And I saw, and behold... a white horse!
Main Article: The Warrant
The Deputy, also known as "Rook" is sent with Marshal Burke, Sheriff Whitehorse, and fellow deputies Hudson and Pratt, to arrest Joseph Seed, a radical preacher who is the head of Eden's Gate. Though Joseph appears to go willingly when they make the arrest, the situation quickly escalates when the cult responds to the arrest with violence and crashes the group's helicopter.
In the ensuing chaos, Deputy Hudson is captured, Deputy Pratt and Sheriff Whitehorse disappear, but Marshal Burke and the Deputy manage to escape the standoff, with Joseph calling for a manhunt to locate them. Following a botched escape attempt to leave the county on road, Marshal Burke is also captured by the cult, while the Deputy is taken away by Dutch, who promptly cuffs them to a bedpost until he decides whether or not to turn them over to the cult. He eventually decides to trust the Deputy, so he supplies them a new set of clothes (so they can blend in easier among the locals), and asks their assistance to liberate his island, thus providing the tutorial missions for the game.
Once the Deputy liberates Dutch's island, they are swept into an armed conflict between the Eden's Gate cult and the rest of the Hope County residents. These include Pastor Jerome Jeffries, a Gulf War veteran and local church leader who has seen his congregation taken by Eden's Gate; Mary May Fairgrave, a bartender whose father was driven to suicide by the cult; and Nick Rye, a pilot who aims to eliminate the influence of the cult in order to build a better future for his children. The deputy must use their help, among others, to build a local resistance to put an end to Eden's Gate.
Where It All Began
Main Article: Where It All Began
After defeating John Seed, Jacob Seed and Faith Seed, and going back to where it all began, the Deputy raids Joseph’s compound with the members of the Resistance, but Bliss is used to control the Resistance members, who then turn on the Sheriff and his deputies, capturing Pratt, Whitehorse and Hudson. Joseph gives the Deputy a choice to either walk away to save their friends or fight him.
Main Article: Resist
If you choose to Resist and fight Joseph, you must fight everyone in the compound to free them from the Bliss by downing and reviving them. After freeing everyone, Joseph attacks, leading to a final battle. After defeating Joseph in the battle, Joseph will quote Luke 23:34, followed by Revelation 16:1 prophetically, as nuclear bombs detonate in the distance, destroying Hope County. In the ensuing chaos, the Deputy, Whitehorse, Pratt, Hudson, and Joseph cram into a pickup truck and make a Hail Mary dash for Dutch's nearby fallout bunker. With everyone either dying from the initial blast or being burned alive in the blazing hellscape that was Hope County, they try to save themselves, but a distressed Pratt who leaps to the passenger seat in which Whitehorse is sitting in, all the while chanting "we're not gonna make it." distracts the Deputy, causing them to hit a collapsing tree, apparently killing Whitehorse, Hudson, Pratt, and incapacitating the deputy. Though semi-lucid, the Deputy is unable to stop Joseph from carrying them into Dutch's bunker. Notably, the way the deputy is carried into the bunker is directly identical to how Dutch carried the Deputy into his bunker at the very beginning of the game. Upon coming to, the deputy wakes up in Dutch's bunker - chained to the very bed they were before - by Joseph, who reveals he broke in and killed Dutch. Joseph forgives you for what you have done and shows mercy, saying he can't kill you because you're the only one he has left. He welcomes you to his family as his child.
Main Article: Walk Away
If you choose to Walk Away, Joseph will forgive the Deputy and his friends. Joseph, being a man of his word, frees Pratt, Whitehorse and Hudson. He lets them go at the cost of the Resistance now being under Joseph's control. However, shooting is heard as they leave the compound leaving their fate unknown. The Sheriff says he isn't gonna abandon them and vows they are going to come back with The National Guard to free Hope County by force. As The Sheriff turns on the radio for the long trip, The Deputy begins to go into flashbacks, through the song, “Only You.” Then the Junior Deputy turns around suddenly. The fate of everyone in the car, including the Deputy unknown, although it is assumed the Deputy kills or attempts to kill everyone in the car. When combined with the “Resist” option, there is currently no way for the player to actually win, no matter what they do.
It has been heavily implied that Deputy's fate will be revealed in New Dawn. It is ultimately unknown whether he/she survived the nuclear holocaust or not.
- While in the Henbane River region of Hope County, the Deputy will often see hallucinations of animals that will change form after taking damage. Harmless deer may turn into much more dangerous bears or wolverines. However, these are hallucinations brought upon the deputy by Faith Seed, prior to her showdown during Paradise Lost. Once Faith has been dealt with, the hallucinations will stop occurring.
- Although the Junior Deputy is conditioned by Jacob Seed, they can still listen to the trigger song, "Only You", at liberated outposts' radio sets without any ill-effects.
- The Deputy is the first Far Cry protagonist that is fully customizable.
- If the player chooses the Deputy's gender to be female, this would technically make the female version of the Junior Deputy the first playable female character in the Far Cry series, if the co-op missions in Far Cry 3 are not taken as canon.
- The closest the deputy gets to speaking is through grunts or pain-induced noises.
- The Junior Deputy is the first mute Protagonist in the entire franchise.
- The Junior Deputy would be the second mute protagonist if one counts Far Cry 2. In that game, the nine playable characters only speak when they are NPCs but are silent when controlled by the player.
- The Junior Deputy is often seen on cult wanted posters. However, the cult posters are generated based on your current appearance; if you change your outfit, the wanted posters are immediately updated, even if you are looking at one of them.
- The outfit worn by the deputy during the prologue is notable for purposely obscuring the player's appearance such as skin tone or body as the player has not yet reached the customization phase to define their appearance.
- Male and female versions of the Deputy have different styles of the same outfits. An example is that the "Badass" shirt is tied up just below the chest for the female, while the male has a tank-top variant of the same design.
- The Deputy is the only Far Cry protagonist who holds their gun at their hip rather than shoulder when standing.
- After completing the main story in the New Game+ mode on the Infamous difficulty the player will be rewarded with the "Rook" outfit as a UPlay reward.