AN: Alright everyone, pairing for this story is now between Samui of Cloud and Shizuka of Nadeshiko Village. I'll try to have a final decision made within the next chapter or two.
AN2: I'm designing Naruto's Mangekyo powers (because of COURSE this him will unlock that). From what I understand (and even if it's not the case in normal canon it's what goes on here) the Mangekyo has one eye with a Ninjutsu, one eye with a Genjutsu, and with both eyes you get the Susanoo (typically at least. There are some exceptions such as Shisui having two genjutsu eyes or Obito having two Ninjutsu ones). I'm making progress on fleshing his Susanoo, I've figured out his Genjutsu, but I'm having a hard time making a good Ninjutsu ability for him to have. Thankfully I have time before that point but if anyone has ideas or knows forums/articles where people discuss Mangekyo abilities, both canon and hypothetical, I'd love to know about them.
A Shinigami's Substitution
Scowling, Hiruzen paced through his office, eyes frequently flitting over to his now bloodstained couch where his medics were working on Shisui Uchiha, the loyal ANBU having appeared in his office via a Shunshin, right eye socket empty and bleeding, the rest of his body in not much better condition. In the next room over he had several of those he trusted or needed to protect. Gai was there, watching over little Naruto and Genin Anko along with Shikaku. He had Kakashi out looking for Itachi, a bad feeling broiling in his gut at what might happen if they didn't find him in time. "Hokage-Sama." Looking over, he saw the medics finishing their work as Shisui was tenderly sat up, "Shisui is stable now and is capable of giving a report."
Nodding, he gestured for them to enter the side room where Shikaku and the others were waiting, waiting till they were gone before staring Shisui in his remaining eye "What happened?"
"I was attacked." The soft spoken Uchiha leaned forward, clenching his hands together, brow furrowed and remaining eye flickering in and out of the Sharingan from his stress, "Their faces were covered and wore no identifying markings but their techniques, their chakra signatures…I'm positive they were Konoha Shinobi. Either a band planning to go traitor or even Root given how they were acting." Sarutobi truly wished that wasn't the case.
"And your attackers? How did you escape?" Hiruzen pressed, needing to have the full scope of the situation.
"They caught me off guard." Shisui coughed, still not fully recovered "I was more on edge thanks to everything going on with the clan and that Naruto kid, but they surprised me enough to land the first strike and take my eye. They clearly wanted both of them as they kept up the attack, although when they noticed there was a chance at loss, the one with my eye shunshined away with it. I killed the remaining attackers before dragging myself to the cliff before using the shunshin to get away, hoping that if they returned, they'd think I died and fell into the river."
"What of your clan? Are they aware of the attack? Are they still planning the coup?" Sarutobi was afraid of what Shisui would say, even if he was already sure what said answer would be.
"I was attacked before I could use my right eye's Kotoamatsukami. My left eye still has a couple years before it can use that Jutsu again. Not only can I not use that jutsu to stop the coup anymore, but whoever organized that attack now has access to using my Kotoamatsukami for themselves." Shisui scowled, before clutching his ribs "Plus I'm in no condition to do anything at the moment. It's up to you and Itachi to try and convince the clan. I know the Uchiha, they respect strength and trying to sway them from my sick bed would send the wrong message."
"I sent out Kakashi to find Itachi but there's been no word yet." Sarutobi had a very bad feeling in his gut as his pacing resumed.
The room was tense and silent as he paced and thought, the atmosphere lasting mere minutes before being shouted by panicked shouts hurrying up the stairs, "Hokage-Sama! Hokage-Sama! The Uchiha!" not even waiting for the one screaming to reach his office, Hiruzen snapped around towards the window, seeing the smoke on the horizon, smoke rising from the Uchiha clan compound. Frantically pulling out his scrying crystal, Sarutobi didn't react as Inoichi burst into the office. The crystal pulled up a view of the compound, moving through it as he saw corpse after corpse, all cut down mercilessly whether they be man or woman, adult or child, shinobi or civilian. He finally came across the house of the clan head, seeing Fugaku and Mikoto dead in a pool of blood, Itachi still holding the blade dripping in their blood as he used a Mangekyo Sharingan on his brother.
"No!" Shisui tried getting up only to collapse on the ground, still too weak to move as Inoichi hastily helped up the man who was now one of the few surviving Uchiha, "Why?! Itachi…you knew that this was a last resort! You wanted peace damn you!"
That sentence, paired with what had been said before, sent shivers down Hiruzen's spine, "He did want peace." Sarutobi remembered countless meetings with both Itachi and Shisui, having even considered naming one the next Hokage. He remembered how much both of them loved their village, wished for peace and detested the loss of life that would happen to either side if the coup happened. "Shisui…how long would it take for the one who stole your eye to be able to use the Kotoamatsukami?"
"…If they knew about it? They could probably get it to work as soon as the eye was implanted successfully." Shisui knew exactly what Hiruzen was implying. On the crystal, he saw Itachi already leaving alongside a man in a black cloak adorned with red clouds, the two moving fast enough that there was no chance of his forces catching up, at least not without being slaughtered as well given who was already near the compound.
"Cat, bring the Advisors here now." Sarutobi ordered one of the ANBU guard stationed at his office, hearing the sound of displaced air as they rushed away. He needed this handled…and he needed to know if his one last fear about all this was true. By the time his three advisors had arrived, Shisui was tucked away and hidden along with the ANBU, his blood-stained couch sealed away and replaced with a clean one.
"Hiruzen, I see you've already heard about the Uchiha Massacre." Danzo nodded to the crystal ball which he had still been using, desperately searching the compound in the hopes of finding even a single survivor, "I was able to get a report about the situation from my Root agents. It would seem Itachi has grown to despise his clan over the years. I know you wished for a…peaceful resolution to this Hiruzen, but Itachi clearly didn't feel the same." He could hear Danzo's disdain at the word 'peaceful', "My agents even report that he has sought even greater power by attacking Shisui and stealing the young man's eyes." As Danzo spoke, Hiruzen could see the other two advisors being convinced easily. Hiruzen knew the truth though.
"Danzo, you're being placed under arrest for the attack on Shisui Uchiha and instigating the Slaughter of the Uchiha clan." Sarutobi scowled as Danzo and the elders looked genuinely shocked before Shisui stepped from the shadows alongside Gai, Inoichi, and Shikaku, remaining eye glaring hatefully at Danzo.
"Root!" Danzo wasted no time in summoning his private ANBU force, the blank masked shinobi appearing to protect their master, fully aware they stood no chance against Hiruzen and the three able bodied shinobi, not even counting what mayhem the injured Shisui could cause with his Sharingan genjutsu if he got one off. "This isn't the end Hiruzen!" Danzo snarled as his Anbu threw down smoke bombs, those in the office unprepared coughing at the sudden obstruction, "I will be back! And Konoha will be mine, as it always should have been!"
Sitting on the couch next to his new 'big sis' Anko, as she insisted he call her, Naruto observed the Sandaime looking more tired than he'd ever seen before, the old man sitting behind his desk while talking with Shisui Uchiha and Gai-San. Shisui had apparently been working to prevent his clan from performing a coup, trying to work for peace and had his eye stolen by one Danzo Shimura, the man's actions in running the second the accusations had been made indicative of his guilt. Now, the Sandaime was having to restructure the Shinobi, prepare the village, and more given Danzo, a man with one of the highest security clearances in the Leaf, had become an S Ranked Missing Nin with a kill on sight order. "First Orochimaru is shown to be a traitor, and now Danzo." The Sandaime let out a tired sigh, "And the loss of the Uchiha clan…they were the Police force. We need to move fast to get things up to par. Shisui, I want you to take Anko as your new apprentice, help train her properly and make sure Orochimaru didn't leave any lasting issues with her. Use that time to get yourself recovered and back to working shape as well, I'm going to need your help now more than ever. We might have to loosen the graduation requirements at the Academy to allow more applicants through, have their Jonin senseis take a more intensive roll in their training to get our numbers back up."
"Yes Hokage-Sama." Shisui nodded without hesitation, the man's loyalty to the village something Naruto, not to mention the 'voices in his head', could respect, "But what of Sasuke?"
"He's still in the hospital." The Sandaime scowled, "It would seem that during the Massacre he unlocked his own Mangekyo and possessed the jutsu Tsukuyomi that you told me about. He trapped Sasuke in a genjutsu about the Massacre, telling the boy that 'he had to grow up with hate, that only then would he be strong enough to kill Itachi'. I'm unsure if Sasuke would even believe the truth when he wakes up about what Danzo did, especially since we don't have actual proof that he used the Kotoamatsukami to make Itachi do it rather than just his snake's tongue."
"Fugaku Uchiha was a stubborn man, and Sasuke seems to take after his father in many of the worst ways." Shisui frowned "I'll do what I can to help him, but I can't make any promises. I do wish to know who is supposed to be the next clan head. I'm the elder between myself and already a Jonin but Sasuke is the son of the last head. I'm unaware of any protocol for this situation."
"It is an odd one." Sarutobi nodded, "But speaking of Fugaku and the Uchiha there's something you should know. I had the morticians check every body and several Uchiha are missing their eyes. I had the rest sealed, for future transplants for your clan as necessary. But I made sure to have Fugaku's eyes brought straight to me given he also had the Mangekyo. If you wish, I can have his right eye transplanted into you so you're no longer half blind."
"That…would be appreciated." Shisui nods, "It's possible he's close enough of a relative to evolve that eye to the eternal version that won't degrade over time as well."
"I've already ordered Tsunade and Jiraiya back to the village while we consolidate power and get everything organized, I'll have her handle the procedure to make sure it's more stable than Kakashi's." Sarutobi nods "In the meantime I'm going to have ANBU guards stationed for you, Sasuke, Anko, and Naruto. These are dangerous times, and the village has already lost enough as it is."