Five boys stand on a dock and sing a song about the sea. Four of them grab the fifth, tie a cinder block to his legs, and throw him into the water. As he sinks, the boys start singing again. A man who has the circular maze tattoo on his right arm calls them in for supper. He sees the fifth boy under the water but doesn't react.
Later, Nathan and Audrey are called in for a dead body found on the beach, the tattooed man. He has no ID, but they find a photo of the man with a woman, and a handwritten note that says, "I'm sorry to leave you... but I can't go on." Duke visits them at the station, because he heard that the dead man had the tattoo. They show Duke the photo, but he doesn't recognize him or the woman. A search confirms that the woman in the photo is Mary Collins, who works at the soup kitchen out of Reverend Driscoll's church.
The officers visit Mary, who says that the man was Leith Glendower, her ex-husband. She has no idea what the tattoo means and has no idea why he would kill himself, as they were still on good terms and had joint-custody of their son Daniel. She leaves to make a call. Nathan explains that the Glendowers live outside of Haven in a compound. His dad Garland had been on good terms with them and often visited, sometimes bringing him along. Mary comes back and says that Daniel never showed up for school, and he's not answering his cellphone. Daniel had been staying at the Glendower compound and Leith was supposed to pick him up.
Audrey and Nathan go to the compound. Nathan notes that it is strange that none of the children are present, since they are home-schooled. Cole Glendower and his wife Gwen (Leith's parents) come out, doing a double take when they see Audrey. They tell them about Leith's death and show them the note, but Gwen dismisses the note as meaningless. Nathan asks where Daniel is, and the couple says that he is fine and that they will take custody of him now that his father is dead. Nathan demands to see Daniel, but two Glendower men come out with guns. Cole tells Nathan and Audrey that they are not welcome unless they get a warrant. As they walk back to their car, the boy who had been tossed into the water walks up and says that they can't have Daniel because he is one of them now.
Nathan finds that Mary told Reverend Driscoll what happened when Daniel sent her a text confirming that he is at the compound. The Rev and his followers are planning to storm the compound and take Daniel by force. Nathan asks them to wait for a peaceful solution, but the Rev says that the Glendowers are filth and must be destroyed. Nathan appeals to Mary, who reluctantly agrees to wait. The Rev says that with Daniel's soul at stake, they won't wait forever.
Audrey tells Nathan that she did some research and found that the Rev's wife Penny had disappeared in 1983 and Driscoll had accused Cole. Three days later, Penny was reported dead in a car accident and her body destroyed in the fire. Chief Wuornos refused to pursue the case against Cole. Audrey suggests they rescue Daniel during the night.
That night, Audrey and Nathan sneak into the Glendower compound. At the refrigerator, they find a photo of Lucy Ripley posing with Chief Garland Wuornos, with a handwritten note saying it is for a wedding in 1983. In the bathroom, they find Daniel lying in the bathtub, underwater. Nathan pulls him up, and he starts gasping for air. Cole walks in and holds the officers at gunpoint. Daniel starts gasping harder and harder, and Cole says that he must stay underwater or he will die. Nathan protests, but Audrey says that she can tell that Cole is telling the truth. Daniel goes back in the water, and he calms down and comfortably breathes the water.
Duke tells Evi about Leith and his tattoo. She suggests that Leith was involved with Driscoll and that the reverend may know more about the tattoo. Duke agrees based on his previous conversation with Driscoll, and suggests that Evi get close to the reverend and distract him.
Cole and Gwen explain the Glendower's Trouble: the males in the family gain the ability to breathe water, but gradually lose their ability to breathe air. When they fully lose the ability to breathe air, they will go to the sea until the Troubles end. They are preparing to go in about two days. Nathan points out that Leith drowned, so Cole and Gwen suggest that he stayed longer than his limit, as he had not fully transitioned to breathing water. Chief Wuornos knew their secret and helped them during the 1983 Troubles. Lucy Ripley had been a dear friend as well, which is why they were surprised when they saw Audrey, because she looks just like her. Leith never told Mary about the family secret because she is a follower of Driscoll.
They question Cole about Penny. He admits that he had an affair with her, but says that he didn't kill her. Audrey compares the handwriting on the photo with that of the note and finds that they are identical. The secret is out, the note is actually Gwen's, as she is actually Penny, having faked her death to be with Cole, the man she loves. Suddenly, a Glendower woman comes in and informs them that someone has kidnapped all of the boys. Nathan finds truck tracks and figures that Driscoll kidnapped the boys and plans to "cure" them of their Troubled affliction. Cole warns Nathan that if they don't get the boys back, they'll suffocate in two days when they complete their transition.
Gwen tells Audrey that she once loved Driscoll, but he began to pay more attention to his work and became emotionally abusive, so she had an affair with Cole. Realizing that Driscoll would be murderous, she faked her death. Cole prepares to storm the town and rescue the boys, but Nathan warns him that Driscoll and his followers with be expecting that.
While Evi talks with Driscoll at the docks, Duke sneaks into his office. He finds a secret compartment with a list of citizens killed by the Troubled. One of the names is Simon Crocker, Duke's father. Nathan and Audrey break in and explain the situation. Duke agrees to help.
The trio confront Driscoll at the docks. Driscoll says that he didn't do anything, he's been at the docks all day, and Evi confirms this. Nathan figures that Mary had kidnapped the boys. Suddenly, two Glendower men leap out of the water and drag two of Driscoll's men under. Cole leaps out of the water onto the dock and demands the boys back. Duke sees that Cole has the tattoo and draws back. Nathan tells Cole that Driscoll doesn't have the boys, Mary does, and asks him to trust him like he did his father. Cole reluctantly orders Driscoll's men released, but warns Nathan that if the boys are not returned soon, his family will start killing. He and his family swim away.
Nathan checks Driscoll's cellphone and finds that Mary had called him several times that day. Driscoll refuses to tell them where she is. Evi suspects that Mary is holding the boys in a barn. They ask Driscoll to convince Mary to release the boys but he refuses.
In the barn, the boys are suffocating, but Mary fanatically declares that once Driscoll arrives he will perform a miracle and "cure" them. When the guys arrive, Mary threatens them with a gun. Gwen arrives and Driscoll recognizes her. He asks Penny why she abandoned him and their daughter. She gives her reasons, and insists that Cole and the others are just like everybody else, and that if the boys don't get to the sea soon, they will die. Driscoll asks Mary to release the boys and she does.
Later, Nathan receives a coroner's report that says that Leith didn't drown, he was murdered. As the Glendower males prepare to walk into the sea, Nathan and Audrey confront Cole. He confesses to the murder, because Leith had threatened to blackmail Gwen with the suicide note because he wanted money in his accounts to provide to Mary. Nathan notes that they can't arrest Cole because he would suffocate. Cole solemnly promises to turn himself in once the Troubles are over, and asks Nathan to protect the Glendower females. He agrees.
Audrey asks Gwen about Lucy Ripley. She says that Lucy was only in town for a few months in 1983, and that she and Garland Wuornos worked together to help the Troubled. A few days after the Colorado Kid murder, she vanished without a trace. Gwen adds that seeing the Colorado Kid's body was the only time she ever saw Lucy cry.
Duke asks Cole what the circular maze tattoo means. Cole says it is a symbol for those who defend the Troubled against those who would harm or oppress them. He says Duke should watch himself or he will share Simon Crocker's fate. Duke demands to know who killed his father, but Cole only says not to follow in Simon's footsteps.
Driscoll and Evi watch the proceedings from a distance. Evi wonders if they are doing the right thing. Driscoll cites the attack at the docks as evidence that the Troubled are evil, and now that Duke knows that a Troubled person killed his father, he will eventually join them in eliminating them.
Mary assures Daniel that she will always love him. Daniel joins his brethren in the sea, while Gwen and the other Glendower women comfort Mary. Nathan is worried about how he barely knows anything about his father. Audrey notes that they've been following in Lucy and Garland's footsteps without realizing it.