After the massacre, on a yearly basis Itachi used to update Konoha about Akatsuki activities.
His top secret scrolls were retrieved by Root shinobi.
There was something about them that seemed off.
On one occasion the Uchiha examined one of them, an incredibly pale young man, whose dark hair and eyes looked a little like Sasuke's.
His brother had never had such a blank expression, though. The love and admiration he had felt as a child had turned to fear and hate.
The shinobi had a seal on his tongue; Danzo had indeed polished his methods since he left.
Even if Hiruzen had disbanded his squad, paradoxically the war hawk had managed to do exactly what he wanted.
Itachi's Tsukuyomi was no match for the old man's countermeasures.
It was easy to penetrate the nin's mind without breaking it, and see a nameless orphan raised with an older boy through the hardest training and isolation, subjected to the disgusting treatment he knew too well. The pale one got used to offer his body to please Danzo as it were another task required of him; the older one did no different, but he tried taking the most upon himself.
Itachi couldn't help thinking about Shisui.
He saw Shin, this was his name, dying from illness, thus assuring his younger brother to live, and his thoughts went to Sasuke. Unlike the Root shinobi, his brother would be happy to see him die.
He was experiencing the symptoms of an illness too, caused by overuse of the sharingan.
He thought he deserved it, just as he deserved the increasing blindness and the tiredness caused by the constant use of chakra, the burning in his lungs and every cough fit that left him breathless and aching in every fiber of his body.
He struggled to stay alive, though. He could not leave this world without giving Sasuke what he wanted, his revenge, and what he needed, even if he wasn't aware of it; his eyes, so he would never end up sick and blind as he was, and all his powers.
Sasuke had escaped from the village, but he would be forgiven. Killing his clan's slayer, the responsible for every wrong action he may have committed, would make him a hero.
He would never fall into Danzo's hands, as he, and the unconscious Root had.
The old man was now teaching his shinobi to erase every emotion, using him –the man who slew his entire clan –as a role model of loyalty to the village.
Ironically he also used Itachi to show the only fault of the Uchiha massacre: leaving one person alive, according to the old man a terrible mistake, proving that he hadn't properly erased his emotions, and that the current Root training was the only way to create perfect shinobi.
To avoid the miscalculations and mistakes made by the one who was dreamt about leading his clan to a peaceful coexistence, the Root enrolled only orphans, taking them when they were too young to have other memories, raising them in couples, isolated from the world where they would learn about other values and lifestyles.
Finally they would have to fight each other to death. The trauma erased every emotion from the winner, turning him into the perfect weapon.
As Shisui and he had never been, thought Itachi, imagining spiky unruly hair and a lively look on the Root shinobi, before releasing him from his technique and disappearing into a flock of crows.