When Nate Sefton goes missing, his brother Jeff, a tarnished reporter, goes looking for him. Jeff discovers that Nate's disappearance is tied into the underground following of a TV show, Cult. He joins forces with a research assistant on the show, Skye Yarrow, and they soon discover that a secret group of fans may be responsible for a series of murders and abductions. Meanwhile, in the series itself, FBI Agent Kelly Collins closes in on the men who abducted her sister and nephew on the orders of cult leader Billy Grimm.
Jeff has a tech friend, E.J., trace Nate's phone call on the night of his disappearance. Meanwhile, Skye expresses her concerns to associate producer Peter Grey, who is less than concerned. and on the show within in a show, Billy tries to help Kelly solve a murder with connections to The Blood, his "family" of followers.
Jeff meets his brother's girlfriend, college student Laura, and learns that a new craze sweeping the nation: Being Billy, a game where students recreate scenes from the series. When one recreation leads to murder and Jeff learns that Nate ran the game, he wonders if his brother is a killer.
Jeff makes contact with a woman, Alma, whose husband Rami disappeared under the same circumstances as Nate. He and Skye make contact with her and Terrence Ross, the cult deprogrammer that she's hired. Meanwhile, on the show, Billy abducts a cult deprogrammer, Professor Parker, who is writing about him and has a personal chat with his unauthorized biographer.
Jeff discovers that one of Nate's friends, Dustin, is planning on attending a Cult fan costume party held by the network. Skye gets the two of them in posing as Billy and Kelly, and soon discover that Dustin is slipping hallucinogenics into the punch... and Skye inadvertently drinks one. Meanwhile, Roger meets a mysterious stranger who claims to be a big fan of the actor's non-Cult performances.
Skye collapses from the aftereffects of the hallucinogenic and the doctors soon confirm that she will die if they don't obtain a sample. Jeff sets out to get a sample from Detective Sakelik with the help of a friend. Meanwhile, Skye confronts figures from her part and present as she tries to determine what is real and what isn't.
Jeff and Skye look into Sakelik's past and trace her to a mysterious house. There they encounter a woman, Annabelle, who holds the key to Sakelik's past. Meanwhile, Sakelik visits a friend and seeks redemption.
Jeff and Skye get a lead on a video that can tie Sakelik to the murder of Olivia Leland, and the trail takes them to video store owner Louis Beal. Meanwhile, on the show Kelly makes a deal with Billy to get her sister Meadow back.
Songs: Murder by Death -- Go to the Light
A former initiate gives Jeff and Skye the information they need to let Skye infiltrate a gathering of new recruits for the True Believers. However, Jeff soon loses her trail only to make some startling discoveries of his own. Meanwhile, on the show, Andy is abducted and Kelly suspects that Billy is responsible.
Songs: How to Destroy Angels -- Keep It Together
Skye discovers that one of the actresses on Cult has ties to the Moon Hill children, and the trail leads her and Jeff to a church dedicated to television. Meanwhile, Stuart asks Roger for a favor, leading Roger to a shocking discovery. And on the show, Billy pens his magnum opus while his sanity cracks.
Phillip's book leads Skye and Jeff to the missing Professor Robert Kimble. His assistant Allegra provides them with clues to the secret of neural interface, and they soon make contact with Kimble and learn of his connection to the Moon Hill parents. Meanwhile, Roger confronts Kirstie and on the show, Kelly goes to therapy with her sister Meadow.
After abducting Allegra, Stuart puts her to work "reading" Cult to find out the secrets to his father's whereabouts. When she meets Nate, Nate asks her to deliver a message to his brother Jeff if she escapes. Meanwhile, Jeff and Skye come up with a plan to locate Stuart's headquarters. On the show, Billy's plan to force a confrontation between Kelly and her parents' murderer proceeds with some help from Meadow.
Jeff trades the location of the Moon Hill parents to Stuart in return for Nate, reuniting the two brothers at last. The Moon Hill children disband after discovering the fate of their parents, but Stuart vows to continue the search for his father... and joins forces with Jeff, Skye, and Nate to learn the truth. Meanwhile, in a live webcast broadcast, Billy and Kelly have their final confrontation and Kelly must make an impossible choice.