The war was over. People rejoiced and people mourned. Some went to count their blessings, others, their losses. But overall, everyone rejoiced. The prophecy was true. They were saved and they wanted to embrace their saviors. Sakura, the apprentice, Sasuke, the redeemed and Naruto, the Child of Prophecy.

Searching...
A cabinet slammed shut.
Searching...
Another one opened
Searching...
That one was soon closed
Searching...
One more cabinet was opened and everything became still.

In one of the Sound Village's many forests is a tree. One just like all the other ones around it, yes, but this one held truth just beneath it. Because deep under the tree was a lab. And within the lab was a very confused person. Which was a very rare thing.

They stood back as they looked at all the scrolls that may or may not have been copied from the Konoha. Each scroll contained information about a certain clan and the mission that was given to the clans killer. And surprisingly, there wasn't that much.

Something was wrong.

They went back to the scrolls and read each one carefully.

It was missing.

The scroll containing Itachi's mission was missing.

But why? They wondered.
Didn't old man Sarutobi at least eight down the mission on a scroll for future evidence?

Unsatisfied with their lack of knowledge on the matter, they closed the scroll and left the lab.

The village they were currently in was devoid of human life as the figure darted through the shadows and streets. They stopped in front of a red building with a giant sign that held the kanji for fire on the front. They stood for merely a second before continuing inside.

Past the office, past the room that said important scrolls and into...a broom closet.

Once they entered, they tugged on the drawstring that was for the light three consecutive times.

Then they fell.

Unlike how most people falling down a mysterious hole that somehow appeared in a broom closet would react, this person just looked down with their hand to their chin wondering about where they went wrong.

They landed on the ground with a soft thud before heading to the file cabinet titled S.U. and opening it. They quickly let their fingers glide past the multiple files inside before bringing their hand up. Their eyes shifted down to their hands where a file titled Coup D'etat rested. Inside was a detailed description of a mission that was assigned to the man with the initials S.U..

His mission, hm?

Their eyes glazed over the report and halted once they reached the end of the paper.

Shinobi Status: Dead
Additional Notes: Body missing

Now it was starting to make sense.

The figure quickly used body flicker, leaving a puff of smoke in there place.

Itachi's missing file.
Shisui's missing corpse.

Ah, so that was what all those weird heat signatures were that were under Amegakure. He must have had to remove some of their memories along with others memories in order to do it though.

Itachi's file was missing because there was never one in the first place.

Shisui's corpse was missing because there wasn't one to begin with.

They opened a scroll with purple trimming and wrote:

After the war
Otogakure base
Uchiha archive

I have recently discovered a truth about Konoha, mainly about its oh-so-powerful Uchiha clan. It seems to me that Shisui Uchiha never did die. Interesting, hm? He succeeded but altered his plans a bit. He cast his Kotoamatsukami on the Uchiha and the whole of the Leaf. Then he only removed it after bringing the Uchihas under Amegakure and erasing their memories. Leaving Itachi-kun and Sasuke-kun behind and replacing their memories with new, darker ones and the rest of Konaha to believe that the clan was whipped out.

The truth is-

Thud!

The noise caused them to drag out a character making it like a line. They turned around just in time to lift up an elegant hand which held a kunai and deflect another kunai that was aimed at their throat.

Standing in front of him was an eerily familiar shadow with glowing red eyes.

"Orochimaru."

His lips tugged to a curve at seeing his theory proven correct with his own eyes.

Turning their whole body they fully faced the figure that dared to attack him.

"Shisui."

The Uchiha clan never died.