Omakes
Naruto (beginning around the time of the month break following the capture of the Yonbi):
Naruto watched as a subdued Team Ten entered Konoha. Not even all of it. Sarutobi-san wasn't there and neither was Choji. Shikamaru limped slowly, his only remaining arm around Ino's shoulders. His face was a nightmare of burn-scars caked in dried blood and mud. His left eye was ruined, just a pit in the midst of the burns. His left arm was gone and a crude bandage was wrapped around the shoulder, stained with bodily humors and more dirt from the field. His left leg was wrapped in bandages and splinted, but he still left bloody footprints every time he had to put weight on it.
By comparison, Ino looked the picture of health. Her hair was a mess, both chaotically displaced and grimy. Her clothes had severe scorching on them and much of them were rags that looked like they had been torn to supplement Shikamaru's bandages. Actually, there wasn't really much left of them. The Ino Naruto knew would have been absolutely livid about this, but she just had a dead look in her eyes.
The news spread quickly enough. Asuma had died at the hands of Konoha's second most wanted ninja. Rumor said that Orochimaru had toyed with him before the death and bragged about working on collecting the whole set. Choji had died too, using his ability to grow to try and shield his teammates from a contemptuous blast by the snake. It hadn't been enough. Shikamaru had thrown himself in the way to protect Ino, costing him his arm, his eye, and his career in the field.
DIE
Naruto had volunteered to come on the mission to hunt Orochimaru and Kakuzu. There had been some resistance to the idea, but he had pointed out that he needed to live-fire test his newest technique and S-rank missing ninja were excellent targets to apply S-rank techniques to. Also, he refused to not be part of the mission. He had failed to bring Sasuke back, but he could at least kill the one responsible for him leaving. It wouldn't be enough, but it was all he had.
DIE
A specially selected squad was sent to hunt the pair. Maito Gai, Hatake Kakashi, Yamato, and Uzumaki Naruto. It wasn't hard to catch up to them near a bounty office. The fight had quickly escalated.
DIE
Naruto was out of his depth and he knew it. Next to Maito Gai, he really didn't belong here. The man continued to pressure Orochimaru while the snake flung jutsu at Yamato and Gai, keeping them from managing to actually harm him. His ability to swap with a suddenly created clone meant that Gai had yet to land a convincing blow and had been forced to constantly dodge swipes from the kusanagi that left nearby trees in pieces.
Orochimaru was clearly trying to get out of the forest where Yamato had plenty of free sources of material and had taken to wide-area fire attacks to defoliate the region as a literal scorched-earth denial. Still, Gai was moving faster than Naruto could track and Orochimaru was somehow keeping up, if only barely. It was clear that the sanin was having trouble, but all Naruto could do was throw swarms of clones into the mix to keep the man having to track multiple targets. He'd yet to even come close enough to hit.
The chirping of birds drew his attention. If his sensei was breaking out that technique, then things had escalated. He threw a last, sorrowful look at the battle between titans and decided to take the high road. One fewer Akatsuki was still a win. A pair of clones helped him stabilize his Futon: Rasengan.
DIE
Kakuzu heard a whirring screech like glass bells being thrown into a whirlwind of blades. He was about to dodge when he felt the lightning in his chest. His body froze as the energy crackled out of the fist in his chest, nerves locked by the attack. His hearts began to climb out of his back and then the electricity was gone and a grinding, slicing feeling carved through his skull and downwards, obliterating him.
"Excellent timing, Naruto," Kakashi said. "Orochimaru?"
"I couldn't do anything to help," Naruto admitted.
"Yosh!" Naruto jumped as Gai spoke from behind him. "Orochimaru fled quite effectively, I am ashamed to admit."
"He lost an arm first," Yamato supplied as he wiped sweat from his brow. "We'll call it a victory for us."
"Your arm?" Kakashi asked.
"Not great, sensei. I think I could hold a kunai, but I'm not going to be using Futon: Rasengan again anytime soon. Tsunade-baa-chan will have my head for this as it is."
"It is a most effective attack, Uzumaki-kun!" Gai cheered. "It is only a shame I could not hold that fiend Orochimaru in place."
"In retrospect," Kakashi murmured, "it might have been best to have you engage him from a distance. If we'd surprised him, you might have been able to manage."
"Doubtful. He is most slippery. Had I not used the gates, he would have eluded me completely. He was unable to fight me properly, but he has a devastating array of attacks that forced me to fight without the full advantage of my speed. He truly is a genius."
"Would have been nice to try. But with them in the middle of a village, we didn't have much choice but to force them out first."
"Agreed. Shall we race back to Konoha to share the good news?"
DIE
Naruto stared at the Hokage Monument, unseeing. They had been riding high on the success of eliminating Kakuzu, marred only by the escape of Orochimaru, when they returned to Konoha. There had been a pall over the village, though none of the citizens seemed aware of it. An ANBU had appeared with a summons to the Hokage that had emphasized the presence of Yamato.
At first, he hadn't believed the news from the elderly toad on the Hokage's desk. He'd thought it was some sort of prank or joke or something. It had to be. Jiraiya couldn't be dead. Only the look on the toad's face—defeated, a little lost, and angry—had said otherwise. It should have been a bad dream. He'd had plenty of those while on his training trip, all too aware of his failure to save Sasuke from his own darkness.
The disbelief hadn't lasted and in place of it had come the anger. Bloody red, raw, cold. He'd expected it to feel like a fire, but it just felt as if all the heat left his body and was replaced with the desire to rendtearkill. He'd felt the parting of flesh under claws, tasted the tang of blood as he tore with fangs. He'd had to throw back his head and let out a roar just to allow some of the hate out. It was so clean. He could slip into this fury and let it wash away the hurt and the loss and the confusion. It would be easy. Just lose himself in the feeling of death.
He could feel them, tail after tail extending from his body as the Kyūbi spoke to him. It promised all the vengeance he could ever desire and the power to bring ruin to those who had hurt him. It had offered before, but this time he was tempted to accept the offer. It roared in anger and this time it felt like it roared with him. It new the pain of helplessness. All he had to do was let it help and he'd be able to hunthurtslaughter those in Ame who had turned their backs on the dream of peace.
Naruto came back to himself as a wooden cage fixed itself around him, hammering the Bijū in his gut back to its own prison. It drained away, taking the comforting cloak of numbing rage with it. All that he had left was the loss and it bubbled out of him in wracking sobs. He wasn't aware of the damage he'd done to the Hokage Tower, the ninja who had gathered, ready to strike him down if the beast had broken free. He just let the tears flow as he'd sworn he never would again after the death of the Sandaime. Long after his eyes had dried and his body had given up on it, he lay curled up in the conjured wood. He didn't want to move and would have happily lain there forever, but a slimy hand rested on his shoulder.
"I miss him too," the old toad had said in a croaking voice. "He was betrayed by someone he thought was going to save the world. I am sad and angry. I will not tell you not to feel as some would." The voice was calm and kind, sorrowful, but tempered by something Naruto didn't have a word for. "Feeling nothing makes you nothing. But there is danger in too much anger or sadness or envy. For you, that danger is greater. Your rage could burn the world down. Do you want these people who care about you to be turned to ash?"
Naruto had raised his head to see Kakashi and Tsunade and Sakura surrounding the wooden cage, concern on their faces. Tsunade and Sakura were busily using medical chakra to cleanse the taint of the Bijū from Kakashi's arms. The cloth of his shirt had melted into his flesh where he had tried to shake Naruto out of his fit.
"No."
"Then you need to learn control, boy. Master yourself. Avenge the fallen if you will; hate his killers, too. Never let it rule you."
"Can you teach me?"
The toad shrugged. "Maybe. I can try. If you don't learn to leash yourself, one day you won't be able to be stopped."
Now Naruto faced a long period of study to master senjutsu. He would leave in the morning for an unknown length of time to be in a place where people would be able to stop him if he lost himself to rage. He could feel it bubbling away still.
DIE
Naruto got the message from Gamakachi. He'd been about ready to return anyway. It had taken time and effort, but there was a sense of peace now. It fell about his shoulders like a cloak, like the one he wore. It had been given to him by the toads when he had completed the steps of mastering his own darkness and been anointed a sage by the elders.
"Konoha is falling."
He landed in ruins. Half the village had been obliterated. The dead were in pieces, scattered around. There were a cadre of orange-haired figures standing at the outskirts, all wearing the distinctive cloak of the Akatsuki.
"I repeat," they said together, "send out Uzumaki Naruto, or we kill the rest of the village."
Naruto considered fighting. He knew he could hurt them. But Jiraiya had been unable to do it. And if he fought and didn't do it right, the village would die. He didn't hesitate. He stepped out of the shadows. "My life for my village."
DIE
Naruto woke a second time since he had expected to die. His vision was very strange, slightly purpled and his eyes hurt. Granted, the rest of him was pretty achey, but this was more . . . sharp. It dug into his skull.
Well then, brat. Naruto froze. The Kyūbi had been completely silent since his sage training had begun to take. He knew it wouldn't last, but since his emotions had come under control, he'd had nothing and had hoped it meant it was cut off. You've got my father's eyes. So the giant fox had a father? I do indeed. And now I know why you're familiar. Welcome back, Asura.
Naruto wandered into the ruins of Konoha, still talking with the beast in his gut. It had been learning senjutsu along with him, hoping to use it to overpower him and had instead found peace. For all its displeasure at being offered up to someone who wanted to use it, the Bijū had nevertheless been impressed by his willingness to save others. Without Uchiha Madara, or its hundred-years-long rage, it was reminded of its favorite brother.
"Naruto!" Sakura shouted as she spotted him.
"Hey, Sakura. The Kyūbi says that we can help. Where're the dead being gathered up?"
DIE
The army of Iwa approached Konoha. It had taken them a few months to gather enough forces to be sure of crushing their hated foe, but the village should still be reeling from the destruction that had been visited onto it.
Standing in the distance was a single figure. With yellow hair. A robe flapped in the wind. Then two more joined it. The pair flanking the central figure knelt into seiza.
"I am Uzumaki Naruto, son of Minato Namikaze. This is your warning: go home now."
The Tsuchikage made a dismissive gesture and his ninja charged.
DIE
"Congratulations, Naruto," Tsunade said, her grin huge. "Younger than your father and you managed to make it to Hokage."
"I'm so proud!" Kushina cheered, her own grin threatening to remove her head.
"I have a promise to keep." Naruto picked up a sheet of paper and began to write.
(A/N John)
The omake on the other hand . . . it's definitely shorter than it could have been, but it's not really supposed to be a full story, just a bit of story to fill in some of the blanks. Like my idea that in this world, senjutsu requires control partly for the harmony with nature and partly because the toads wouldn't want someone who's a loose cannon to be able to use senjutsu.
(A/N 2 John)
About Kushina: yes, Naruto used the Rinnegan to bring her back, just like he had a pair of paths gathering nature chakra for him during the fight with Iwa. Well, I say "fight" but that's really a bad way of putting it. More like "making them wish Minato had been there instead". He also brought back most of the casualties from the attack on Konoha. He can use nature chakra to cheat the cost since that is essentially life-energy. Does that apply in other stories? We shall see.