And I saw, and behold... white horse!
The mission begins after all three heralds are defeated. One must simply approach the (now empty) compound in Joseph Seed's region and come to the church from the prologue.
Joseph will then meet the Deputy and offer them the same choice he was offering in the prologue. The Deputy can either fight Joseph (as well as Bliss-hypnotized allies from the entirety of the game, including both of his active companions), or take their friends and leave the Hope County for good.
Choosing to Resist will anger Joseph, leading to him ranting about the Deputy's primary sin being not Wrath, but Pride: refusing to stand down even if it means dooming everyone. He will then trip over two barrels of Bliss while quoting the Revelation. This begins the boss battle in a middle of the nightmare vision of the compound.
Joseph occasionally warps in, firing his assault rifle, and vanishes for a short time if enough damage is inflicted upon him. He cannot be defeated for good, however, until any of the Deputy's hypnotized allies remain on his side.
There is a total of 12 characters fighting on Joseph's side. Depleting their health will send them to Unconscious state, from which they can be Revived. If Revived by the Deputy, they will revert to their normal selves and once again become friendly; if Revived by Joseph, they will fight on his side. Each ally can go through multiple cycles, so it's not enough to just Revive them once, one needs to continue Reviving them if they fall to more damage.
Stage one requires to revive 3 allies, before more join the fight. Stage two requires dealing with 7, and stage 3 with 12. Only liberating all 12 will make Joseph defeatable. Obviously, the more allies the Deputy has, the easier it becomes to subdue others.
The battle ends with Joseph being finally defeated, captured and shackled. This will, however, cause a nuclear explosion to go off across the lake, forcing the party to immediately retreat to Dutch's Bunker while on a car. While player is in control, this is pretty much a scripted event: drive there within a limited time.
Arriving to the bunker triggers the ending. All except Joseph and the Deputy die in a car crash, and Joseph drags the Deputy inside. Upon waking up, the Deputy is bound to bed, alone with Joseph, and Dutch is dead. Joseph will narrate that his prophecy has come true: the world ends in nuclear war, and although he should kill his arch-enemy for devastating his flock, Joseph will instead make them his new child. Together, they will wait until the surface is habitable again to restart the civilization in the image of the Project at Eden's Gate.
As the credits roll, We'll Meet Again by Vera Lynn plays.
If Walk Away option is chosen, Joseph will immediately release the Deputy's original group. One might think that "friends" includes all allies, but in reality, only Staci Pratt, Joey Hudson and Earl Whitehorse are allowed to go. No combat occurs, as they leave the compound.
Hudson is outraged that they would leave everyone behind like that, but Sheriff Whitehorse tells her they're all going to Missoula to get federal backup.
However, as they drive away, the trigger song used by Jacob Seed Only You by The Platters plays on the radio, and the Deputy's vision goes hazy. Apparently visibly distraught, Whitehorse asks the deputy if they're alright, before the scene cuts to black and the credits roll, as Only You continues playing over them.
Once the credits end, the game reloads the last auto-save.
- There is an option to kill Joseph while in the car by using a sidearm to kill him; however, doing so results in another explosion instantly killing the Deputy.
- After choosing the "Resist" ending, the song that plays over the end credits is Vera Lynn's 1939 song, We'll Meet Again; The use of it in this context is a reference to the ending of the 1964 Stanley Kubrick film, Dr. Strangelove, where the world ends in a nuclear holocaust, with the song playing over footage of nuclear explosions.
The following section needs to be cleaned up to conform to a higher standard, as it is possibly too long, too detailed, lacking objectivity, unclear, or lacks citations.
- The ending involving the nuclear detonation ("Resist") sparked a huge discussion among players regarding whether the nuclear war is real, with 3 major theories:
- The Collapse is a real event unrelated to the actions taken in Hope County, and Joseph was right all along. The radio broadcasts about the international crisis add to it (although how the radio was transmitted with all communications to the outside world cut, is still unclear; this led some to believe the message is actually Cult's forged airwave).
- The Collapse is a hallucination from overexposure of all present parties to Bliss. Quite a few facts add to it, including unrealistic nuclear explosion physics (see below), absence of missile trails, Joseph's knowledge of the exact moment when it happens, the fact that he tips two Bliss barrels over when the fighting starts, and that it does not occur in "Walk Away". Another fact that increases the plausability of this theory is that Hurk knows Jack Carver, the protagonist of the original Far Cry, however the original Far Cry takes place in 2025, seven years after the events of Far Cry 5. This obviously means that a) Hurk and Jack Carver exist in the same Far Cry universe, b) Hurk knew Jack before the events of Far Cry, c) since they exist in the same universe and Far Cry dates after Far Cry 5, there could not have been a global nuclear war. However, this does not preclude the possibility of a localized nuclear incident.
- The detonation is real, but Cult-orchestrated and limited to Hope County only (since the Cult had connections to both American and Russian government, and the detonations are occurring roughly where the Cult bunkers used to be).
- If you chose the "Resist" ending: when you leave the compound and turn right to head south, the second nuclear burst's blinding light is almost immediately followed by the sound of the explosion. This is, however, impossible - if the same thing happened in reality, the Junior Deputy and everybody else in the car would be permanently blinded and suffer serious burns as the explosion would be closer than 0.5 miles (the speed of sound in air is about 1,125 ft/s), not to mention the Deputy, Joseph and others being able to drive and walk after the landscape starts to burn around them without suffering the same fate.
- During the scene where the Junior Deputy is offered the choice of resisting or walking away, you can catch a glimpse of the fence at the left corner of the small church behind Joseph Seed. However, when the fight is over and Joseph Seed is crawling towards the lake, the fence with the gate is gone, and it is not destroyed as no wreckage is seen (before and after Where It All Began you can visit Jacob's Compound and destroy the fence, but the debris will be visible on the ground). While this may be due to a deliberate design decision to offer an unobstructed view of the nuclear blast going off beyond the ridge of the mountain, it also supports the theory that everything is happening in a Bliss-induced vision, just like the fight against Faith.