A/N: I got bored and watched a couple filler arcs from Naruto Shippuden and did some reading on the Naruto wikia page and had a interesting fanfic idea pop into my head so I thought I would run with it and see what happens. Because the scope of this idea is so big and you can only list 4 main characters per story I am going to write and update a couple stories at the same time that will be interconnected with the characters crossing over. You WILL NOT have to read both stories to understand the plot since each story will focus on the listed characters with cameos and quest appearances of other Naruto characters. Enjoy!
Fugaku Uchiha stood in the office of the Hokage with his hands loosely clasped behind his back as he stared out the large window taking in the view of the village below him. It was early morning and the sun was just barely beginning to creep over the horizon. As the sun cast a new day on Konoha Fugaku's mind wondered, and not for the first time, to that fateful night three months ago. A night that had forever altered the fate of Konoha. The night of Konoha's quick, decisive and brutal civil war. When the Uchiha had rebelled against the very village they had once defended. Fugaku couldn't help but remember each of the shinobi he had killed that night and it saddened him that he had been forced to kill so many of his own clan members in order to preserve the peace of Konoha. Thankfully the sound of the door opening pulled the patriarch of the diminished Uchiha clan from the worst night of his life.
"Ah, Fugaku you're here early." Minato casually greeted his advisor and former Genin teammate.
"Good morning Hokage-sama." Fugaku calmly greeted Minato Namikaze.
"How many more times am I going to have to tell you to call me Minato when we're alone?"
"At least once more Hokage-sama." Fugaku deadpanned as he turned to face the Hokae he had chosen to support over the rebellion of his own clan. A choice that had left wo dozen Uchiha dead and almost twice as many Konoha Jonin dead and a handful of ANBU scattered lifelessly in the immediate area surrounding the Uchiha's vast compound. For his loyalty Fugaku was rewarded with watching his once great and proud clan reduced to the smallest clan in Konoha with barely 28 members, many of who were simply Uchiha in name and had married into the family and did not possess the Sharingan. His loyalty had also brought a great deal of mistrust from many of the current active duty shinobi for simply being an Uchiha, as well as mistrust of the various clan heads for not preventing the uprising of his own clan.
Minato simply pinched the bridge of his nose at Fugaku's response. The two had known each other since their days in the academy and had been rivals of sorts, with both boys consistently being the top two students in every subject and constantly trading victories. Even back then Fugaku had been a by the book staunch traditionalist. It was what had made him so effective as a shinobi and commander of the currently near defunct Military Police Force. As Minato moved to sit in his chair the blonde Hokage heard the soft shuffle of Fugaku's feet indication the Uchiha patriarch had turned form the window to face his old teammate, a gesture Minato returned in kind while remaining seated.
"Fugaku are you sure you don't want to take today off? I know the past three months have been exceptionally hard on you." Minato softly address his old friend.
"No. The elders chose their fate when they decided to incite rebellion among my clan." Fugaku instantly and bitterly replied in an angry tone. "For too long the Uchiha have slowly become arrogant in our possession of the Sharingan. The Sharingan may be a powerful dojutsu but it does not make us any more privileged than the other clan's of Konoha. Without the Sharingan many of the Uchiha would simply be mediocre shinobi at best." Fugaku took a second to slowly let ou his breath and compose himself. "With the execution of the Uchiha elders being carried out today and the other active members of the failed coup being imprisoned or assigned to labor camps with their chakra sealed away today marks a rebirth for the Uchiha, and the start of a legacy both my clan and village can be proud of." Fugaku held his head upright with pride as he said this.
"I have no doubt of that last part." Minato said with a smile as he turned back towards his desk. "Do you plan on keeping your Mangekyo Sharingan from your clan?" Minato tried to casually ask since Fugaku had been forced to activate it when the duo fought the elders during that fateful night.
"I have kept it a secret since it active when Hiroki was killed saving my life during the Third War." Fugaku finally admitted to Minato referring to their fallen teammate. "The Mangekyo has been a near legendary pinnacle of the Sharingan's power and has only been achieved a handful of times. Because of this the truth about its activation has been misinterpreted. Many of the Uchiha that have sought this power have murdered their closest friends and loved ones in a horrific attempt to seize power." Fugaku's demeanor took a darker and more somber tone. "The truth is that an Uchiha must witness the horrific death of a truly loved one to have the potential to unlock the Mangekyo Sharingan, but only those who are direct descendants of the first Uchiha can achieve this level of Sharingan."
Minato wanted to ask so many questions but knew that it was rare for Fugaku to be so forthright and open about himself or his clan, and out of fear that his interruption would cause Fugaku to return to his normally reserved and stoic demeanor Minato kept his questions to himself for now.
"If the Elders had found out to truth of the Mangekyo Sharingan I feared they would have taken drastic and horrific measures to activate this level of Sharingan in our clan. A fear that recent events have proven justified." Fugaku paused as he turned his head to look out the window to the village below. "But enough talk of such a dark matter. Today is a day to rejoice and hope for the future." Fugaku allowed himself a small smile "Our sons, and the children of many of the clans of Konoha start the Acadamy today. It's been a long time since a entire generation of Konoha's future has been so close in age. Maybe this will allow the Will of Fire to grow even stronger in the future."