The Bellevue PD is called to outside the scrapyard where there are signs of an altercation of sorts. Included within the evidence at the site are a jean jacket, a bicycle, a tooth, blood covered pieces of what look to be a torn adult magazine, and a cell phone. The phone in particular points to the fact that a person involved is sixteen year old Jesse Sweetland, arguably the best hockey player his age in town, he who has now been reported officially missing. Some within the police department initially don't take Jesse's disappearance too seriously if only because he, only recently known, is gender fluid, the thought being that he may have left on his own volition to explore this side of himself more fully outside the glaring eyes of Bellevue, the small town where he grew up. He may also be escaping what is perceived to be a bad home life, his mother, Maggie Sweetland, known to imbibe too much. Everything at the site, including the tooth and the blood, are eventually positively identified as Jesse's. Concurrently, the police are given the head's up that a known pedophile has entered town, Annie who investigates the possibility that he may be involved with Jesse's disappearance. Instead of finding information about the pedophile, she is confronted with issues from her past, most specifically issues concerning her life immediately after the death of her father. The case in which he was killed, that of murdered teen Sandy Driver, also has overtones to Jesse's case. Annie frequently still deals with Sandy's mentally unstable father, Neil Driver, who never recovered from Sandy's death. Putting some of the pieces together, Annie believes there may be some religious bases to what happened to Jesse, partly from the cross emblazoned on his hand as seen in a photograph on his cell phone.

In the continuing investigation of Jesse's disappearance, Annie has been receiving messages from the unknown person who tormented her with riddles when she was a child following the death of her father. Beyond the evidence gleaned thus far from those riddles, Peter does not want Annie following any of those leads, knowing how traumatized she was as a child from those riddles. Those current leads point to Jesse being exposed to aversion therapy, whether it be voluntary or involuntary being unknown. That aversion therapy lead points back to a person the detectives had previously questioned, who at that time stated that he had no formal ties to Jesse. Although already questioned by uniformed officers, the detectives decide to question Jesse's peers, most specifically his classmates and those people on the hockey team. The detectives may have a difficult task in breaking through the unofficial code of silence among that group, who in general do not trust the police. The one piece of information his classmates do provide is Jesse's ties to "the rez", Virginia who decides to follow that lead as an indigenous woman herself who may gain the trust of those on the reservation. But Annie discovers a tie between a piece of evidence already in possession and someone with connections to high places in town.

The missing persons case of Jesse Sweetland turns into a homicide investigation when Annie discovers his dead body on the shore of the lake, he having died from blunt force trauma to the back of the head, with preliminary evidence pointing to his head being held under the water during whatever the altercation that killed him. Information also comes to the detectives' attention that Jesse was planning on running away with his boyfriend Danny the evening he went missing, Danny who saw Jesse in a white truck when Jesse was supposed to meet him for their departure that evening. Annie divulges to Peter the clues that led her to the body being from the riddler - although Annie is uncertain if the riddle was supposed to point her to the body or something else - and the other anonymous contact she has had with "him" during this investigation. Annie believes she has a special bond to the riddler who knows what happened to Jesse, and probably knows what happened to Sandy Driver. While Peter is upset with Annie for disobeying direct orders to not pursue leads from the riddler for her own sanity, Peter allows her to cultivate their relationship to discover more information, with Peter cautioning her that the riddler may be Jesse's murderer. All this new evidence points to another well respected person in town as a suspect, Annie who can see on the surface the motive that this new suspect would have in wanting Jesse dead. The investigation begins to have an effect on Annie's home life as Daisy begins to follow up on her class project regarding Sandy. Daisy's actions do not sit well with Eddie, who wants to protect his daughter and who partly blames Annie.

The latest evidence discovered in Jesse's murder points to known but never charged or thus convicted ecstasy manufacturer "Rainmaker" Jed Martin, who, despite not being indigenous, lives on the rez due to his largely absent wife being First Nations. Upon questioning, Jed does not deny knowing Jesse - or Danny for that matter, and Jesse and Danny's relationship - but does deny everything else, including his drug dealings. More and more evidence piles up on Jed, which leads to him being charged with Jesse's murder. While Peter, Brady and Virginia are certain Jed did it, Annie believes the evidence is a little too convenient, her gut telling her that he is not guilty of murder. While Peter does keep to his promise to follow up on the Riddler, if only for Annie's protection (although he does not tell Annie his specific actions on the matter), Annie cannot help but believe that Jesse's murder still has something to do with the Riddler and Sandy Driver's unsolved murder from over twenty years ago. Annie works partly on the remote possibility that Neil Driver is the Riddler. In her investigation of this matter, Annie discovers a tie between Jesse and Sandy - although she doesn't know what that piece of information actually means - and discovers that someone, probably the Riddler, has found a new way to observe her goings-on. The dealings of the case begin to take their toll on Annie, who has a passive-aggressive reaction to the current goings-on in Eddie's life.

Maggie is preparing for Jesse's funeral, she wanting to honor her daughter the best way she knows how in light of she not truly yet understanding the transition that Jesse was going through when alive. There are two somewhat unexpected attendees at the service, both who affect the proceedings in different ways. Beyond the official service itself, Jesse's true friends remember her in their own way. Meanwhile, Annie decides to make direct contact with the Riddler through the surveillance camera in her house. She not only wants answers, she both trusting yet not trusting her unknown surveiller, but also wants to find out who he is, she asking Jim to help her track him through the Internet connection. Annie also has crossed certain people off the list as either Jesse's killer or the Riddler - despite some of those people still be considered as the murderer by her colleagues - but she knows that certain people, such as Maggie, still are not disclosing some pertinent information. The strongest key Annie believes is who planted Rainmaker Jed's drugs in Jesse's room. What the Riddler tells her, continuing in cryptic form, leads Annie down a path which hits a little too close to home. And Annie can see that there is something wrong going on with Eddie, she suspecting that he may be on drugs himself, which in turn affects if she will allow Daisy to be with her father alone.

Annie is now certain that Jesse's death has some connection to Sandy's death. With what she now knows, Annie figures the next logical step is to review her father's old evidence, the new and the old which she hopes will fill in the missing pieces. She knows that it will be a painful process, as her father killed himself two days after closing Sandy's case. In reviewing her father's notes, Annie learns Sandy's death coincided with the production of that year's Christmas pageant at the school where Sandy, Mrs. Spencer's first but perhaps not most obvious choice, was to play Mary, she who was replaced following her death. Mrs. Spencer, still directing the school's Christmas pageants, this year's which is currently in production, now takes the path of least resistance in casting. That evidence collected by her father leads Annie to a person who seems to be key to what was going on with Sandy's death, the connection to people around her which is not as clear cut as it first appears. These findings take their toll on Annie who needs to deal with the painful emotions in any way she can, destructive or not. With what Annie discovers, Peter feels the need to address certain aspects especially with regard to the Riddler and his relationship to Annie's father through Sandy's case. And Virginia finds a hole in some testimony regarding Jesse's murder case.

The stories of three of those initially questioned by the police in Jesse's death now have holes in they purposefully lying in their official statements. They are requestioned with each detective taking one of the three. Those new stories do corroborate each other, especially in the fact that all three were with Jesse together the night that she died, which either means they were able to discuss this new story ahead of time, or that they are now telling the truth, the latter which the detectives believe. In further investigating the story, Annie believes there was a fourth unknown person at the scene who saw and heard everything between the three and Jesse. Annie also believes she knows the name of the Riddler and why he has had such a connection to her. She is still uncertain if he will do her physical harm, intended or otherwise. Peter, learning the story from Annie, does whatever he can to ensure that the Riddler remains out of her life forever. The police get an unintentional and unexpected clue in Jesse's murder based solely on a freak incident with Daisy and Bethany visiting the site where Jesse's body was found. Annie and Virginia discover one more important piece of the puzzle in Annie accessing internal police information without authorization. What Annie eventually discovers hits a little too close to home, with issues of obsessive/possessive love, what she admits she feels for Eddie and what she admits is not right.

Adam is able to save Annie before Jesse's killer is about to kill her, that person killed in the process. Before Adam takes off into the night, he tells Annie that she has to understand why things have happened - the reason for the riddles - and that the cycle has to stop. Within his comments, he implies the identity of the Sandy Driver's killer. Annie slowly begins to understand part of that cycle when a group of three who were involved with what happened to Jesse the night he was killed are targeted in various ways, they who also have ties back to what happened to Sandy. But she will also learn Adam meant the cycle within their own family, that understanding when something happens to Daisy in the process. Through these issues, Eddie wants to take action in protecting Daisy with or without Annie, the possibility without based on what she decides to do with her own life.