The Atonement (Story Mission)
When you've finally pushed John so far he can't be pushed no farther (ie, his Resistance meter is full), you'll get this mission.
You can still pursue other missions around the valley, if you want to tie up any loose ends. Note that, with the exception of Hit the Gas, all side mission should still be available after this. Even Hit the Gas wil register as 'completed' in your mission log. When ready, go the church in Fall's End.
After getting knocked out by a so-old-it's-got-whiskers-on-it cliche, you'll get a long cutscene with Fashion John.
Jerome will eventually produce a revolver from his bible. Say 'Yes' to take it. You will then be immediately reunited with all your usual weapons.
Secure the church and its environs. The safest spot is from just inside the church door.
Jerome, however, doesn't share your big-city notions about 'shooting from cover,' and may need a revive or two if you want to keep him in the fight.
When these goons are down, hop in the turret truck with Mary May.
Another rail-shooter sequence. The characters will advise you to disable vehicles by shooting out the tires, but shooting the driver is at least as effective.
After a few trucks and ATVs, you'll be attacked from the sky. Your turret only elevates so high, but once the planes are in range they go down pretty quickly.
There are three planes- then it's just a few trucks and ATV's between you and the ranch.
When you get there, it's dog-fighting time. This begins the Wrath story mission.