Here's my though on how it happen
Madara and Izuna had a plan and that was the infinity Gen jutsu.
So it starts of with Madara and Izuna planing a sacrifice since they were the most feared and respected of all Uchiha. If one was to die, and given a reason it would have change the Uchiha clan to go to war with the Senju Clan.
However, since many Uchiha refused that had raged Madara since the death of his brother meant nothing so Madara left the Uchiha and fought Hashirama being defeated by the 1st, Madara had survived but with near death he retreated and hidden for a long time. During his time period he created Zetsu, to watch over the hidden leaf and Zetsu must have heard that there some Uzumaki still leaving in a certain village. Zetsu then went on to tell Madara,Madara realising that this is the chance that him and his brother had plan.
Madara went on to find the boy, 'Nagato,' Madara had worn the mask That had flame mark on him and spoke to Nagato parents before him being born. He told them that if you want your child to be the most powerful ninja and told them the tale of the sage of sixth path. Nagato Parents both believing in the man had allowed Madara to place the uchiha blood in him, however, it would only awaken when the person experience a close person death.
So during the time when konoha ninja killed nagato parents he had awaken the rinengan and disappeared n formed the group with yahiko, konan. and Jeriaya had trained dem later for them to form the group called akatsuki. (Uno there story....)
So during Minato Arc....Obito had died but was found By Orochimaru who knew madara was alive, so he brought Obito to Madara and zetsu had shown him what had happen. Madara was dying..So he asked orochimaru to fix obito body and obito had use zetsu body to fix obito. But since obito was Dead they needed a soul n that soul was non other den izuna madara had placed Izuna soul in obito.
However, since obito was brought back he had remember who he was but izuna was inside of him....MAdara had train Obito and gave him access and strength to control the fox.
Now heres the twist Obito had attack the village when he was fighting Minato he had swapped with zetsu(IF you remember, zetsu has the ability to become you) they swapped so when they fought minato was able to defeat him n if you remember tobi touched his left side which wasnt crushed and somehow zetsu body part fell of.
All tobi was planing to do was try and get the hokage killed since minato passing tobi went to speak to Nagato and Nagato remembers Tobi because of the mask that why he had always considered him to b madara. So later one Tobi had notice that there was someone else leaving inside of him and he had tried to figured out who it was and when tobi messed around or when tobi was on low chakra the soul of izuna would take over and that when tobi was feared he would retreat to avoid both being killed.
When nagato had died tobi had when to get the rinengan and placed it on himself..however when madara died way before orochimaru had taken his dna...
IF you remember minato died using the reaper death seal so there was no possible way to resurrect him so when orochimaru resurrected 1st nd 2nd the 3rd coffin was suppose to b madara!
I stop writing because i cba atm i was to busy...N sorry if i had miss some fact this is just my opinion...N by the way minato consider tobi to b madara because only madara was known has the ninja to summon the fox.
