3-4 years later:
Sakura Haruno at 4 years old:
Danzo sat in an underground meeting room in the ROOT Headquarters, with several men and one woman, and one Orochimaru.
"Consider Sakura as your own daughter, Fu Yamanaka and Torune Aburame, Tatsuma Aburame, and Yoji Aburame. I trust you each to babysit Sakura while I'm off doing official business, taking turns. Make sure the secret of her Rinnegan does not get out," Danzo instructed his henchmen.
"As for you, Nono Yakushi, you healed Sakura during your first day meeting Sakura. You know about her Rinnegan. You must also ensure that secret does not get out, or else I will personally slaughter your entire orphanage."
Nono nodded. "Yes, Danzo-sama."
"Good. Nono, you are in charge of healing my daughter from any side effects of what's about to get administered to her: Poison. Both Orochimaru's poisons, and the Aburame's variants of poisonous bugs; the poisons generated from each unique bug. Yamanaka, you are in charge of making sure that Sakura does not suffer any brain damage, from any of this. Right now."
"Yes sir," they all saluted, although the less-jaded Root members were internally cringing at the heartlessness of all this. Fu Yamanaka stepped forwards and placed his hand over Sakura's forehead.
"Shit!" Oni retreated and zapped herself out of Sakura's mind. Sakura was alone now (mentally.)
Fu Yamanaka began doing constant brain scans of Sakura's brain to make sure no brain damage happens and to cure anything that might happen. "You may begin."
Danzo pulled a cart of 100 needles and vials; this entire thing was a custom gift from Orochimaru. "Nono, stick each of these into Sakura. We will be here all night. We will be doing this everyday for a few months. We're trying to get Sakura immune to all poisons."
Nono stuck several of the needles and vials of poisons, all liquids mixed and invented by Orochimaru, into Sakura. Sakura felt the pain from each needle sting, and she felt Orochimaru's liquids, ninja viruses, and infections entering her body, but she did not react outwardly. Nono stuck more needles into Sakura, shuddering and healing Sakura whenever she had a fever flare up.
"Don't worry, Nono, Sakura. These are vaccines," Danzo smirked smugly.
"Danzo, her immune system is getting overloaded!" Nono protested.
"Oh, then we will do this over the course of a few months, until every single vial has entered her and until she's gained immunity to all poisions. One last thing, Aburames and Nono, meet up here again with Orochimaru next week. I'm getting Sakura immune to your bugs too. Make sure to steal all of the Aburame bug variants. Procure them somehow, whether through social engineering or outright stealing. Bring them all here. Then Orochimaru will create vaccines for them. Orochimaru will also bring Snake poisons. Orochimaru will be dorming here for a few months until we get Sakura's immune system to be as impenetrable as a God's."
"Aye, sir."
The following week, Orochimaru was there; Orochimaru brought along various snake vipers and venoms, along with vaccines and antibiotics. The procedure to make Sakura immune to all the poisons was a delicate task. Sakura was the first test subject for this program.
The Aburames had various bugs bite Sakura with their most lethal poisons, and Orochimaru and Nono Yakushi worked together and gave Sakura vaccines to the poisons, and healed all her injuries too.
Orochimaru tsked, "Wouldn't this process be a lot faster and easier with Tsunade-hime here? Why is this second-rate healer here anyway?" Orochimaru made a dig at Nono. Nono grit her teeth.
"Orochimaru-san, don't distract me, I'm just trying to heal—"
"Shut up, Orochimaru, unless you have the capacity to bring Tsunade here yourself," Danzo growled.
"Never mind," Orochimaru chuckled. He continued summoning baby snakes filled with viper to bite at Sakura's arms. Then he administered special vaccines and antibodies to cure Sakura. The Aburames also assisted by letting their poisonous bugs bite Sakura, and having Orochimaru and Nono cure Sakura of them too.
Sakura's eyes looked cold and heartless, glazed over, over while this was happening. Vaccines hurt.
Next, Orochimaru had Sakura drink many different poisons, and drink the cures to those poisons. They mixed that into her food, her soup, and her milk.
But eventually, she gained immunity to all poisons.
"This is great news. This guarantees that the Rinnegan user won't die. I swear, I would rip these eyes out myself, but."
Orochimaru smirked smugly. "Well, your daughter's not dying anytime soon. And the longer she lives, the closer we get to immortality, because the longer we have to experiment on her. Every experiment that we conduct with her, we walk closer by one step towards immortality. Am I allowed to touch her eyes yet?"
"How far along are you to actually know what to do once you have Rinnegan?"
"Ahh… Not yet, no. I need more children to experiment on. But I've almost made breakthroughs with the Senju cells. Once I made the breakthroughs, I'll be ready for immortality experiments. Give me a few hundred more live bodies, Danzo, please."
"Granted. We've burned down some foreign villages, so you may use those live bodies. Most of them are imprisoned. You may leave, Orochimaru."
"Thank you, Danzo," Orochimaru left the Root hideout.
"Nono, Aburames, and Yamanaka, your work here is done. Yamanaka, stay with me. Aburames and Nono, you may leave." Nono and the Aburames left the room as a result.
"Fu Yamanaka, now is the time to implant all the Academy Jutsu basics, and the entire Ninja education curriculum and the ROOT curriculum, into Sakura's head. I know this is a cheat, and not a literal way to teach, but she is a literal baby. She's not that smart and I don't have the patience or time to tutor her. Implant into Sakura's brain, the basic language, the entire alphabet, mathematics, science, and all cyphers and codes that we ANBU and ROOT use. That would make it like multiple languages. Sealing knowledge too. And all your knowledge of the world. I've vetted your brain and we've gone over what material is fine to implant into Sakura's brain, so you should be fine to do that now. Do this in increments whenever you suspect brain overload on Sakura."
"Yes, Danzo-sama," Fu Yamanaka agreed. "I'm not as good as Inoichi Yamanaka, but I will do my best."
"Good. You'd better. We stole so much training material from the Yamanakas, so there's no way you'd fail on me. Your services are needed, for this is about the future of the Shinobi World and the protection of our Village."
"Yes, Sir." Fu Yamanaka placed his head over Sakura, and implanted all memories into the young toddler's brain.
Sakura fainted from the information overload.
Danzo merely shrugged. "We'll just do more of this tomorrow, then. And the following day, and the day after that. We'll keep going until Sakura reaches adulthood, as the smartest ninja in Konoha. Fu, always keep absorbing useful memories from smart shinobi, and implanting those memories into Sakura. We need to kidnap more civilian NOBLES who have a good language understanding, and implant their memories of elegant nobility lessons onto Sakura. That way, Sakura can masquerade as nobility someday. And act the part as my daughter, as well. Either way, nobles are well-read than shinobi, so get their memories too. And steal the memories of Konoha's cipher division. They're smart code crackers, and I want that for Sakura."
Fu panicked but nodded. "Yes Danzo-sama. I will make sure to do this everyday to Sakura, and give her a few days off when I sense that her brain can't handle all the experiences and knowledge."
"Good." Danzo nodded. "Add some of Root's kills to her memories to desensitize her to death."
"Yes, Danzo-sama."
So they proceeded to do precisely that. Everyday, Sakura would get "Tutoring lessons" from Fu Yamanaka, but they were merely life hacks where Fu would place his hand over Sakura's forehead, and implant all the memories and comprehension into her head.
In a few months, Sakura was able to speak verbally and eloquently. Sakura knew the entire alphabet, and several thousand vocabulary words, and was able to string together full sentences. Sakura knew mathematics, fuuinjutsu, and basic Academy Jutsu and how chakra works, and how to mold chakra. Sakura knew and understood the theory of almost everything a regular high-ranked Root shinobi understood, due to the Yamanaka memory cheats.
Sakura literally knew how to read and write anything.
Sakura is now 6 years old. Sakura Haruno (Sakura Shimura) is the same age as Itachi Uchiha. Kabuto Yakushi is canonically 2 years older than Itachi.
"Great work, Sakura," Danzo headpatted Sakura for the first time, as he lead Sakura to an underground library, a secret clan archive by Root. "Now study all these books, of stolen clan material. I have not even shown any of these to Fu Yamanaka to implant into your brain, because much of these Jutsus are forbidden jutsus and techniques. Many of them are Fire Release techniques stolen from the Uchiha clan. You must study these on your own. I will be hunting down an Uchiha Tutor for you. I've got my eye on Shisui and Itachi, likely clan traitors who agree with my vision.
"Because your new job is going to become a terrorist for me and bomb all the minor villages with the Fire Release. I can't wait for you to gain a name for yourself, and that's before your eyes have even matured to unleash hell upon the world. Who knows, perhaps after you blow up a few villages and cause a few hundred hellfires across the world, your eyes will activate the same way the Uchihas' eyes do." Danzo chuckled, and began tutoring Sakura with fire release techniques basics.
Danzo handed Sakura chakra-paper to practice making the paper burn.
Sakura was able to finally get the chakra paper burning. However, since Danzo didn't have a Fire Release nature, Danzo's lessons ended there for now.
"Don't worry, Sakura-hime, I will recruit Itachi or Shisui into Root, and you'll have a new tutor," Danzo headpatted Sakura and gave her a Japanese snack, which she ate reluctantly expecting poison, but fortunately the snack turned out to not be poison.
Danzo then took Sakura out of the Root archive library, and into Root's cypher division.
Sakura, six-years-old, was startled to see a 8-year-old white-gray-haired boy.
"This is Kabuto Yakushi. Nono's son. You already know Nono, your healer. Sakura, you will be teaching, or helping, or learning, from Kabuto Yakushi. Kabuto will be your partner in the cipher division of Root from now on. Kabuto enlists on various missions throughout the elemental nations, to spy on them and gather intel. He brings that intel home, to our Root HQ, and we decipher. You and Kabuto will work together to crack codes of all the Nations, for the protection of Konoha. Sakura, you already have your brain loaded with all foreign languages thanks to your training programme" Fu Yamanaka "So you will be of great help to Kabuto. You two will be equal partners. Now get to work." Danzo pointed at a massive scroll filling up an entire 20-feet-long table, that Kabuto brought home. There were lots of foreign inscriptions and codes.
"Sakura, this will basically be your assignment. Work and learn with Kabuto while you're not training in elemental releases, or while you're not training your body. When you are training your body or in ninjutsu, Kabuto will be on foreign missions gathering intel. But every time Kabuto returns home to the Root HQ, you must greet Kabuto, escort him to the Cipher room, and decrypt his intelligence, and submit them as reports to me. Think of them as homework reports, my dear daughter."
"Okay, dad," Sakura nodded. She never truly got to play, she never knew what playtime was. It was 24/7 work all the time for the child. She considered the Taijutsu lessons that Danzo had Sakura attend, as playtime.
Fu Yamanaka implanted so many spy memories into Sakura, that Sakura knew everything there was about spying and knew about Kabuto's missions, how they worked, and was able to decrypt much of Kabuto's foreign language scrolls. She was a massive help for Kabuto.
Kabuto saw Sakura as a mere co-worker. They were both very mature for their ages.
8-year-old Kabuto just wanted to help his adoptive mom, Nono, so Kabuto kept working. He didn't want to get too close to Danzo's daughter. That was dangerous. She was basically his surveillance, designated to keep an eye on him and make sure he didn't step out of place. So Kabuto worked diligently for Root, and worked diligently and respectfully with Sakura, deciphering foreign shinobi codes with her.
One day, Sakura wondered what happened to the other gray-haired boy who wasn't Kabuto who tutored her. She asked Danzo, "What happened to Shin?"
Danzo replied; "You think those Vaccines that we used on you came cheap? How do you think you survived all those vaccines? Orochimaru and I concocted them under careful testing, and we used him as a voluntary test subject to test the vaccines on, before we used the vaccines on you. Shin is currently recovering and re-assigned into a non-combat department on paid leave. And by paid leave, I mean that I'm payingfor his hospital stay. Be grateful."
Sakura gulped. But she didn't know any better, so she said "Okay, father."
Kabuto and Sakura worked together in Root, for several years, before Kabuto's eventual defection of Root. Orochimaru himself, had defected a few years prior, and when Orochimaru caught Kabuto in Iwagakure after Danzo's blotched mission to have Kabuto and Nono take each other out, Orochimaru had stolen Kabuto from Root.
When Kabuto never returned home one day, Sakura was stunned. Sakura also noticed, that her healer, Nono, hadn't been around the HQ for many years either. Nono hasn't been around the HQ ever since Kabuto joined Root's Cypher division. Sakura hasn't had a healer for years. And now, Kabuto was gone.
Sakura didn't have anybody close to her age to hang out with now. She didn't have any real friends—Sakura wouldn't consider the Aburames and Fu Yamanaka as friends. They were scary and always forced shit onto Sakura. Nono and Kabuto at least never laid a (harmful) hand on her, and now they are both gone.
But that was okay, said Danzo, before Sakura could mourn Kabuto or even Nono because when one son was gone so abruptly despite being in the middle of an important encryption job with Sakura, it occurred to her that the mother might possibly be gone for darker reasons than simply retirement.
It was okay, Danzo said. I will replace your friend. Now, let's prep and practice what you shall say to him, Danzo said. We've practiced and been over this for years. If you fuck up, make sure to brush it off as you having been sheltered your entire life in my mansion as a Councilman's daughter. Relate to Shisui, and tell him to train you hard, and to not go easy on you, because you are only three years younger than him.
…
"Your new friend," Danzo said, ushering a young boy in front of him, towards Sakura. "And training partner."
"Pleased to meet you, Sakura-hime," a black-haired boy with curly hair and red eyes— Shisui Uchiha, bowed. "I've heard a lot about you. I'm three years older than you. I'm Shisui Uchiha, a new ANBU member of the Root division."
Sakura was only six years old, and Shisui was nine years old. They were both prodigies.
"Nice meeting you too… Shisui." Sakura didn't use honorifics on anyone. She didn't need to, because of her rank and nepotism. "Yeah, I'm six years old. And I need fire release training for my upcoming missions. Please."
Shisui smiled dazzlingly, "I would be honored to teach you, princess." Shisui bowed his head.
Danzo smiled. "Itachi Uchiha will be joining us next year, when he graduates from the Academy at age seven. He accepted my offer to join ROOT. Shisui, your recruitment of the Uchiha Clan Heir was a success. This is all thanks to when you approached Itachi in that forest at the back of the Academy, and befriended Itachi. Now, a future civil war can be averted." Danzo hummed to Sakura. "Sakura, Shisui here is nine-years-old and graduated from the Academy 2 years ago at age 7 as well. He's been working with us since graduation, and has been working with us for 2 years. He's already recruited the Uchiha Clan heir, who will be joining us in 1 year. You should treat him well, Sakura. These two Uchiha boys have the same goal as us, the goal of peace and safety for Konoha. I can't say the same about the Uchiha clan themselves, they want conflict and war. But that's why it is urgent that we work hard and train hard. We cannot afford to have another war, so shortly after we've just survived and won the 3rd shinobi war. Shisui was in the war with me. I caught wind that Itachi witnessed the aftermath of one of the battles, and that's why I think we can recruit Itachi; he's no longer a sheltered boy."
Sakura blinked. "Shisui here is only 2 years older than me, but he's already been in a war?"
Shisui nodded. "Yeah. I'm currently 9, but I graduated from the Academy at age 7 and was immediately placed on a genin team and put to fight in the war. I fought for one year before the war ended. I lost so many comrades. While heavily injured, my eyes transformed into the Mangekyou Sharingan when I watched my best friend die in the battlefield. The war ended a year after I graduated, so I'd become a war veteran at age 8. I don't want to witness anything like that ever again. So when my war commander, Danzo, reached out to me post-war to come work for him, I accepted his offer. I've worked for him for a year, and now I'm nine years old."
"Wow...I'm amazed. My father is so amazing," Sakura swallowed, staring between Danzo and Shisui. Sakura decided to share a little about herself in return: "I was born to Danzo Shimura, no mother. And I've lived inside this ROOT Facility for my entire life, training and getting stronger, in hopes of becoming useful for protecting Konoha in the Shadows, via ROOT." Sakura glanced at her father, Danzo, hoping that he'd be satisfied with her answer.
Danzo smiled and headpatted Sakura. "That's a good girl. You two are my most valued ROOT assets, after the Yakushi traitors defected from us. We have a lot of workload to pick up. You two, start training now. I have to go organize and clean up after the Yakushi traitors' messes. I'll be back to check on your progress incrementally. Shisui, teach Sakura all the ropes so she'll be useful to the organization. Teach her everything that you know." Danzo concluded as he started walking out of the dojo room, leaving Shisui and Sakura alone in the Root HQ room, for training.
Shisui was one of Danzo's first converts, and Itachi will be next. The hate and spite of the Uchiha clan, are radicalizing their children to come to the other side.
Shisui was going to train Sakura in Fire Release techniques, to prepare to send Sakura out onto the field. It was all Danzo's plan, to replace two significant agents that he'd unfortunately lost; the two Yakushi traitors.
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Join please. Also please read the rest on ao3, just google sakura's rinnegan. Will update this site when I have time but not always.