So this story will be kind of a kingdom building story but that will come later.
MC awakens in Amegakure, arguably the worst possible village to live in.
MC will be the same age as Yahiko, Konan and Nagato. You could possibly make the MC related to one of the Characters previously mentioned.
Due to this being an Ame based story, you want to focus on the life in Ame and how terrible ths living conditions are due to the War.
They meet and start living together, Eventually they meet the 3 sannin and end up trained by Jiraya.
Eventually you want to kill Hanzo and his men while making sure that Yahiko and the others don't die.
Once they killed Hanzo, the kingdom building begins. You start to learn fuinjutsu, make an academy, an orphanage.
Write about the relationship and meeting between Ame and other villages etc.
You will have to adjust the story so the 4th war still happens.