Disclaimer ; I do not Own Naruto
This is an AU ending to the 4th War that I will be using for many of my crossovers.
Feel free to use it in your own crossovers as long as you leave a comment with the name of your story in a review and you point your readers to where the original came from.
Near the end of the fourth war, during the tug of war with Obito for the tailed beasts, Obito was able to split his attention long enough to launch off a single attack, but that attack was all he needed as it was able to kill Sakura. The death of Sakura broke Naruto's concentration long enough for him to lose the struggle. Naruto and B, along with their respective Bijuu, were sucked into Obito and into the Demonic Statue. Despite his conviction, it wasn't enough as Naruto found himself melding with the consciousnesses of all the Bijuu and Jinchuuriki. No longer simply Naruto, he watched as Obito beat down Sasuke and killed him, ending the last of 2nd generation Sannin. Naruto regained hope when Sasuke seemingly came back to life with one of his eyes turning into a Rinnegan as he then proceeded to call the Demonic Statue out of Obito before killing the man just before Kakashi could stop him.
For a moment, the war seemed to have been won, but everything seemed to go to hell when one of the Zetsu took the Rinnengan, still in Obito's eye socket, and used the life force of the few remaining white Zetsu to truly revive Madara. For a while, it looked like Sasuke would still be able to beat Madara and succeed in ending the war, as Madara had been revived without eyes, but Madara was able to create a lull in the battle and use it to implant Obito's, originally Madara's, rinnegan into himself and seal the Demonic statue within himself, once more leaving the Shinobi army at a disadvantage.
Madara quickly subdued Sasuke and performed the infinite Tsukuyomi before freezing as the latest twist in a long line of twists occurred. Behind Madara stood the black Zetsu with it's arm impaled through the Legendary Uchiha.
As Kaguya once more revealed herself onto the mortal plane, the small spark, inside her near infinite chakra, that was once known as Naruto watched as the eternal genjutsu spread throughout the world. It watched and tried to fight it's way out. It tried do something to end the root of evil that it was a part of. By itself it would have never have achieved anything, so it reached out. First it let itself connect to the dormant sparks of the other jinchuuriki, waking them up. Seeing what Naruto intended, the Jinchuuriki connected to the small fragments of their Bijuu that they could still access and provided Naruto with just enough chakra to carry out the next step of his plan.
It took days, but slowly, Naruto used tiny tendrils to connect to the Divine tree, and through it to the thousands of people that were now a part of it. None of the now connected people had any chakra to lend Naruto, but they did have plenty of will as they each realized that they were living inside a lie. They sent their defiance and mental strength to Naruto.
With the will of Humanity behind it, the node that was once Naruto forced itself to be acknowledged by the vast amount of chakra that was under the control of Kaguya and tore it from her grasp. Kaguya fought back, but was helpless against the onslaught of the collective force of humanity. Naruto's presence toppled that of the Rabbit goddess, and what was once Kaguya became Naruto.
Quickly, after coming to consciousness, Naruto had ended the Infinite Tsukuyomi, removing the remaining Biju and B from himself so they could once more be themselves. People rejoiced at the end of the war, happy that everything was over and that they had escaped. The celebration came to soon though as Naruto had forgotten about Black Zetsu.
Seeing that Kaguya had fallen, Kuro had quickly moved to the still recovering Sasuke and slowly took over his body. Before anyone realized it, Zetsu, masquerading as Sasuke used his Rinnegan to seal the 1 through 9 tails within himself before attacking Naruto.
Naruto, seeing that Sasuke was no longer himself, had grabbed hold of him and transported the two of them to one of the dimensions Kaguya had created long ago. They fought for months on end. Naruto's new existence as a god and Sasuke's absorbed Bijuu allowing them to far surpass the limits of even the Sage of the Six Paths. Eventually, even the combined chakra of the 9 bijuu ran dry as Sasuke threw more and more into bigger and more devastating jutsu he created by merging his unparalleled lightning release with the equally devastating natures of the subjugated Bijuu. Finally defeating him without ending his life, Naruto tried to separate Sasuke from Black Zetsu but found that, at some point, Sasuke had already overcome Kuro, meaning that Sasuke himself had chosen that he wanted to take the power of Naruto.
At this point, Naruto was faced with a decision, to allow Sasuke to live, or to kill him. Naruto really didn't want to kill Sasuke to live, but with the power of the 9 bijuu sealed within him and kept there by the power of his now Rinne Sharingan, something even Naruto couldn't break apparently, Sasuke was too dangerous to allow to roam the Elemental Nations. Seeing no better option, Naruto allowed himself to absorb Sasuke, hoping that the Uchiha would reform over time so Naruto could allow him to be recreated.
As the last vestige of Sasuke was absorbed within himself, Naruto allowed a second for the chakra to settle within him before feeling himself being attacked from within.
Black Zetsu had foreseen his loss and allowed Sasuke to overcome him, biding his time. Once he was within Naruto, Zetsu reconnected with Kaguya, who was still present, and allowed himself to once more become a part of her. Zetsu had been created purely out of Kaguya's will and, as he returned to her, a bolstered ex-Rabbit Goddess attacked Naruto from within, trying to regain control of the power Shinju.
Without the rest of humanity behind him, Naruto only had his own will and the wills of the 9 Bijuu within him to fight back against the ancient will of Kaguya. For nearly a hundred years, the two fought within the six dimensions. Naruto repeatedly tried to travel to the human realm but, everytime he tried, Kaguya interfered with his control just enough to land him in some other dimension.
Near the end of the hundred years during a small break, made possible because both he and Kaguya knew when the other was going to attack, Naruto finally discovered another aspect of himself known as Ashura. When they assailed each other the next time, Naruto was able to bring the weight of his numerous reincarnations to bear and was able to subdue Kaguya. Knowing that she would forever be a risk if she was allowed to be a part of him, Naruto disgorged her from within himself, leaving her what she was before she became a part of the Shinju.
Kaguya was still around the level that Madara had been during his original life, but was nothing compared to the might under Naruto's control. Naruto quickly made an expansive Truth Seeking Ball and, before she could gather any nature chakra in her new body, threw it at Kaguya. Naruto watched as the Bōchō Gudōdama anihilated Kaguya before it complete erased the mountainous dimension they were in as well, deeming that the loss of one dimension was worth the end of Kaguya.
As the last of the dimension was erased, Naruto felt himself being forced to leave as chose to use his Amenominaka to travel back to earth, wanting to see how much the world changed in the last 100 years, hoping that events of the Fourth Shinobi War and absence of the Tailed beasts had lead to peace.
As he materialized back on Earth, the first thing that had caught his attention was that it was hot. Much hotter that it had any right to be. Looking around, he hadn't been worried to see a land filled with lava, merely assuming he had teleported into a field of volcanoes. He had flown straight up, attempting to gain his bearing, but only becoming more concerned the higher he got. Eventually, he was no longer even in orbit and was able to see that the part of Earth that was visible to him was just a mass of volcanoes.
In denial, he had rationalized that he was probably just on the wrong side of the earth and flew at the speed of light to see the other side. Two seconds later, he was on the exact opposite side of the earth and it wasn't any better. Naruto spun around, thousand of miles away from earth, trying to understand what was going on. coming back to face the earth, he realized that he hadn't seen the moon.
Naruto shot around the planet, wondering if he had somehow missed it, before coming to stop above a portion of the earth that was deformed. coming back in from space, he hovered a couple miles above the deformation looking around to see that it stretched into the distance. The dark fumes that now covered the planet made it hard to see what the deformation actually was, so he gathered chakra within his lungs, nearly a tenth of what he used to have but nearly nothing to him now, and blew it out, converting it to wind as it passed through his mouth.
The fumes cleared away to show a white surface. Naruto realized that, at some point during his fight with Sasuke and Kaguya, the moon had impacted with the Earth. Concentrating, he used his senjutsu and tried to sense something. He delved as deep as he could to make his range encompass the entire planet. Naruto sighed as he felt nothing, not even a plant.
Naruto lowered to the surface of the grounded moon. Sitting there cross legged, he allowed himself to cry. To cry for Sakura, for Sasuke, for Neji, and for all the other lives that had been lost during the war. To cry for Tsunade, for Hinata, for B, for Kakashi, and for all the others who had died while he was fighting Sasuke and Kaguya. Finally he allowed himself to cry for himself. He had fought against the will of a literal god for a century so that he could save everyone from her tyranny, only to come back to see that his efforts were in vain as everyone had already died.
He had lain there for ages, his body no longer needing nourishment, and cried his pain and frustration away as he finally rested from the 101 year day. Eventually, as the wobbly planet completed a revolution around the still blazing sun, Naruto ceased his sobbing and stood up, noticing that his tears had created a tranquil sea upon the surface on the moon.
Naruto reached within himself and lightly 'poked' the bijuu and Sasuke, waking them up. After explaining what happened and having a short discussion, Naruto finally decided what to do.
He once more left the surface of the planet and floated a few hundred miles above it. With the unparalleled water manipulation of the Isobu and vast amount of chakra available to him, Naruto picked up the sea he had accidentally created and flung it off the moon and onto the earth. Then, with the Rinne Sharingan Sasuke had unlocked, he grabbed the moon with a gravitational pull and attempted to pull it out of the Earth, using a Chibaku Tensei to keep it in one piece. Naruto absently noted that it was smaller than it used to be, but decided that it didn't really matter before once more placing the moon in orbit. Naruto looked back at the earth, and realized that there was a huge crater in it. It was so huge that he could see into the lower mantle. Once more using Sasuke's Rinne Sharingan, Naruto grabbed onto the Earth's natural gravity and squeezed. The Earth shuddered and then began compressing into itself as it tried to reform itself into a ball under the effects of the immense gravity.
Naruto felt what the amount of chakra he was channeling through the spirit of Sasuke was doing to his brother in all but blood. Naruto was about to tell Sasuke to stop as he felt the black haired boy's spirit tear under the strain of moulding the earth before Sasuke cut him off. This was how he was going to pay for his sins. Naruto tried to cut off the chakra supply, but Sasuke had a firm grip on it and refused to let go. Naruto could easily tear control of the chakra away from Sasuke, but doing so would also rip his soul. Naruto could only sit back and watch as his brother let himself be unmade. As the last of the Earth was pieced together, Naruto felt what was left of Sasuke's soul lighten, for probably the first time since his Itachi killed killed the Uchiha clan, and fade away.
Naruto once more cried, this time his tears being caught in the earth's gravitational pull and falling to the planet below as rain. He quickly brought himself back together, taking solace that Sasuke had at least faded happy and under his own volition.
Naruto floated down to ground, seeing it no longer littered with fissures and molten lava. He quickly sat in the crosslegged stance and held himself in the stillness that was necessary for senjutsu. Instead of gathering Nature chakra, he took his vast reserves and pumped them back into the earth. Slowly, over the course of centuries, his reserves depleted and the world refilled with the Nature chakra it had lost with the death of it's inhabitants. Naruto had planned to pump every last drop of his chakra into to Earth, but before he could commit the last of his reserves into the process, the Bijuu had shoved him out of the way and took over. Naruto watched as they let themselves dissipate. He wanted to stop them, to yell at them to let him take on the burden so that they could live on, but he only watched, respecting their obvious last wishes.
Naruto woke from his trance and realized he was already in Sage Mode. That the entire world was now filled with his chakra meant that he would always be in sage mode. Naruto bent to look at the small pool of water that had formed sometime the last couple thousand years while he had been replenishing the world. He focused intently and felt the microscopic organisms that were now living in it. Smiling, he delved deeper into his sensing, once more feeling the entire earth. Around the planet, he felt the millions of places where similar microscopic life now lived.
Naruto had always been an active person, loving to travel. He longed to run around and explore this new world he had helped to create, but calmed himself down. The Nature chakra he had introduced into the world might be boosting the rate of evolution immensely, but it would still take millions of years for there to be sentient life. So he sat back down, closed his eyes, and decided to sleep until the world was a little more exciting.