Disclaimer: I still only own my OC's :)
Kaze no Uchiha
As promised Kenji and Jenki visited as often as they could without arousing suspicion, steadily becoming more 'human' and gradually developing their own opinions. They were continuously evolving and Jenki especially was very good at bending their orders, as long it didn't endanger the village. That was how Aya found herself in the surreal situation of pretending to be a root-operative patrolling with Jenki, while said nin told her what he could about ROOT.
The reasoning Jenki had employed to get around their secrecy was very backwards, involving a lot of free interpretation. He wasn't allowed to talk about or mention the organization to the uninitiated unless being ordered to by Danzo-sama. But Jenki reasoned that Danzo-sama always did what was best for the village, no matter how distasteful it was, and had created the organization for this reason. Therefore he should, as a member of this organization, strive to do the same, even if he had to act to protect it from said organization. Furthermore he concluded that the village wouldn't exist in any meaningful form without its people, so they had to be protected. The one charged with protecting the people was the Hokage, meaning he made the decisions these people's security depended on. Withholding crucial information about the village's shinobi force was a security-risk, as he could not make the right decisions if it was based on bad information. It was his duty to correct this breach in security and the most effective way to do this was to inform the Hokage. He could however not do this himself, since it was unlikely that the issue could be resolved immediately and this fact made having an operative inside the organization necessary. Should he be seen near the Hokage without being ordered there, he would be killed and Kenji's loyalties probed, which would seriously hinder said person's ability to find information too. The logical solution was to use a middle-man without any connection to Danzo-sama, one that could be trusted to only report the information to the Hokage, and one that the Hokage would believe. Aya lived up to all of those criteria. She could also be considered to live up to ROOT's core view of itself, being an unseen one who supported the great tree of Konoha from the depths of the earth, since she served the village with only the Hokage knowing it. She already knew about ROOT, who they reported to and was currently wearing the uniform while performing a mission for the organization. This shouldn't have been possible if she wasn't initiated, so it followed that he was in fact not going against his orders, when he talked to her in order to do what was best for the village.
That this arrangement allowed his brother, Kenji, to spend time with his pet was just an added bonus.
It was only years of hearing politicians and officials talk circles around each other that allowed Aya to somewhat follow the convoluted argument.
During the patrol Jenki told her what he could about being raised and conditioned to have no personality, name or personal connections, killing the one closest to them to complete their emotional conditioning and finally how the organization only answered to Danzo-sama. He also showed her the cursed seal all operatives had on their tongue, preventing them from ever disclosing information about said person. She could see how he struggled to reveal even that much.
After Aya reported her findings to the Sandaime, he set in motion a longsighted plan concerning ROOT. He first recruited her to help identify members of the organization, since she was one of the few he could be sure Danzo couldn't influence and because she would be able to recognize members even after only seeing them in uniform. He then called in Nara Shikaku to a private meeting, explaining the situation to him and assigning him the mission of basically unraveling the mess. Shikaku, needless to say, found it all very troublesome and wanted to know whom he would be working with.
"I will introduce you to an operative of mine, who will brief you on her findings. During this mission she will also be supplying identities of possible operatives along the way, to give you more to work with. I am completely confident in her loyalty," – 'After all, she already knows a good chunk of Konoha's ugliest S-class secrets and still hasn't deserted' Hiruzen thought to himself – "so I ask that you have the same, even though you won't be able to verify her identity. Other than that, I trust your judgment on who to recruit for this mission, Shikaku"
Then he called in Aya, who was in the guise of Kurohyou and wearing a voice-distorter to protect her civilian identity. When the privacy-seals were up, he said "This is Kurohyou, Kurohyou meet Nara Shikaku. Please brief him on everything you have found about ROOT and their operatives, every little detail could be crucial".
When Aya got home that night, she fell like a boneless pile onto the couch, mentally exclaiming 'Finally! Having Shikaku milk your brain for information isn't something I will ever wish on anyone'
But at least now something was being done and they had the beginnings of a plan. Saru-jii-san was trying to reach Jiraiya, as they planned on having him look at the cursed seal, possibly while she was taking the place of either Kenji or Jenki. 'Probably Kenji, since we are closer in height' she mused
Until then Aya would be perfecting her ROOT-persona, slowly getting the other operatives subconsciously used to the extra operative. It helped that none of them formed any bonds to each other or knew all other operatives. Kenji and Jenki would also be showing her where the ROOT-chambers were located, so that she could keep a figurative eye out for signature-presences entering it. When she was ready she planned on faking a trip somewhere, while she was in reality infiltrating the chambers. Her unnoticeable chakra, sensing- and stealth-skills made her uniquely suited for the mission. This would however not be before she was prepared to handle the traps sure to be there and Jiraiya-sama had figured out if the cursed seal perhaps functioned as verification of identity too.
It wasn't long after the first meeting that Kakashi was brought in on the mission too, with one of his jobs being to prepare her for the aforementioned traps 'Joy, now Kakashi actually has a reason to trash me with those traps of his' she thought miserably. And he did, mercilessly drilling her.
To himself Kakashi admitted that he was probably being more throughout than strictly necessary, but the thought of her infiltrating the equivalent of the ANBU-headquarters made his heart clench with worry.