He'd felt the presence again, the one he felt while traveling to Uzu. Fortunately, his extensive security seal the Iron Palace Seal not only buttressed his sensory abilities but also offered offensive and defensive responses to unwanted intrusions. Jiraiya had to find that out the hard way. The seal alerted him to the oncomer and Naruto could sense it was approaching them. He didn't know what annoyed him most, the intruder, or that he'd have to leave bed to deal with the sad intruder as he was still holding Itachi as her head lay on his chest.
"Itachi" Naruto whispered, "do you know of someone or something that can merge with trees?"
"Zetsu, the Akatsuki's main source of intelligence. He could seemingly get anywhere almost undetected."
"Oh. Anything else you can tell me about him?"
"He eats people."
"I want to be judgmental but given recent events, I'd be something of a hypocrite," he said while wiggling his eyebrows.
"You've been around Jiraiya too long, I believe Kushina-sama was correct in attempting to beat his influence out of you."
"I'm just trying to keep the mood light given I'm about to go torture this… thing? I don't think it's human."
"So, what's your plan?"
"The next time he reveals himself I'll restrain him and we can go from there."
It didn't take long for Zetsu to once again emerge from the vegetation and just as Naruto said, he had a series of seals to restrain him, block access to his chakra, and burn him in an eternal flame if Zetsu didn't talk. It was a similar array to what he used for Danzo, a flame that just caused constant pain but would never truly burn the victim and was sustained by the victim's very own chakra reserves. Naruto wasn't a fan of his torture seal but he realized it had utility.
Zetsu talked but not because of the threat of torture. Kaguya's will just understood he'd overplayed his hand, his time was up and he'd ultimately failed in his mission to revive his mother. Naruto almost felt bad for the bastard until he relayed that Tobi was commanding an army of white zetsu that could mimic anyone and not even a byakugan nor most sensors could tell the difference. Along with dozens of edo tensei of the strongest shinobi in history, the alliance was in trouble. Itachi burned Zetsu with her Amaterasu and the couple found Jiraiya so they could head off to battle. Once the trio was ready, Naruto made them vanish in a flash of yellow.
The scene they arrived at was bad. All five sitting Kage were barely clinging on to life as some long-haired Uchiha zombie mocked them. Tsunade's torso was separated from her legs as she was slowly dragging herself toward her legs to reattach them. Jiraiya was dismayed, Itachi was surprised to see just who the Uchiha was. Naruto was livid. Beside himself. Downright murderous and fortunately for him, there were no moral qualms to killing a zombie and an army of plant people. He helped Tsunade on her path and then shared Kurama's chakra with her so she could fully heal herself and the other Kage. Madara, Itachi identified, didn't seem bothered by any of this and just let the jinchuuriki do what he wanted. Naruto surmised that the Uchiha clan must have parables about how arrogance in battle assures victory because that's the only way that makes sense.
It took some doing but Jiraiya and Itachi agreed to go face Tobi with the small army of shadow clones Naruto provided while he would stay and face Madara, the duo only agreeing to it after he promised he had a plan for the man. Tsunade wanted to argue against Naruto doing this but she had already failed and the shame of it made her stay quiet.
Naruto slowly approached the notorious Uchiha, trying to remain calm as undue haste would result in his death.
"Come to face me alone, boy?" Madara asked. "What can you do that those five Kage couldn't? Even with the power of my pet fox, you're nothing compared to me."
"Tsk. A couple of questions before we start. It's not every day you get to meet a legend." Seeing Madara consent, Naruto continued, "Is it true, Hashirama-sama tried to shove a tree up your ass at the Valley of the End but it was blocked by the ten-foot pole you normally kept up there?"
This caused the Uchiha to go wide-eyed before narrowing them to slits. "That's question one, brat. One more before we dance and you die."
"That question was for you to ask me. Like I said, it isn't every day you get to meet a legend. You should be honored, teme."
"I'm going to enjoy this but I doubt you'll last even five minutes."
"When this is over, I'm going to want to see that same energy."
A blinded and restrained Madara has a look of disbelieving rage plastered on his face. How a shinobi he outclasses in every area managed to do this to him is still something he can't understand. Naruto, however just looked ready to finish this stage of the battle. And what a battle it was. Madara spammed high-level jutsu after high-level jutsu only for Naruto to continually dodge but inch his way to his opponent. Eventually, it became a taijutsu battle and Naruto baited Madara until he revealed his trump card. The chakra arms he could produce. No one knew about them and Naruto made sure not to reveal them until he could strike and strike he did. Naruto created three arms, each designed with a specific seal in mind. Two would seal Madara's eyes, robbing him of his Rinnegan and the last, well the last would end the bastard for good.
"How?" Madara grunted.
"I'm just so tempted to say ninja and leave it at that but I'll be quick. There was an asshole that killed my grandfather using the jutsu that brought you back. I was determined to never allow myself to be defenseless against it so I took a look at the village's forbidden scroll of seals. It turns out the Edo Tensei isn't that complex. There needs to be a physical body because dead bodies still contain yang chakra. The jutsu calls back the yin chakra of the intended and the dna or blood; along with the chakra provided by the user is the anchor that allows the yin to merge with the foreign yang. You separate the two and the jutsu ends. I essentially did that except when your yin releases it'll be more like a very small star collapsing and hopefully you'll take that fake with you."
"What's your name, boy?"
"Naruto Uzumaki."
"Of course, that clan of second rate shinobi. Fighting with ink like a bunch of cowards."
"Oh no, Mr. Zombie don't insult my clan. Whatever loser, just sit there and wait to be of use."
Before he departed Naruto had something he needed to tell her. He whispered it in her ear, she looked mildly shocked but his firm head nod confirmed he meant what he said. He then disappeared in a yellow flash.
"Tsunade, what did the boy tell you?" asked Ay.
"The person controlling the Edo Tensei was Sasuke Uchiha."
The battle against the eventually revealed Obito was hard fought. He pulled some broken, hax ability to avoid being killed by Naruto's Madara bomb but it still injured him. The fight against the other bijuu was epic, Naruto, Killer B and Itachi worked very well as a newly formed team, much to Obito's ire. He became increasingly unhinged, going for wide area effects jutsu and abandoning tactics. It managed to keep the Alliance from landing a killing blow but Obito was no closer to getting the two remaining bijuu. Then Sasuke arrived and literally stabbed Obito in the back, ending the war. Except he had a deranged look in his eyes. He started shouting Naruto's name repeatedly and Naruto was more than willing to meet the challenge. Sasuke had crossed the last line, there was no rehabilitation to be had. He was a mad beast and Naruto would put him down, promises be damned.
Itachi stopping and kissing him before he went to face Sasuke surprised him. For one, she didn't strike him as the type to be overly comfortable with public displays of affection. Two, the emotion behind it felt off. He couldn't quite figure out why but something was wrong and the look in her eyes didn't help. It was when she turned toward Sasuke's direction he realized what she intended to do. She was saying goodbye, finally going to sacrifice herself for the sake of her brother and Naruto was having none of it but before he could stop her or even move he felt an arm around his neck. It was Jiraiya, executing a choke hold and even with one arm it was damn near impossible to break.
"Jiraiya, stop! Let me go!" Naruto bellowed as if suffering the greatest anguish of his life. "Please, Jiraiya, let me go!" But Jiraiya wouldn't release Naruto and the lack of blood flow was starting to affect him. Naruto immediately tried to call upon Kurama's chakra, only for Sakura to slap a seal on him. Naruto was blacking out fast, his last sight was of Itachi's back as she marched toward her death.
He awoke three days later. Apparently, Sakura and Kakashi thought it a good idea to place him in a medically induced coma so they could subdue Sasuke without Naruto killing him. Why? Comrades don't abandon each other. When Naruto awoke, Jiraiya was there and it took a great deal of Naruto's self-control not to lash out at the man, even more after Jiraiya's first sentence.
"She's gone, Naruto." And there it was. Confirmation that she finally completed her mission to die by her brother's hands. Aided by his godfather, friend, and Jounin Sensei. In that moment, Naruto wanted to kill all three and was finding it almost impossible to come up with a reason not to.
"Tsunade had been working on a prosthetic since I came back from fighting Nagato. When you turned over Danzo's body, it gave her some ideas. Three weeks, Naruto. I'm asking you to sit on this for three weeks and then you and I can fight it out and no matter what the result is, you won't be held responsible." Jiraiya said and saw Naruto nod. Jiraiya started to head toward the door but was stop when Naruto spoke.
"Why?"
"Because she felt like she had to. Whether you accept it or not, Itachi blamed herself for how Sasuke turned out and for his inability to fight off the darkness. She needed to atone and I couldn't take that away from her. She'd sacrificed everything for the village, she at the very least deserved that."
"She deserved a future, to have her name cleared and be acknowledged as the loyal kunoichi she was."
"True but she didn't want that, she wanted to try to save her brother."
"Then she wasted her time."
"Naruto, let it go. Sasuke is in a holding facility, chakra sealed and guarded by a small army of black op ninja. Whatever designs you may have on his life, let it go."
"Why do I have to have designs on his life, he's going to be executed, right? Right?"
"When the advisor's deeds came to the attention of the Daimyo, he pulled some strings. Felt Sasuke wasn't completely responsible for his actions, not even helping Obito so no, no execution but he'll likely never be released from prison."
"Well, isn't that grand. Leave, Jiraiya. I'll see you in three weeks."
The duel between the two Toad Sages destroyed three training grounds by the time it was done. Kakashi ordered all other ninja to avoid the surrounding areas so no one truly witnessed the details of the battle but the destruction of the land told the story of two high level shinobi going at each other with intent and a tier of power most ninja couldn't truly comprehend. Both combatants managed to leave under their own power but Jiraiya did have to go directly to the hospital whereas Naruto simply vanished.
Three months after the end of the war, Naruto received a request from Sasuke to visit him in prison. Naruto knew the asshole wanted nothing of importance but decided to go, to have one final conversation with him. It started off how one could predict, Sasuke admonishing Naruto for his betrayal, how if he'd be a true friend none of this would have happened, and how it was his betrayal with Itachi that was truly unforgivable. All of that was more or less boilerplate and easily ignored, it was his final statements that sealed Sasuke's fate.
"Does it hurt, Naruto?"
"That she's gone? Yes, Sasuke, it does."
"No, not that. Of course, it hurts my nee-san is gone. Does it hurt that she loved me more than you? That she chose death by my hand over being with you? Does that burn? Does it keep you up at night? Your inability to protect your precious person because she didn't value you enough? Did, hahahahaha, did she even tell you she loved you? Because she told me, right before my Kirin vaporized her. She sounded so sincere. 'I'm sorry for all the pain I caused you Sasuke and I'll always love you' she said."
"And for that love you killed her."
"No, you killed her. This village killed her, just like it killed the rest of my clan. My best friend and my sister, screwing behind my back. Laughing at me, plotting and planning and manipulating me. You had to answer for your betrayal. One of you had to die but truthfully I wanted it to be you. I think it's because I've always hated you, at least a little."
"Well, this has been a blast, Sasuke. Enjoy your time in prison."
"Oh, I will. No matter what, I'll always be the person that took your love from you and there is nothing you can do about it. You won't seek revenge, it's not your way. Goodbye, Dobe. Live in misery."
As Naruto was exiting the visitors' area he felt a familiar presence arrive in the shadows.
"What are your orders, Naruto-sama?" asked Sai. One of the many former Root members that had slowly transitioned back into village life and while many wouldn't ever fully have their emotions back, they were getting some and were thankful to Naruto for no longer being beholden to Danzo.
"Is it all set?" Naruto asked.
"Yes, we have successfully infiltrated the prison, be it guards or inmates."
"Good. I want you to do nothing."
"Nothing?" Sai asked in confusion.
"Yes, nothing. No beatings, no rapes, no violence of any kind, and prevent others from doing the same. I also want him to have no allies, no friends, no one to even share a conversation with. Sasuke knows the hell of loneliness but it's time for him to be reintroduced to it. As far as anyone is concerned, while in there Sasuke Uchiha doesn't exist. The only voices speaking to him should be the ones in his head. Let's see how strong he is."
"It will be done, Naruto-sama."
Meanwhile…
Jiraiya was glad Tsunade hadn't left the village yet and could only hope she'd be willing to help him. He didn't have a lot of people he could trust with this but it also wasn't a small ask. She'd been less than thrilled with him, Sakura, and Kakashi after they subdued Naruto as they did. Not only was it a betrayal of their bond but they had no way to be certain all enemies had been accounted for and Naruto was the only one who could point out the Zetsu that may have remained or had the reserves to face a strong opponent should it have emerged. She understood honoring Itachi's final wish but she also knows the heartache of watching the person you love die and being able to do nothing to stop it. Things had been tense between the two remaining Sannin since.
"Tsunade, I need your help?" Jiraiya stated, seeing no reason to be less than direct.
"Concerning what?"
"I have a VIP in need of medical care."
"The village has-"
"Tsunade, this person isn't in the village but needs help; the best, which is you. Your absolute secrecy is also required."
"Then I need details, Jiraiya."
Jiraiya faltered, wondering if he should tell her now and risk her sharing this information.
"It's a high-risk pregnancy. The patient has a degenerative disease but has managed to prevent much of the damage associated with it however the disease, the pregnancy, and recent events may stress her body to the breaking point."
"Who is this person, this sounds serious."
"If I tell you, you cannot share this information Tsunade. Please, promise me."
"She'd be entitled to doctor-patient confidentiality, Jiraiya."
"It's Itachi, she's alive."