To handle the matter, a joint operation between the United States Marshals and the county sheriff's department consisting of Deputy Marshal Cameron Burke, Sheriff Earl Whitehorse and his deputies Joey Hudson, Staci Pratt and an unnamed junior Deputy came to town.

They have arrive at an Eden's Gate church to detain Joseph Seed with a federal arrest warrant on charges of kidnapping with the intent to harm. Although Joseph offers no resistance, he claims that God will not allow him to be taken. The Deputy Marshall calls it all as a bluff and cuffed him. As he is escorted away, some cult members attack the task force and cause their helicopter to crash. Joseph escapes and commands the cult to capture the task force members. However, the Deputy survives and escapes with the help of Dutch, a resistance member from the town, who explains that the cult has interpreted the attempt to arrest Joseph as the fulfillment of his prophecies. Believing the end of the world is upon them, they have begun "the Reaping", a concentrated effort to purge Hope County of non-believers and gather all material needed for war. As the county is now cut off from the outside world, Dutch tasks the Deputy with contacting the young resistance scattered throughout Hope County to gather allies, rescue the task force and destroy the cult's operations to erode the influence of Joseph and the cult members.

Joseph's younger brother, John lures the Deputy to Holland Valley by broadcasting a message showing Hudson as his captive. This mad the deputy furious knowing that his friend is captured by a madman. John indoctrinates residents to the cult's beliefs by subjecting them to a forced baptism to "cleanse" them, tattooing their "sins" onto their bodies, and carving out the marked skin as part of their "atonement". John captures the Deputy and concludes that his sin is Wrath. When the Deputy escapes, John escapes by taking over the town of Fall's End where he forces the Deputy to confront him and atone for his sins. When all hope seem lost, a counterattack by the local Resistance came to the rescue. 

John was dumbfounded. He narrowly escapes.

This causes John to flee, leading to the Deputy engaging him in an aerial dogfight and mortally wounding him. As he lays dying, John remarks that the Deputy will not save anyone and asserts that Joseph is right. The Deputy rescues Hudson and the captive survivors and destroys John's bunker. But all is not over if that maniac Joseph is still around. the battle goes on.