Beneath the village of Konoha in one of the many secret bunkers created by the late snake Sannin a man set at his desk. He commanded the black ops of Konoha's military. Both the Godaime and Rokudaime Hokage believed that this section had been disbanded since the death of its previous leader.
'For thirty years I have been here and now the peace that I have been striving for is coming to its end.' He was brought from his thoughts as he heard three knocks at the door.
"Enter" at his command a tall pale man his hair was black with small streaks of grey walked into the room, "Report."
The man knelt on one knee staring at the ground.
"As you predicted it has begun, and we number too few to be able to have the desired effect on the outcome. Per your orders the initiates have taken to relocate the potential recruits to a safer place." His voice was low and emotionless; whatever he had gained over the years had been lost.
Both men sat in silence for a moment, before the man at his desk spoke again, "Rise Sai" he watched the man in front of him stood awaiting orders.
"I wonder did Danzo ever regret some of the choices he had made or was he always able to be the cold logical tool that he believed all Shinobi should be." He couldn't help but feel whimsical he had never really known the man in life. It was only after he had been passed up the spot of the Rokudaime that he came to know of the man more.
"I don't know, but he was a firm believer that emotions were dangerous, that they breaded hatred and hate bread war." Sai could remember the day that Danzo had told him those words. It was the day that he had wanted to be permanently assigned to team Kakashi.
"He was both right and wrong with that, it's why we still have the emotional conditioning. But they can give us great strength. The problem with most Shinobi is that they can't leave their emotions on the battlefield." He couldn't hold back the small chuckle at that thought. "I am probably a living example of that fact; you would think that they would have been happy with the defeat of the Kyubi but there hate stayed with them. We were heroes of the fourth war and defeated Pain, but there hate and fear still stayed. Maybe that is why I wasn't able to do more."
Sai stood silently listening to the man that he had followed for years. He was not like the man that had taught him the ways of being a Shinobi, no the two were very different in that regard, but as time moved on their similarities became strikingly clear to any who paid attention. He wasn't sure when it happened maybe after the fifth war, but he knew that the last thirty years of peace in Konoha was all thanks to him. And now all that he could do was watch as the peace that he had strived to keep began to crumble around him.
"Is there nothing that we can do?" Sai already knew the answer if there was something that could have been done to prevent this then it would have already been done.
"Both the Roots and the Leaves are needed for the tree to prosper, but when the centre is rotting the tree is doomed to fall. Tell me Sai if you could do it all again would you do it any differently?" he was curious he had been thinking about the question himself a lot recently. What would he do differently?
"I don't know Naruto-sama but…" before he could continue he was cut off.
"What did I tell you when we are speaking freely?" Naruto looked at Sai with a bored expression.
"Of course" reaching into his pocket he brought out a small note book and flipped through it, "I don't know Oh great Toad Sage of Mount Myoboku, Man that has been known to bring both men and women to their knees for different reasons, crusher of armies, wooer of…"
Naruto couldn't hold back his laugh he didn't think he would be able to laugh at all on this day but Sai had managed to find a way, "One time Sai, I introduced myself like that one time and you still hold it against me."
"It seemed to help moral in the fifth division during the last war. Though I don't know, I don't think I would do anything differently. What about you any regrets?" Sai asked.
Looking around the room that had been one of his offices for the last thirty years Naruto had to wonder if there really was anything he would change about his life. Like everyone else he had his regrets, the people he couldn't save, the people that he let live that he really shouldn't have. It was a long list but at the same time everything that he had done had brought him to where he was today.
Maybe there was a lot he could change but there is no guarantee that it would make a difference in the long run. 'Heck there's every chance that the same outcome would have happened sooner.'
It was definitely a sobering thought that no matter how hard you tried that your home was doomed to fall.
"Regrets Sai, yes I have many regrets. Would I change my life, I don't know. If I did maybe I wouldn't be the man I am today." With a sigh Naruto glanced around the room again.
"You know Sai if someone told me when I was a genin that this was needed to protect the village I would have scoffed at the idea. Part of me is amazed at how long Danzo managed to keep the village alive without anyone ever knowing it." A sad smile came to his face at the thought of the man, "I bet he would have been able to keep the village together. That what is happening tonight could have been avoided."
"I don't know Naruto, Danzo-sama was one to make the hard choices like you and do what was needed for the village. Maybe this was just unavoidable." Sai spoke quietly he didn't like what was going on outside the walls. He was as close to heartbroken as he had ever been at the thought that the village that his teacher and his friend had both loved was crumbling around them.
"Sai your in charge" there was no waver in his voice no change he had decided on his course of action and he would stick through to the end. "If I don't make it back you know what to do." And before he could hear a reply he was gone.
00—00
Standing on top of the Hokage monument Naruto looked down on his village, he could hear the sounds of battle the screams of the civilians. It was truly a terror, the worst type of war, Civil war. 'Brother against brother, friend against friend, family against family. Is there anything worse?' Looking to his left and right he could see the heads of the previous Hokages and the current one.
"I wonder what you would say if you could see how far your village has fallen."
"So you finally came out of your hole Naruto?" A voice said from his left.
"Yea Shikamaru I decided that I should see the destruction of my home first hand. You know I warned you of this day. I told you that this would happen after you cut out the civilian council" Naruto said as he turned to see the current Hokage, a tall black haired man with a spikey ponytail, dressed in the standard Jōnin outfit.
"I was always surprised that you had managed to get so many of them to listen to you before they were cut. They were too troublesome after the forth war they kept trying to butt their heads into Shinobi business." Shikamaru let out a sigh at the memory of the council.
"Yea but after the fifth when you realised the reason they were needed you gave them too much power. Then it was just a slippery slope down." Naruto let out a sigh as he pulled off his Hitai-ate taking a long look at it he dropped the metal plate on the ground.
"So you have chosen your side." It wasn't a question Shikamaru was proud of his reasoning and deduction skills. The blonde man may have become more of an enigma over the years but he was certain he could still read him.
"No Shika, I never had to choose, always for the village, since the day I put on my Hitai-ate it has always been for the village." Reaching into his jacket Naruto withdrew a white porcelain ANBU mask.
"And today is no different, the tree is rotting neither the leaves nor the roots can nurture it any longer. But we will plant a new tree and the roots will nurture it until it is ready for the sun." Naruto spoke with finality as he placed the mask on his face.
"So that's it you cut your ties and start anew" Shikamaru asked as got ready for an attack.
"It's not cutting ties the village is dead, you have seen to it." There was no emotion, no anger or sorrow that his beloved village was dying. "Trying to appease the different factions within the village has only made others angry."
Naruto looked at the man in the eyes though Shikamaru would have a hard time to see through the mask. "We are Shinobi of the Hidden Leaf, we are meant to protect our home and fight our enemies that want to take what is ours. Now they will take because we have started to fight between ourselves."
"Tell me Shika just how fast is that shadow of" before Naruto could finish his question he realised that he was caught in Shikamaru's shadow. "No hand signs impressive."
"I'm sorry Naruto but you are to blame for this, your actions over the years have made the other shinobi wary. And the fact that you control a branch of the military power who answers only to you has not helped with the fears that the Ninja population has." He didn't want to kill the man but once they put down this civil war they couldn't have any rouge factions within Konoha.
"Konoha is dead Shika; it is time to understand that they are tearing themselves apart down there." Naruto spoke calmly as he tried to overpower Shikamaru's hold on him to look at the man one more time.
Shikamaru watched as his onetime friend suddenly flashed away from where he was standing, he wasn't fast enough to stop the sudden drilling into his lower back. "And with this one of the five nations fall."
The pain was immense Shikamaru never thought that he would ever see the day when he would have to take an attack from the Rasengan. He was barely holding on to consciousness.
"Danzo spent so long in the shadows that he could no longer see the Will of Fire, I am different I can still see it burning. It may have dimmed over the years but it is still there. I know this Shika because I spend my time in its shadow guarding it from whoever may wish to do it harm." Looking at his friend he couldn't help but feel guilt at what he had to do. But the village always came first.
As he left the man to die on the head of his father's monument Naruto left his final parting words, to a question Shikamaru asked him so long ago. "I remembered who was king of this village and I will always protect my king."
And with that Naruto left his old friend, for tonight his village had died, for tonight he had lost what he had fought for so long to protect. But the king was still in the village and if he was going to rebuild he would need to protect it.
A.N
This was an idea that has been kicking around my head for a while I don't know how it turned out some feedback would be much appreciated but hope you enjoyed it.