Everything originated from the Nine-Tails Rebellion that frightened Konoha civilians and ninjas. Konoha's heroes Namikaze Minato and Kushina died and sealed the Nine-Tails in the body of their newborn son Uzumaki Naruto, but what they didn't know was what kind of treatment their sons had suffered since their deaths.
The choices Naruto Uzumaki made later also made the Third Hokage and his faction regret for what they had done.
Konoha Village? Oh, what does the village have to do with me? You must be ready to bear the consequences of what you have done, right?