After killing Bob, a Soc, Johnny and Ponyboy escape to this church out in a pretty remote, mountainous location (which is wonderfully symbolic after Ponyboy's dreams of a simple life in the country) based on Dally's advice. After staying there for a while, Dally comes to check on them and takes them for a quick meal before leaving them again.
Interestingly, it is just before they are all aware of the fire that Johnny has a couple of pertinent revelations. First, he considers turning himself in to the police because he sees that as the best possible outcome for both him and Ponyboy. He also asks whether his (abusive) mother has asked about him, and Dally tells him that she hasn't. Pony realizes that as much as the group of friends support and love Johnny, they are no replacement for the actual love of a mother that Johnny has never had.
When they return the the church, they stop short when they realize that it is on fire. A group of kids has gathered in what seems to be a school picnic, and someone becomes frantic, yelling that some of the kids are missing.
Johnny and Pony leap into action, believing the church is ablaze because of one of their cigarettes. They knock out a window, climb into the church, and get all the kids out. Unfortunately, Johnny is hurt badly in the process.