A/N: Yes, it's a Rinnegan!Naruto story. Yes, it's been done to death. Yes, there will be similarities with other fics, but only accidental I hope. I found that there is another fic that has Shisui transferring his eyes to Naruto minutes before posting this story. I had not read that story and it has not influenced this one, so I hope I can make this one sufficiently different. Hope you enjoy this.
Shisui Uchiha stood broken. His emotions were already wrecked from the stress of dealing with his clan, which was poised to revolt. Losing his right eye to Danzo's treachery was like rubbing salt in his wound. He had intended to use his Kotoamatsukami to protect the village, to guide the Uchiha down a path of peace. Now, that hope was all but shattered. He struggled to control the feelings of anger and betrayal threatening to consume him. He couldn't afford to falter now. The village's future still hung in the balance.
Danzo had poisoned him while taking his eye, so he suspected he didn't have much time. His left eye was still intact as he had managed to get away from Danzo before he took that as well. But it would die with him thanks to the poisoning. He couldn't allow that to happen. He needed to find someone worthy to inherit his power, someone who could carry on his mission and safeguard the peace he had fought so hard to maintain. His mind immediately jumped to Itachi. But he discarded that thought as soon as it came to him. Itachi treasured the village above all else bar his little brother. He had a suspicion that if the worst came to pass, Itachi would carry out Danzo's will to eliminate the Uchiha clan if Sasuke is spared. This was not something he could condone. Kinslaughter for the sake of peace was a slippery slope, and he wasn't confident that Itachi's choices would be best for the village.
Leaving out Itachi presented a problem. There was no guarantee Sasuke would live, even if Danzo promises this to Itachi. Even if he did, the poor kid would suffer so much trauma that Shisui couldn't guarantee that he would be mentally stable. There were very few people apart from the Uchiha who could handle the chakra requirement of the Sharingan. In fact, he would say that the Senju and the Uchiha were a tier above the rest in terms of quality and intensity of chakra. Kakashi was living proof that transplanting Sharingan to a non-Uchiha may not be the best idea. Shisui believed that Kakashi's true potential was held back by the implanted Sharingan leeching his chakra. So if he was going to give his Sharingan to a non-Uchiha, they better have a hell lot of chakra with high quality.
The Hokage was too old, and the whereabouts of the loyal Sannin were unknown to him. This left him with precisely one option. Naruto Uzumaki, hailing from a clan related to the Senju and possessing exceptionally strong chakra. He had watched the kid often during his patrols or as part of his duty, since the Jinchuriki is a high-value asset of the village. Even though he suffered a lot of hate from the villagers, Naruto did not resent them for it. He still sought to be acknowledged by those who scorned him. As far as Shisui could see, Naruto did not have the capacity to hate. This, more than anything else, made him the ideal candidate in Shisui's plan for his Sharingan.
His time was limited. With his mind made up, Shisui headed towards Naruto's apartment. There were two ways to give the Sharingan to Naruto. If he implanted it on him, it would be next to impossible for the boy to control it. The other option was to transfer the special chakra that resided in his brain to Naruto. This chakra was responsible in converting a normal eye to the Sharingan, and Shisui theorized that transferring that chakra would also transfer the kekkei Genkai. The only problem was that the transfer would probably cost him his life, and the one receiving the transfer should be well equipped to handle it without allowing it to overload their brain.
Shisui was already a dead man walking thanks to Danzo. To ensure that his ocular chakra would not harm Naruto, he would have to seal it within Naruto until he became adept at controlling chakra. As an academy student, Naruto did not have anywhere near the level of control required to use a Sharingan, let alone his Mangekyo. In a couple of years, Shisui was sure Naruto would be able to control the onslaught of his ocular chakra by virtue of him possessing an equally exceptional chakra.
Little did Shisui know the consequence of melding the chakra of an Uchiha descendant with the chakra of a Senju descendant. The result of his interference would awaken within Naruto a power that makes even the Mangekyo sharingan pale in comparison. But this would not occur until several years later...