The three qurans you are thinking of are when their prophet lived in Mecca before he was outcast to Medina. This was the peaceful verses. Then comes the Medina verses which get harsher chronologically and the final is after their so called prophet retakes Mecca and begins the conquest of all Arabia. These are the most violent verses in their book. The ninth book is supposedly said to have been one of the last books written in the Quran. This is the book that contains 9:5 which states to go kill all the mushrikun wherever you find them and tells how to collect the jiziyah (protection money) by humiliating the non-believers (jews christians etc. iow mushrikuns).
One other thing here is that the books of the quran are not in chronological order which is why you will have in book 40 peaceful verses towards jews and christians but in book 2 you will have them killing jews and christians. Its helpful that when you read the quran to have an idea of which book was written.
At one part early on....the Quran was in Chronological order. Then, all copies got called in and a rewrite occurred.
I can only speculate but I think the out-of-order rewrite was done for two purposes. First, if you realize there’s two eras of Muhammad (the Mecca-peaceful period and the Medina-violent period)....then you’d ask stupid question why he had to change.
The second reason is that you’d need someone to continually keep you focused on the writings and what was being said here and meant....so you’d need a Islamic scholar at every Mosque meeting. In the way that the Catholic Church controlled their empire with a Bible only in Latin...this same technique was used by the Islamic empire. Both wanted their ‘customers’ to seek only authorized readers or scholars.