that the Glendowers live in a compound outside of town and that many consider them a cult. Chief Wournos checked on them occasionally and took Nathan with him. Mary calls the school and learns that Leith never dropped Daniel off at school, and Daniel doesn’t answer his phone. She last saw Daniel a day ago when Leith picked his son up and took him to the compound to stay with his cousins.
Audrey and Nathan drive to the compound and notice that none of the children are present. They meet with Cole Glendower and his wife Gwen, who appear shocked to see Audrey. Nathan explains that they found Leith’s body and it appears to be suicide. Gwen glances briefly at the note and says that it means nothing to her. When Nathan informs them that they’ve come to see Daniel, Cole insists that Daniel’s place is with them now that Leith is dead. He explains that the family was trying to get custody. Audrey asks where the children are and Nathan demands to see Daniel. Two men come out with guns and Cole tells Nathan and Audrey that they’re not welcome there despite Chief Wournos’ friendly relationship with them in the past.
As Audrey and Nathan go back to their car, they see a boy. Audrey asks him if he knows where Daniel is, and the boy tells them that they can’t have him because he’s one of them now.
Nathan drives to see Mary, who has gone to the church. Driscoll has his members preparing for an attack on the compound. Mary explains that she got a text message from Daniel saying that he wants to live at the compound, but Nathan warns Driscoll to stay out of it. The reverend calls the Glendowers filth and insists that that they should have been wiped out long ago. Nathan tries to convince Mary not to start a war and she agrees. He tells Driscoll of Mary’s decision and Driscoll agrees, but the reverend warns that Daniel’s soul is at stake and they won’t wait forever.
Back at the station, Audrey tells Nathan that she found a case in 1983 when Driscoll’s wife Penny went missing. The chief suspect was Cole, but Wournos’ report doesn’t say why he suspected Cole. Three days later Penny died in a car accident and Driscoll thought it was murder. However, Chief Wournos didn’t pursue his accusations. Audrey suggests that they sneak into the compound that night, but Nathan is reluctant now that he’s chief. He figures that she’ll go anyway and agrees to her plan.
That night, Audrey and Nathan sneak into the compound and find only one locked house. They break in and Audrey finds a photo of Lucy, Chief Wournos is in the photo, meaning he knew Lucy. On the back is writing identifying the photo as from a 1983 wedding celebration. They hear water running and go to the bathroom where a tub has overflowed. Daniel is immersed inside and opens his eyes when they approach. He rises out of the water, gasping for air, and Cole comes in, wielding a gun. He insists that he’s doing what needs to be done, orders them back, and tries to push Daniel back under the water. When Audrey and Nathan draw their guns, Cole insists that he’s trying to help the boy. Audrey sides with Cole and pulls Nathan away. Once Daniel is back under the water, he starts inhaling the water.
On his boat, Duke tells Evi that a man with the tattoo washed up on the beach. He figures that Leith is tied in with Driscoll, who may know about the tattoo. Duke suggests that Evi talk to Driscoll because he hasn’t met her yet.
Gwen and Cole explain that Daniel can only breathe air for short periods of time now that he’s transitioning. For generations, all Glendower men lose their ability to breathe air when the Troubles come. They migrate to the sea when they can no longer survive on land. The boys transform first and spend extended periods underwater. The couple believes that Leith panicked and went into the water too soon. On the ebb tide of the next new moon, the Glendower men go into the water together as a matter of unity. Chief Wournos knew the Glendower secret and the couple figured that Audrey and Nathan knew as well. Cole insists that Daniel has to stay with them and the change comes in two days. Since Mary follows Driscoll, Leith refused to tell her about his Troubled condition. Cole admits that he was having an affair with Penny but he didn’t kill her, and Driscoll wouldn’t let it go.
Audrey realizes that the suicide note on Leith’s body belonged to Gwen, who wrote it in 1983 to Driscoll. She actually is Penny Driscoll and faked her death to get away from him and be with Cole. A woman comes in and tells them that the boys have been kidnapped. The next morning, Nathan finds tracks from the truck and confirms that Driscoll kidnapped them so that he could “cure” them. Cole warns that if they don’t get the boys back, they’ll suffocate when they’re no longer able to breathe air.
Gwen talks to Audrey and explains that she initially admired Driscoll’s passion, but when he came to Haven he grew obsessed and angry. She hoped to turn him back to the way he was but eventually realized otherwise. When Driscoll learned about Gwen’s affair with Cole, she worried that he’d murder her.
Evi goes undercover at the church soup kitchen and tries to get Driscoll out so Duke can break in to his office
Cole warns Audrey and Nathan that there’s no reasoning with Driscoll, and Mary will do whatever Driscoll says. Nathan warns that Driscoll will be waiting for them with men of his own.
Duke searches through Driscoll’s office and finds a secret compartment in a chest. Inside is a list of citizens killed by the Troubled, and one of the names is Simon Crocker, Duke’s father. Audrey and Nathan burst in and Duke tries to hide the list without success. Nathan yanks it away and Audrey tells Duke that Driscoll is involved in a kidnapping. Duke offers to tell them where they can find the reverend in return for the list.
At the docks, Nathan prepares to arrest Driscoll for kidnapping. The reverend informs them that he has been at the docks all morning. Evi confirms his alibi and admits to Driscoll that she’s Duke’s ex-wife. Nathan realizes that Mary has the boys and demands to know where she is. Before Driscoll can respond. Two of the Glendower man leap out of the water, grab Driscoll’s men, and jump back into the water with them. As Nathan and Duke try to get everyone off the docks, Glen leaps out of the water and demands Daniel’s return. Duke notices that he has a maze tattoo on his arm and refuses to turn over Driscoll. Nathan informs Cole that Driscoll doesn’t have the boys and asks the man to trust him like he trusted Chief Wournos. After a moment’s hesitation, Cole tells his men to release the church workers. As they leave, Cole warns that if his boys die, the beaches will run red with their blood.
As they get off the dock, Driscoll starts to condemn the Glendowers and Nathan slams him into the wall, warning the reverend that he was close to letting Cole take him. Nathan then takes Driscoll’s phone and confirms that Mary has called him three times in the last hour. Audrey realizes that Driscoll told Mary about the Glendower affliction, provoking her into kidnapping the boys. Driscoll refuses to talk, but Evi overheard Mary and Driscoll discussing a barn outside of town where they store the soup kitchen supplies. Driscoll refuses to tell Mary that he was wrong, and Nathan warns him that he’s condemning the children to death.
At the barn, Mary calls Driscoll to tell him that Daniel and the other boys are dying. Daniel accuses her of lying but Mary insists that everything will go back to normal when Driscoll cures them. He insists that she has to let them go back. Mary hears Nathan and the others pull up outside and gets out a gun. She tells them to stay away and that she’ll only talk to Driscoll. The reverend offers to help in return for them coming to Sunday service so the town can see that they stand together. When Nathan refuses, Driscoll stands his ground. Nathan then has Gwen come over. Driscoll realizes who she is and accuses her of leaving him and his daughter. Gwen insists that Cole and the other Troubled are just normal people, and the children will die if he doesn’t talk to Mary. When she accuses him of acting out of jealousy, Driscoll goes into the barn without a word.
Nathan and Audrey wait and finally Mary release the boys. Audrey thanks Driscoll, saying it was brave of him to accept that more is required than prayer. Driscoll agrees and warns that a good shepherd always takes care of his flock. Meanwhile, Nathan receives a report on Leith’s autopsy and confirms that there was no water in his lungs. There were pre-mortem bruises, meaning he was murdered.
The Glendower men gather at the beach and Nathan and Audrey meet them. Nathan informs Gwen that Cole murdered Leith. Daniel had heard Leith arguing with Cole about how he would find money for Mary. Leith planned to sell Gwen’s note to Driscoll and reveal where she was. Cole insists that Driscoll would have destroyed the compound while he was in the water with the others. Nathan admits that he can’t arrest Cole without condemning him to death out of the water. Gwen promises to wait for Cole no matter how long it takes. As they go to the beach, Cole tells Nathan that when the Troubles are over, he’ll turn himself in. Until then, he asks Nathan to watch over his family and keep Driscoll away. Nathan promises to do it.
Audrey asks Gwen about Lucy, and she says that Lucy was only in Haven for a few months and spent most of her time with Chief Wournos. One day Lucy just disappeared, a few days after the Colorado Kid murder. Gwen tells Audrey that the only time anyone ever saw Lucy cry was at the murder scene. Meanwhile, Duke approaches Cole and asks what the tattoo means. Cole explains that there are those who fight when people rise up against the Troubled, and they are watching Duke in case he follows in his father’s footsteps. When Duke asks who killed his father, Cole only tells him that if Duke wants to stay alive, he should stay out of Simon’s business.
On the hill, Driscoll and Evi watch the procession. Evi has doubts but Driscoll says that there shouldn’t be any doubt given what she’s seen. When he wonders if they have Duke, Evi assures him that now that Duke knows who murdered his father, they have him on their side.
As the Glendower men enter the water, Mary tells Daniel that she’ll love him and think of him every minute until he comes home. Gwen approaches her daughter-in-law and tells her that it gets easier, and offers to help her. Mary embraces Gwen, crying, and they watch as the men walk away.
Nathan and Audrey watch, and Nathan admits that he didn’t know the right questions to ask about the secrets his father had. Audrey has learned from Gwen that Chief Wournos helped many of the Troubled and that they’ve been following in his footsteps without knowing it.