Synopsis
When Itachi got asked to spy on the village for the clan, and spy on the clan by the village. Itachi decides to take more things into consideration and discovers that the higher ups of the village aren't as good as they appear to be. He discovers the inhumane experiments on the civilians and orphans by Danzo and Orochimaru, he discovers that the higher ups let Uzushiogakure be destroyed and that they were the ones that leaked how to get passed their seals to their village, but the worst of all was when Itachi discovers that Danzo abducted and ambushed many Uchiha's during the 3rd Ninja War so he could take their sharingan.
After discovering all of Konoha's misdeeds, he decides to side with the Uchiha Clan along with Shisui Uchiha and rebuild Konohagakure.
This would also allow Itachi to get closer to his goal of bringing peace to the element nations.
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1. Itachi decides to take the Uchiha Clans side and fight the village.
2. The MC is reborn as Itachi and also takes side of the Clan. (MC would have future knowledge and would be able to prepare for Obito, Madara and Kaguya.)
In order for Itachi's plan to succeed he would still have to eliminate some of the elders of the Uchiha Clan (including his father.) in order for the Clan not to treat any other clan as their slaves because of their arrogance. (Itachi's goal is to make the village better and not enslave other clans.)
(You could also get some of the other clans on board like Yamanaka or Hyuga which sluld have been cool maybe even get Jiraya on board.)
Then comes the day where the remainder of the village takes on the Uchiha Clan and the Uchiha Clan come out victorious.
(Uchiha would have 3 or 4 Mangekyo users. Itachi, Shisui, Fugaku (who they would let die.) and possibly Mikoto)
(It said that Mikoto was good friends with Kushina so you could say she awakened MS when she found out Kushina died.)
Itachi would also make sure that absolutely nothing would happen to Naruto and Sasuke because they will be necessary in order to seal Kaguya (Use this if you decide to have the MC be reborn as Itachi.)
You could have Mikoto adopt Naruto and raise both Sasuke and Naruto as brothers. You cluld also help Naruto control the Kyuubi and make him stronger than his canon counter part.
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In Iwa
After hearing news of what happened in Konoha, Onoki believes that the village would be weakened too much so he decides to send a decen sized army to try and destroy the rest of Konoha, unfortunately for him, none of his army will return because they would be slaughtered by Itachi/Shisui.
From here on you could follow some of the canon. Or add in completely new events etc.