Johnny affected Ponyboy a lot throughout the story. When Pony was drowning Johnny has to kill Bob to save Ponyboy, this affected both of them. This makes them have to run, They went to a church, and there was a fire, and they have to save kids. They managed to save the kids but Johnny pushed Pony out, and Johnny was hit with a piece of lumber. Johnny died and that put Pony in disbelief, and he wanted to believe that he never died, but the letter he wrote helped him accept his death. He said that the kid's lives were more important than his life was.
When Johhny kills Bob it made a very big influence on both Ponyboy and Johnny. When Johnny kills Bob it made then get help from Dally to run out into the country for hiding. This makes Johnny very scared and worried and makes them go to a church in the country for a hideout. They are being searched for and targeted by both the police and the Socs. Johnny only kills the Socs out of self-defense, he has to save Ponyboy and has to save himself.
The church serves as a hideout for Johnny and Ponyboy after Johnny killed Bob. When Johnny killed Bob, both the Socs and Police were after them. They had to "lay low" while the only person who knows where they are is Darry. The church also was a conflict, when Johnny and Ponyboy's smoking caused a fire. This created a problem because after Ponyboy runs to save the kids, they all have to go and help get the kids. This caused Johnny to get hit by a piece of lumber.