The first raid
When Nancy Lunde and the undercover FBI agents Emily Prentiss and Spencer Reid arrive at the ranch, Ben greets them warmly and sets up an impromptu interview room in the schoolhouse. As Nancy and the agents talk to fifteen-year-old Jessica Evanson, discovering she is actually married to Ben, the ranch gets a tip that the police are planning a raid. Placing the women, children, Nancy, Reid, and Prentiss in the tunnels beneath the ranch, Ben and his most dedicated followers get into a heated firefight with the SWAT agents when they arrive. In the chaos, three of the cultists are killed, while two of the SWAT agents are wounded, and Nancy is accidentally killed by one of the agent's stray bullet when she ventures above to talk to Cyrus. Ordering a ceasefire, Ben allows the agents to leave with their wounded (one of whom dies en route to the hospital).
When the authorities and the BAU team set up outside the ranch, Ben is contacted by Rossi, who begins negotiations, Ben tells him about Nancy's death during their discussion. Having agreed to give the cult medical supplies, Rossi drops off several bugged boxes the next day, Ben lets him inside and shows him the women and children, who he refuses to let go when Rossi asks him to. When Rossi leaves, Ben pours each member of his congregation a cup of wine, telling them after they drink it that the wine is poisoned. After instructing his lieutenant Chris Cole to write down the names of those who panic after hearing the announcement (to know who his true followers are), Ben tells everyone there is no poison and he is giving them a test.
The turning point
Later, after seeing a news broadcast mentioning that an undercover FBI agent is in the ranch, Ben, when Prentiss admits to being that agent, takes her to an empty room and beats her unconscious, telling Chris to keep her tied upstairs. Getting advice from Reid, who realizes the ranch is already being bugged, Ben calls Rossi and claims he will release a child if they give the name of the FBI agent inside, as a trust test. Releasing a young girl, whose parents were two of the members killed in the first raid, Ben is told by Rossi that Prentiss is the agent before expulsing the members who failed his wine test, leaving only his most dedicated followers. Lying to Rossi, Ben claims the cult will surrender at noon and demands the press be present; in actuality, Ben is planning on a mass suicide as a last act of defiance and has his faithful followers rig the ranch to explode.
The final stand
As 3:00 a.m. approaches, Ben offers Reid the chance to leave, an offer the agent declines, telling the cult leader he wants to be the one to tell the cult's story. Moments later, Ben notices a squad of Humvees approaching and, enraged by this development, goes outside and fires a machine gun in the air to get the attention of the press. Preparing for the inevitable attack, Ben, after seeing Reid trying to talk sense into Chris, beats him into submission just before Morgan and several SWAT agents burst into the room, having sneaked in through the tunnels and evacuated Prentiss, the women, and the children. Both Ben and Chris are shot to death by Morgan and the agents. Having run back into the chapel after realizing her mother tried tricking her into leaving by claiming that Ben wanted her to bring everyone into the tunnels, Jessica, upon seeing her dead husband, grabs the detonator he had dropped and activates it, setting off the explosives that are spread throughout the chapel, killing herself and any of the dedicated followers still inside while Reid, Morgan, and the other agents manage to escape. Jessica's mother is later revealed to be the one who called in Prentiss, Reid, and Nancy to the ranch in the first place, to investigate the allegations of Ben's sexual relations with a minor.
BAU and SWAT Casualties
- Emily Prentiss and Spencer Reid (both held hostage):
- Emily Prentiss (assaulted to near-unconsciousness by Benjamin)
- Spencer Reid (assaulted by Benjamin and later nearly killed by the chapel explosion)
- Bower and a second unnamed SWAT agent (both injured in the first raid; Bower died en route to the hospital)
- Derek Morgan and numerous SWAT agents (nearly killed in the chapel explosion)
Separatarian Sect Casualties
- Three cultists killed in the first raid:
- Benjamin Cyrus and Christopher Cole (both shot to death by SWAT agents)
- Jessica Evanson and numerous unnamed members (killed when Jessica blew up the chapel with herself inside)
- Nancy Lunde (a federal agent; was accidentally shot by a stray bullet by the SWAT team)