After Pain ... alternate Naruto Shippuden Ending

Warning: SPOILERS AHEAD Up to EPISODE 175 of Naruto Shippuden

After watching episode 175 of Naruto Shippuden I thought it would be a great place to end the series neatly, with Naruto having achieved his goal of getting the respect of the villagers and becoming their hero. I was, however, excited to see what would happen next. (read my full post about it here )Unfortunately, much of what came after that was pointless and the ending was very disappointing. Aside from the Obito vs Kakashi fight, which was done so well in the anime, I almost wish none of it had happened.

So I've decided to put down my idea (developed with my siblings) in the form of fanfiction. I know. It's been ages since I finally stopped writing Harry Potter fanfiction and I never thought I'd go back, let alone to a different fandom, but what can you do! I can't get this alternate ending out of my head unless I write it down so I might as well share it. 

So here you have it. For now I'm calling it After Pain. 

This tale is set after episode 175 during the rebuilding of Konoha. Many of the things that happened during the rebuilding, and the build up to the five Kage summit will still happen, just in a slightly different way or order. 

UPDATE: This fanfic is now complete. Links to each chapter have been added below. 

After Pain 

Chapter 1: Wanted: Sasuke Uchiha

Chapter 2: For a Friend 

Chapter 3: Anbu 

Chapter 4: The Hidden Leaf Jounin 

Chapter 5: A Worthy Opponent 

Chapter 6: Kakashi Hatake 

Chapter 7: In the Open 

Chapter 8: The Right Moment 

Chapter 9: The Quiet Before the Storm 

Chapter 10: A Man of Many Shadows

Chapter 11: A Leaf on the Wind 

Chapter 12: The Konoha 11 

Chapter 13: Epilogue 

Chapter 1 - Wanted: Sasuke Uchiha 

When the team of cloud ninja entered the leaf village they did not make any attempt to hide their presence, they strolled into town arguing about a pebble of all pointless things and ignored the leaf ninja, focusing on whatever their important mission was. Despite all this, they did not raise much attention because the villagers had, by now, become used to ninja from other villages coming in and out with messages and reports and threats and offers of help and so on. They were escorted into town by two Chunin skilled at disarming and quick capture. No one seemed worried. That worried Shikamaru.

It was quite a drag, but Shikamaru and his classmates had developed a habit of butting in where they weren't needed - or authorized - to. His mom told him it was a sign that they were ready for promotion to Jonin, Shikamaru wasn't so sure, he saw it as a sign of Naruto's influence on the group. To Naruto, there was no such thing as rank and chain of command and minding your own business. He saw himself as the future Hokage and so he saw any issue that interested him as an issue that he could interfere in. Whatever the reasons, Shikamaru found himself attaching a shadow trace to the nearest of the three and then excusing himself from his current task of inserting window panes into the new Academy windows.

No one cared. The other Chunin there were perfectly aware that Shikamaru had been misplaced in the rush to get the rebuilding done as quickly as possible, many of them were also out of place at this task and were simply waiting for an excuse, or an opportunity, to go do something that better fit their abilities. His feet took him to where Choji was automatically and his mind was relatively free to think about the bits of conversation that he had heard from the three Cloud ninja. They were here on a very secret and sensitive mission, but they had no problem casually throwing the name Sasuke Uchiha around in their conversation.

Choji had abandoned his task of wall-building and returned to his normal size by the time Shikamaru got to the site of the new village gates. He looked seriously worried, which meant he knew a lot more than Shikamaru did right now.

"You saw the three Cloud Ninja?" Shikamaru asked. He didn't need to elaborate any further. Choji had been waiting for him.

"They're after Sasuke," Choji said. "I heard them talking to the guards when they came in, showing their official mission papers... Sasuke went after someone important from their village, the RaiKage's brother or something, and they want us to help capture him. They say he's with the Akatsuki."

That didn't make any sense. Sasuke had reportedly killed Orochimaru to avoid being used - and his mission had had nothing to do with the Akatsuki organization's goals. Why would he go and join them? Why would he want to attack any Cloud Ninja? Had he achieved his goal of revenge on Itachi and just got bored? Shikamaru needed more information.

"Did they let anything else slip?" he asked Choji hopefully.

"No," Choji said, "But they demanded to be taken to see Lady Tsunade, I don't think they realize she's..."

That was another thing that worried Shikamaru. Without a Hokage at the helm even the simple task of rebuilding the village was being done in a haphazard way as each of the Jonin on the Jonin Council took on one aspect of the rebuilding and worked without any oversight from one leader. That was how Shikamaru had ended up making windows. He wasn't very confident that the Jonin Council could handle it if these Cloud Ninja got offended and decided the whole village was at fault.

"Let's go find Ino," he said. Ino was bound to have more information.

...

"The team from the Cloud have arrived at Konoha and spoken to the new Hokage," Zetsu said.

"What did Danzo say?" Tobi asked impatiently.

"He's declared Sasuke a Rogue Ninja and he plans on attending the Summit. They may very well succeed in capturing him. Especially since Sasuke wants to confront Danzo."

"That's not what I'm worried about," Tobi said. "Sasuke is an amusing tool that I still have some uses for, but he's too much trouble. It wouldn't be too great a loss if he was captured. But the Summit... it can't be allowed to go smoothly."

"What is there to fear from the Summit?" Zetsu asked. "It's not like they're going to agree on anything - even going after Sasuke. Might be a chance to kill one of them on the road though?"

Tobi shook his head. He would be stupid if he didn't learn from Nagato's loss... it had been a bigger blow than he was willing to admit and it infuriated him that he still didn't know what had caused it. If Pain had simply been killed it would have been bad enough, but to betray him? Tobi was not going to underestimate his enemies again. He wanted to know what they had that could possibly cause such a change of heart - he had to find out before they used it to unite against the Akatsuki. After all, this Kage summit wasn't convened just because of Sasuke, it was the RaiKage's reaction to the Akatsuki's attack on the two and eight-tails. One of the Kage, at least, understood the danger that his organization posed to their comfortable seats of power.

...

They found Hinata and Lee before Ino and so of course this meant that by the time they did track down Ino Shikamaru found himself looking at a small army of Ninja instead of just his two friends. He didn't mind, they had all heard different bits of information and it would all help. Unfortunately, it also meant they were all talking in quick succession, not allowing him a moment's silence to think. Gaara's name was bouncing around in his head, but he couldn't keep anything straight in there. Kiba was too loud. Even without Naruto there Shikamaru was already developing a headache.

"We're not kids anymore, Sakura," Kiba protested. "We can't always be trying to save him. He's older now too and he chose the path he's on."

"What do you mean, are you trying to say Sasuke-"

"It's not about Sasuke!" Shikamaru raised his voice so that he could be heard over their passionate and completely pointless argument.

Silence.

He fought the urge to say that it was a troublesome bore, there were more important words to say now, no time to complain. Kiba was right, they weren't kids anymore, they had to grow up.

"It's not about Sasuke," he repeated. "This is much bigger than one Ninja or one attack on the Cloud village. The Akatsuki brought our entire village to the ground and killed some of our strongest Jounin. And this Kage summit ... it could go very badly for us if the Cloud decides that the entire village is at fault for not taking care of Sasuke sooner - or for not being cooperative enough in helping them search for him."

"Where's Naruto?" Lee spoke up. "I think he should be here, Sasuke was his teammate."

"No, Lee," Neji spoke for the first time. "I think it best that Naruto not be here for this conversation. He won't be able to think about the matter seriously, his emotions will get in the way."

"He did save the entire village from Pain," Tenten said. "And he may cause more trouble - be upset - if he finds out we had this discussion without him."

There they went again. How was he supposed to gather his thoughts when they kept going off on tangents like this.

"Look," Shikamaru said forcefully. "We're not kids anymore, we looked for Naruto and we can't find him and we need to act."

"Act?" Neji sounded skeptical. "It's not our place to act, Shikamaru, the Jounin Council, the elders, the clan leaders..."

"You're a Jounin, Neji," Shikamaru reminded him. "We're operating without a Hokage here, everyone is overwhelmed with all the rebuilding, it's time for us to grow up and start protecting this village ourselves. It may mean reporting to our clan leaders or elders, but we can't just sit idly and make windows and paint and pretend we didn't hear the things we heard. we can't pretend that you're not one of the most skilled users of the Byakugan or that Ino isn't skilled at the mind transfer or that Sakura wasn't on Team 7 with Sasuke..."

"Shikamaru," Ino said softly, in that tone that meant he continued to surprise her.

"Yeah!" Kiba growled.

"Do you have a plan, Shikamaru?" Lee asked.

"I think we need to make a decision," Shikamaru said, avoiding eye contact with Sakura. "I think we need to bring Sasuke to justice on our own. We have the best chance of doing it, and this time we won't be blinded by the shock of his leaving the village or our emotions... we know how far he's fallen. If we bring him back and bring him to justice there might be a chance to salvage this mess with the Cloud, stay on good terms with the other villages."

"But we can't just leave our duties here," Neji said. "Not all of us, and without Lady Tsunade I don't think it likely we can get this approved as a mission by the Jounin Council."

That was when Hinata's younger sister came running up to them. She went straight to Neji and spoke to him very formally and respectfully, asking him to report to her father, the leader of the Hyuga clan immediately.

"What is it, Hanabi?" Neji demanded. It was more of an order than a question.

"Danzo has been named Hokage," Hanabi replied without hesitation.

Neji looked towards Shikamaru and they made eye contact. Sometimes it was difficult to read Neji's thoughts, but not today. Today Shikamaru could plainly see the worry and shock behind Neji's Byakugan. If Danzo had been named Hokage despite all the opposition this put the village in a very bad situation.

"But Lady Tsunade's not dead, is she?" Sakura called out.

"No," a new voice replied. "She is still the same as when you saw her last. The coming of the
Cloud Ninja has necessitated this move."

It was Sai.

"You should all know that Lord Danzo is already on his way to the Five Kage Summit, and that Naruto has followed him on a quest to go meet the RaiKage and beg mercy for Sasuke. I was ordered to report to Lord Danzo, but I thought you should know this before I left. Someone must make Naruto understand that this gesture may do more harm than good."

"Wait, Sai!" Sakura said. "Can you tell us anything about Lord Danzo... what will he do about Sasuke?"

Sai turned around and looked Sakura in the eyes as if trying to understand something. Unexpectedly, instead of talking he just opened his mouth and stuck out his tongue.

"I cannot tell you anything secret, Sakura. But you will soon hear that Lord Danzo has announced that Sasuke is a rogue Ninja and he has allowed the cloud team to look at Sasuke's file in the records. He will not have any mercy on Sasuke."

Sai took off without waiting for a response. For some reason, even though they had all just been discussing killing Sasuke off themselves Sakura seemed even more downhearted to hear about Danzo planning the same thing. Did she know more about Danzo than she was supposed to? Shikamaru turned to Neji.

"Please stay in contact with us, Neji," he said. "I think our efforts will be needed now more than ever and we should be united in this." At least as classmates they could be united, because Danzo's reign might create a lot of division.

He didn't need to explain further. Neji understood what he meant. He gave a small nod before taking off, followed by young Hanabi. The others lingered.

"For now," Shikamaru said. "We should probably report to our team leaders and superiors to see what's going to be done and who can be spared... the new Hokage will not approve all of us going on a mission to get Sasuke by ourselves and he's already left the village. But Sakura, if you could go after Naruto and stop him..." He hadn't trusted her to help bring back Sasuke all those years ago, but this time he knew that she would have the greatest chance of bringing Naruto back to his senses and as his team member she had a perfectly good excuse to go after him.

"I'll go with you," TenTen said. "I think I know where we can find Kakashi sensei..."

"And my insects will find Naruto for us."

Shikamaru nodded.

"Hinata," he said. "Can you keep an eye on Lady Tsunade's tent, please?"

Hinata nodded and Lee turned to follow her. "I'll help you," he said.

Shikamaru had to go find his Dad and - if he was in the village - Yamato as well. Naruto was being such an idiot going out alone like that! Now they had to rearrange their entire plan, but with Danzo as Hokage it was even more imperative that they do so quickly. Dad would probably be able to send them off on some kind of herb-gathering mission.

"Let's go," Ino said in a businesslike manner.

...

By the time they caught up to Naruto he was face first in the snow at the RaiKage's feet, begging for mercy for Sasuke. Even Sakura seemed to think this was going too far, Kakashi could see a deep frown on her face as she regarded her teammate. She had grown up a lot since those first days on Team 7. Naruto on the other hand, continued to display the same boisterous childishness as always, no matter how much more powerful he got. It was one of the things that fascinated people about him, but in this case, even though Kakashi had agreed to help him find the RaiKage, he knew it could have disastrous consequences.

The RaiKage left Naruto in the snow and continued on his trip, and while this put Naruto into a deep well of depression Kakashi hoped that their encounter had left enough of an impression on the RaiKage to help smooth things over at the Kage summit. Gaara's presence would be a great asset there, but he wasn't sure it would be enough to counter the shrewd manipulation that Danzo was capable of. It was crazy, but he feared his own leader, the Hokage, most of all at this summit.

"Let's go, Naruto," Kakashi said as firmly as he could. "There's no more we can do. He listened to you and he will be thinking about what you said on his way to the summit."

"Acually, Kakashi sensei," Sakura said. "There's something we can do. The others and I were talking back at the village before we heard about Danzo and we decided that we should take care of Sasuke ourselves... bring him to justice ourselves."

This brought Naruto to his feet in an instant. "What do you mean, bring him to justice?" he yelled. "Sakura this is Sasuke we're talking about. We need to bring him back home. Have you forgotten the promise I made to you? Well I haven't!"

"Naruto," there was a strange look in Sakura's eyes, as if she pitied Naruto or felt guilty about his behavior. That was new. "You heard what they said. If it's true, if Sasuke's joined the Akatsuki and attacked that cloud Shinobi then he's not acting like our comrade anymore."

"Sakura!"

"Just listen, Naruto!" Sakura said firmly. "There's no way the new Hokage is going to be as forgiving to Sasuke as Lady Tsunade or Lord Sarutobi were and if we leave it to them and the other Kage they could end up killing him. If we go after him ourselves we'll get a chance to talk to him and to bring him in as a prisoner instead. They'll have to try him formally, then, and hear his side of things. They'll have to take into consideration things like his age when Orochimaru took him from the village and the fact that he was nearly kidnapped. It's our best chance to help him. Otherwise he gets killed by some assassin somewhere and that's it."

Kakashi let the words sink in before prodding Naruto gently towards Konoha.

"She's right, Naruto. If you want to help Sasuke you need to think about things a little more strategically so that this time we don't go home disappointed. Let's go back and talk to the others."

He almost fainted with relief when he saw Yamato come panting up towards them. Finally. Now they just had to get Naruto home in one piece and hope that someone had come up with a good way to keep him safe this time. Kakashi knew that Naruto was one of the goals of the Akatsuki and he was determined not to let them get him, but he knew that the next time they came, they'd be more prepared. They weren't stupid enough to underestimate him after that battle with Pain.

...

Shikamaru's father had invited several clan family heads to dinner, as he often did, but this time the Hyugas and several random Jounin were also included in the invitation. Even Shizune had been convinced to send a shadow clone to the dinner while her real body sat by Lady Tsunade's sickbed as always. Shikamaru had offered to keep one of his shadow traces with her to help them keep watch and get help to her as quickly as possible if the need arose. His father made no direct comment about this idea, simply asked where else he had been using the new jutsu. Even when Shikamaru explained that he had attached a trace to the shadow of one of the three cloud Ninja his father had made no comment. No compliment or chastisement. No questions about how the new jutsu worked. That night at dinner, however, he had invited Shikamaru to sit by his side and dine with the clan leaders, despite the fact that the table was packed with people. Shikamaru tried not to smile too ridiculously during the solemn meeting, but he swelled with pride at the invitation.

Of course it was a drag having to be formal and polite and watch his every movement, but for once Shikamaru considered the effort well worth it. All the information that he was suddenly privy to, all the little hints and rumors of discontent, the whispers about Danzo's secret Anbu foundation and their less than pleasant means of operation... it was like a treasure. He was starting to see more clearly. It would take a while to process all of this information, use it to formulate a plan of action, but for now he just had to listen and remember and be polite.

Poor Neji stood like a bodyguard behind his uncle as the man ate. Shikamaru tried not to make too much eye contact with him, but he vowed to take him a heaping plate of food himself later on.

"We have no objections about his plan towards Sasuke or any of his declared positions, you understand," Hiyashi Hyuga said. "It is the secret organization and their underhanded methods which worry us. Danzo may be the Hokage, but village law keeps his powers in check through the Jounin Council and the elders and all through consultation with all clan leaders, if he is using his organization to bypass that system that is cause for concern for all clans."

"I agree," Shikaku said. "It is the secret activities which worry me the most as well, but I fear he may use the incident with Sasuke to cover up some other activities. You know what happens when the Anbu get involved in a manhunt. And if it has the seal of approval of all five Kage the Anbu team will be almost unanswerable for any ... mistakes."

"Our position is very delicate now with the village in its current state," a Kunoichi from the Aburame clan spoke up. "And Danzo rushed off to this Kage Summit without consulting any of the clan leaders even as a common courtesy, half the villagers aren't even aware of who the new Hokage is... this could get messy."

"Who did he take with him?" a less involved great uncle that Shikamaru was quite fond of asked. "I heard one of the Yamanakas is on his team..."

Ino's dad shook his head gravely. "The boy is one of Danzo's foundation members, I have no contact with him, let alone any control over him."

"What about his parents?" Hiyashi Hyuga asked incredulously. "Surely they might hold some sway over the boy...?"

Inoichi shook his head. "He was orphaned in the nine tails attack before he was even old enough to be aware of his own name. It's no use. Not unless we can get him in for interrogation, that is."

Hiyashi pursed his lips, as if biting back a comment about how the Yamanaka clan took care of its members. Shikamaru stole another glance at Neji. Now was not the time to open up that can of worms. Besides, Danzo's organization had been so secret for so long that no one could have predicted this kind of situation.

...

Kakashi was very well aware that despite their efforts this masked man alone could have had Naruto by now if he'd wanted him. Apparently, all he wanted was to bait him into talking about his fight with Pain. For now, anyway. He also seemed to be baiting Kakashi by purposefully slipping in little comments about events long past - events that he should know nothing about. Kakashi kept himself calm, looking around at the situation, trying to find a weakness in the man's strange Jutsu, but his Sharingan eye was responding in a way that it often did without his control...

"And this is the elite squad that the leaf could spare to protect its Jinchuriki?" the masked man mocked, Sharingan connecting with Sharingan. He had surely seen the tear even if Sakura and Yamato and Naruto had missed it. But Kakashi had grown, he would protect his student this time, no matter what it took.

His mind worked feverishly as the masked man's voice took control of the stand off. He tried to focus on analyzing the Jutsu, but all he could do was fixate in horror on the things he was hearing - how could this man know so much about Itachi's story? Even Kakshi didn't know half of these details and he was both a Jounin and a former Anbu member. More importantly, why was he telling it to Naruto now? What could he hope to gain?

Perhaps he was so confident in the strength of his defensive Jutsu that he thought he was just having some fun with Naruto before capturing him. Kakashi's grip tightened on his Kunai. He could not let that happen.

"But why," Naruto yelled. "Why would they do something so horrible to Sasuke's brother? Who would do such a thing?"

"Why your new Hokage, of course," the man said. "Danzo Shimura."