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Naruto: The Best Naruto Neglect/Dark/Banishment Stories

These will be the best Naruto neglect/dark/hate/banishment stories by several different authors. All authors will get credited. Most of the stories will be abandoned stories. Enjoy

Hyuga_Tobirama · アニメ·コミックス
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242 Chs

Chapter 5: Part Three

Part Three

Snafu's Notes: The song used as Konoha is destroyed is fitting. Fee free to listen to it as you read Konoha's destruction. I would love to see the Consequences series on the TVTropes page. And check out my profile for a new challenge.

Find the Street Fighter reference within the chapter. After this, will be the epilogue.

About three weeks after the Konoha envoy had left for Azura...

The tension was very high in Konohagakure no Sato. Their salvation lied in the one they had tried to kill. There were no civilians left in the city. Only ninja. After the last attack, which had destroyed the market district, the remaining civilians were evacuated from the city and sent to other villages in Fire Country. The village was locked down tight.

At the moment, it was nearly dawn. Hanabi and the Hyuuga were patrolling the main road leading to the massive village gates. The Jounin ninja, now reduced to less than half of its strength patrolled the city streets. The ROOT ANBU – now under Tsunade's control following the death of Sasuke Uchiha – patrolled the streets alongside the remaining Jounin. There were no Chuunin-level ninja, as Tsunade had express-promoted them to Jounin.

Things looked grim, but Tsunade and Jiraiya held out hope that Naruto's love for Konoha would save them.

If they only knew...

As the run rose over Fire Country, Hanabi noticed the scroll that was attached to the gate. A quick scan of her Bykaugan showed that was not booby-trapped with exploding tags or poison of any kind. Flagging down a passing ANBU, she ordered her to take the scroll to the Hokage Tower.

Hokage Tower

Jiraiya was summoned to the office of the Hokage minutes after the scroll was delivered. He found Tsunade behind the desk, the color drained from her face, the scroll opened.

"What is it?" the old pervert asked.

With shaky hands, Tsunade handed over the scroll to her former partner. Soon, Jiraiya's expression matched that of the busty Hokage.

What had been delivered to Konoha's doorstep was a copy of the Terms of Surrender, signed weeks earlier by the Fire Lord, Rahoujin Hanzou and Kurotsuchi.

"The Fire Lord sold us out," Tsunade whispered. "We're considered expendable."

KABOOM!

The embattled Godaime and her former partner turned to the window, where the massive explosion had literally blasted the door off its hinges, the massive doors flipping end over end like a pair of oversized shurikens, crushing any Konoha ninja that failed to get out of its way.

Tsunade knew that Hanabi and the majority of the main branch Hyuuga were stationed at the front gates when it blew. She had hoped that the Hyuuga clan head's death was painless.

Ninja came charging in, weapons drawn, wearing the symbols of Rain and Stone.

As the Konoha ninja engaged the invading forces, both former Sanin came to a horrifying realization. Hanzou's demand of a match with Naruto was a decoy to allow his forces and those of the Stone to move in for the kill. Hanzou's gambit had paid off in spades. He knew of Naruto and of his past as a Konoha ninja and had used that against them while forcing the Fire Lord to hand over Konoha to be destroyed by his and Iwa's forces.

Naruto wasn't coming. The Leaf was done for.

The Siege of Konoha has begun.

"Naruto was never going to help us, wasn't he?" Tsunade asked as she and Jiraiya watched from the Hokage Tower the deadly battle that was taking place.

"I don't think so," the perverted hermit replied. "Never thought he would. Should have know that Hanzou would use Naruto against us. We fell for it. Then again, after what we tried to do to him, we're not exactly his favorite people now, aren't we?"

Tsunade nodded. "So this is it, then? The Leaf goes out not with a whimper, but with a bang?"

"Seems that way. Wish I could die in my bed. But dying in battle isn't too bad. Let's make the Shinigami wait a while longer."

Tsunade nodded. If Konoha was doomed, might as well make Hanzou and Kurotsuchi earn their prize. If Konoha was to fall, then they would take as many enemy ninja with them as they can.

One week later...

The Siege of Konoha was indeed brutal. Tsunade and Jiraiya made good on their promise. Iwa had expected a quick victory, but Hanzou knew better. Konoha's back was to the wall and despite inflicting casualties, Konohagakure stubbornly fought on.

On the third day of the siege, Tsunade Senju, the Godaime Hokage, granddaughter of Hashirama Senju, grand-niece of Tobirama Senju, was killed in battle. But not before seriously injuring Kurotsuchi with her super-strength. With their leader injured in battle, Iwa retreated. Hanzou, deciding that discretion was the better part of valor, decided to pull back his forces as well.

Jiraiya, however, did not get through this battle unscathed. The poisons used by Rashoujin's great-grandfather were very deadly, and even now they were no exception. A well-aimed senbon needle laced with the Salamander's poison nailed Jiraiya in the neck, a parting gift from Hanzou before pulling his forces back.

Two days after Tsunade's death, Jiraiya received word through his spy network that Ame and Iwa were now planning to launch a leave-no-survivors assault on the village. Hanzou's previous offer of mercy was now suspended. There would be no mercy.

Jiraiya thanked his informant, then issued his final order: his information network was to be disbanded. After all, why would a dead man need an information network?

Office of the Hokage – shortly before the fall...

Jiraiya knew he didn't have long. The remaining Konoha ninja had taken up positions in the area surrounding the Hokage Tower and in Danzou's underground ROOT headquarters. The protection seals kept Ame and Iwa's forces out, but it wouldn't be long before those seals gave out.

The poison in his veins was taking its toll. Either he would die fighting or he would succumb to the poison. From the look of things, it would be the latter.

His vision cleared long enough to see the unhappy faces of Shikamaru Nara, Tenten, Ino Yamanaka and Chouji Akamichi.

I know, I know I've let you down

I've been a fool to myself

I thought I could

Live for no one else

"You're late," Jiraiya said.

"Where's Tsunade?" Ino demanded.

"Dead. Killed in action just the other day. It's over. Konoha is finished. Hanzou's demand to fighting Naruto was just a ploy to let our guard down."

"He refused, by the way," Tenten said. "After what we learned, I really don't blame him."

But now through all the hurt and pain

Its time for me to respect

The ones you love

Mean more than anything

Now Jiraiya's interest was piqued. He leaned forward, ignoring the pain in his body. "How much did he tell you?"

"Everything. He showed us...showed us the abuse and the assassination attempts on his life by the villagers...our senseis...even our parents," Ino seethed.

"And I'm guessing that he told you the truth about the Uchiha Mission, right?"

The four ninja nodded.

Outside the ruined village, Rashoujin Hanzou and the interim Tsuchikage watched as the seals keeping them outside Konoha were starting to fail.

So with sadness in my heart

I feel the best thing I could do

Is end it all

And leave forever

One of Hanzou's lieutenants approached the Ame warlord. "Your orders, General Hanzou?"

"Leave no survivors," Hanzou ordered. "Show no mercy. Destroy any jutsu you find. Anything else is fair game."

At that moment, the seals sputtered, then gave out. Hanzou and Kurotsuchi – with her torso bandaged, and one arm in a sling – gave the order to move out.

Back inside the office...

"Why? Why did you do this to Naruto?" Ino demanded, while Chouji cracked his knuckles and Tenten had several kunai in her hands. "Why did you lie to us about the banishment orders? If anything, Sasuke should have been banished!"

"For the record, I wasn't crazy about the Uchiha like the council and the Fire Lord was," Jiraiya said, deciding to come clean for once in his life. "The Fire Lord, Danzou and those two elder councilmen, and the Civilian side of the council worshiped the ground that the Uchiha walked on. But we were both united in our hatred for Naruto for our own selfish reasons. His father was my student, a prodigy in the fuinjutsu arts. I should have been happy that he surpassed me in skill. Instead, I became jealous at his success, especially when he created the Hiraishin."

What's done is done, it feels so bad

What once was happy now is sad

I'll never love again

My world is ending

Jiraiya paused for a moment to cough into a handkerchief. Shikamaru noticed that there were specks of blood on the soft cloth. Outside, the forces of General Hanzou and Kurotsuchi began to slaughter the remaining shinobi forces, before being delayed by a second set of seals. Here, three squads of ROOT ANBU delayed them, with orders to kill as many of the enemy ninja as they could before they were brought down.

"I thought that I had some more to teach Minato," Jiraiya continued. "But there was nothing else. Then he married Kushina, who was trained here in Konoha, but was the daughter of the Whirlpool Damiyo. I knew that Kushina was very wealthy, given her status as royalty, and combined her wealth with the Namikaze wealth, they were the richest couple in Konoha. When Naruto was to be banished, I saw my chance...to get a piece of the wealth that was stored inside the estates. I acted purely out of greed."

"Why did Tsunade go along with the banishment? Why did she blame Naruto for her death?" Ino demanded.

"Tsunade and Kushina were very close. Tsunade did not have any children and saw Kushina as a surrogate daughter. Tsunade did not know that Kushina was the jinchuuriki to the Nine-Tails, as was her grandmother was before Kushina, and as Naruto after his mother. Tsunade once told me that 'Naruto took his first breath by taking Kushina's last.' She had opted to kill Naruto herself when we retrieved her after the Sandaime's death, but she stayed her hand."

I wish that I could turn back time

Cause now the guilt is all mine

Can't live without the trust from the those you love

Explosions were heard outside, as the explosive traps were triggered, having been laid there by what remained of the ANBU, decimating the Iwa ninja. Jiraiya and Tsunade had seen that the main city streets were booby-trapped in the same fashion. If Konoha was to fall, then Hanzou and Kurotsuchi would have to work for it.

"Our friends died because of the elders' ignorance!" Ino shouted. "You took the Yondaime's legacy and tried to butcher it! Konoha lost everything because of your hatred towards Naruto!"

"I know, and for that, I deserve no sympathy," Jiraiya said. "Minato entrusted Naruto to the both of us, as we were both his godparents." Off their shocked looks, the dying man continued. "But...Tsunade and I wanted nothing to do with him, and we left him at the mercy of the people. Iruka's friendship towards Naruto was false...Teuchi and Ayame tried to poison him to death. Hell, I even tossed him into a ravine. Naruto summoning the Boss Toad was a fluke."

The remaining ROOT ANBU, led by Sai, confronted Rashoujin Hanzou.

I know we can't forget the past

You cant forget love and pride

Because of that its killing me inside

As the Iwa and Ame forces engaged the emotionless elite of the 'Ne,' Sai fought Rashoujin Hanzou, forcing the Ame warlord on the offensive with his ink jutsus.

Inside the office...

"I confess...that I betrayed the Sandaime...my student...as much as I hate to admit, Naruto held the ideals that Hashirama Senju once had – the Will of Fire," Jiraiya said. He smiled sadly. "Just like his father. He would have brought Konoha to greatness without force. I will tell you all something. It was the Uchiha – particularly Madara Uchiha – who unleashed the Nine-Tails in a frenzied state upon Konohagakure. It was Fugaku Uchiha who plotted a coup d'etat. And it was Itachi Uchiha who slaughtered the Uchiha clan not to test his limits, but to stop a civil war. I let my ego and my pride cloud my judgment. Tsunade let her hatred cloud hers. Naruto was not the Nine-Tailed Fox in a human body. He was just an innocent boy in all of this mess."

Sai's body fell to the ground, his neck broken. Rashoujin Hanzou turned from his men, who were finishing off the remaining members of the ROOT ANBU. He looked at his prize – the Hokage Tower, which sat in the distance. The seals were a hindrance, but he knew that Konoha was finished.

He planned to thoroughly clean out the village of anything that wasn't nailed down. Then he would destroy all of its prized jutsu, be it elemental or clan techniques. The Hokage Tower he would save for last.

Inside the office...

"You four are the last of the Rookie Eleven," Jiraiya said. "You can stay, fight and die...or you can make a new life for yourselves. Like I said, Konoha is finished. The seals will only keep Ame and Iwa out for so long. As acting Hokage...I relieve you four of your duties. Get out while you still can. It's too late for me. But it's not too late for you. Hanzou's forces are coming down the main street, which means you have a thirty-minute window to get whatever you need from your homes. Use the hidden route inside the graveyard behind the Shodaime's grave to escape."

It all returns to nothing, it all comes

tumbling down, tumbling down,

tumbling down,

"We can't just leave you here!" Chouji objected.

"You can and you will," Jiraiya said as he opened retrieved a chest from under the table and opened it. Inside were exploding tags. Chakra-powered exploding tags. More than enough to level the Hokage Tower.

"Something I picked up from Naruto," Jiraiya said, remembering the booby-trapped chest inside the Namikaze Estates. He tossed Shikamaru a storage scroll. "That should be enough for the four of you to start over. I think 20 million ryo should do the trick. You're almost out of time. Get out of here." He smiled. "Good luck."

Shikamaru nodded. Then he and the others left Jiraiya to his fate.

Once they were gone, Jiraiya activated a second set of seals. Exploding seals, with a ten-second delay. He turned to the window and watched as Iwa and Ame made their way down the main streets, block by block. It wouldn't be long now. Turning back to the desk, he found Tsunade's sake stash inside a drawer.

Shrugging his shoulders, he decided on one last drink. Pulling out the bottle of the strong drink, he found several photos at the bottom of the drawer. Jiraiya pulled them out as he undid the cork. Since there were no drinking cups, he decided to just knock the whole bottle back.

It all returns to nothing, I just keep

Letting me down, letting me down,

Letting me down

The first picture was of himself, Tsunade and Orochimaru, back when they were genin, along with a younger Hiruzen Sarutobi.

"I fucked up big time, sensei," Jiraiya whispered. "Konoha fucked up big time when it came to Naruto. If we only treated him better instead of treating him like he was a pariah...Konoha would not be in its final moments. You would be proud of him, sensei. He would have made a great Hokage, had he was given the chance. You saw that in him. He was unlike the Uchiha, thinking he could get something for nothing. He doesn't deserve our forgiveness."

At the residential district, Shikamaru, Ino, Tenten and Chouza went to work. They cleaned out their homes of any cash and of family jutsu scrols. Tenten made a side trip to the Hyuuga compound, where there were several remaining Cadet Branch ninja pilfering the compound.

It was there that Tenten learned of Hanabi's ultimate fate. Knowing well that she was pregnant with Neji's child, the Branch clan handed the weaponsmaster copies of the Jyuuken scrolls, and told her to leave. Tenten nodded in thanks and left the remaining ninja to their devices, but not before warning them that they had less than 30 minutes to get out before Hanzou's forces breached the seals guarding the residential districts.

In my heart of hearts,

I know that I could never love again

I've lost everything

Once they were prepared, they met at the grave of the Shodaime. Their hitai-ates and flak vests were left behind inside their homes, which they set fire to in order to deny Hanzou and Iwa anything of value. Knapsacks slung over their shoulders, they were ready to go.

"So...this is it," Shikamaru said. "Never thought that Konoha would see its last days."

"Where do we go now?" Ino asked.

"Somewhere neutral. Somewhere with plenty of food," Chouji said as he finished off some chips.

Everything

That matters to me,

Matters in this world

"Chouji's right about being somewhere neutral," Ino said. "We're the last of what Konoha should have been. We need to stick together. We'll head for Sea Country and rest up. Then we'll decide on our next move."

With that, Shikamaru Nara, Ino Yamanaka, Chouji Akamichi, and Tenten made their final escape from Konohagakure no Sato. They never looked back.

Inside the Hokage's office, Jiraiya found pictures of Minato and Kushina – on their wedding day, and at home while Kushina was pregnant, along with pictures of Naruto with an elder Sarutobi, and of Minato and himself.

"Tsunade still blames Naruto for Kushina's death, Minato," Jiraiya confessed, the sake now gone. He was fading, and fading fast. "It wasn't the gaki's fault. If my pride and jealousy of you being a better seal master did not get to me, then I would have been at Naruto's side when the banishment orders came down. But you would have been proud of him, both you and Kushina. He's not Hokage, but the Damiyo of Whirlpool. He revived her homeland. I wasn't worth the ground he walked on. Your son was better."

I wish that I could turn back time

Cause now all the guilt is mine

Can't live without

The trust from those you love

Outside the shattered window, he could hear Hanzou shouting orders. "Secure the tower! I know Jiraiya is still alive somewhere! Bring him to me!"

As the ninja charged into the tower, Jiraiya let loose a small smile. With this final act, he would deny Rashoujin Hanzou and Kurotsuchi the pleasure of displaying his corpse for all to see.

"Wish I could go out in style," he murmured as he held the photos close, his heart slowing down. "I was hoping in bed with two half-naked ladies. Oh well. At least I could take out some more ninja before I go." He sighed. "If only we treated Naruto better...Minato...Kushina...Sensei...Naruto...I am so sorry..."

With those words on his lips, Jiraiya breathed his last breath, and died.

I know we can't forget the past

you can't forget love and pride

because of that, its killing me inside

Not long after Jiraiya's death, Ame ninja burst into the room. All they found was one dead (former) sanin, clutching several photos to his chest, and a closed chest resting on the desk.

Thinking that there was something valuable inside the chest, the three Ame ninja opened it...

...and the exploding tags and the seals Jiraiya had set around the office and all over the Hokage Tower activated.

KA-BOOOM!

Outside there was a flash of white, which was followed by the explosion, killing any Ame and Iwa ninja that were inside. The tower the collapsed onto itself, leaving nothing but debris and rubble.

The blast wave threw the invading ninja back, Rashoujin included. The great-grandson of the Salamander rose to his feet, and looked at the burning ruins of the Hokage Tower.

'So...Jiriaya was there after all,' Hanzou thought. 'Well played, old man. But in the end futile.'

It all returns to nothing, it all comes

Tumbling down, tumbling down,

Tumbling down

Indeed, it was futile. Upon Jiraiya's death, the seals had failed, allowing full access to the village.

Turning to the Ame and Iwa ninja, he declared victory. "The Leaf has been crushed! Take whatever spoils you can carry! Destroy any jutsu you find! Konohagakure no Sato is finished!"

With that, the looting began.

The Fire Capital – Fire Damiyo's Residence

With the majority of the occupational forces down in Konoha, the Fire Damiyo decided to act.

After one final visit of his family, he designated his eldest son as his successor before locking himself inside his office. The Fire Lord sat behind his desk, looking over the document which he had signed, turning over Konoha to slaughter. Hanzou was thorough. The civilians who had escaped Konoha were forbidden to leave Fire Country in order to start over. In effect, they were like him, prisoners inside their own homeland.

It all returns to nothing, I just keep

Letting me down, letting me down,

Letting me down

He sat back in his chair, the tanto in his hands. He had hidden it inside his office, and the Ame forces had failed to find it. The blade was unsheathed, already stained with his blood, having sliced his wrists.

The burden of selling out his integrity in exchange for his family's lives had proven too much for him to bear. He had hoped with his final sacrifice, that he would at least find some redemption in the life thereafter.

It all returns to nothing, it all comes

tumbling down, tumbling down,

tumbling down

He would be found dead inside his office an hour later by his Ame guards.

Ruins of Konohagakure no Sato – dawn.

Konohagakure no Sato, once the strongest of the Shinobi villages, was in flames.

Rashoujin Hanzou watched the city burn with an impassive look in his eyes. The city had been picked clean, its jutsu destroyed. He even decimated the remaining ROOT ANBU in Danzou's underground headquarters by flooding the underground base with the salamander's poison, following by destroying all exits with several exploding tags.

Kurotsuchi and her Iwa ninja had long since left the battlefield, taking with them the spoils of war. Out of respect, did Hanzou ordered the graveyard not to be touched.

The siege was over, but he had to admit that Konoha made him work for the victory. Over a quarter of Ame's ninja force had been killed, and it would take some time to recover.

One of his lieutenants approached him. "General Hanzou, we received word that four Konoha ninja has escaped the village."

"Only four?" Hanzou repeated, disinterested.

"Yes, General. Shikamaru Nara, Ino Yamanaka, Chouji Akamichi and Tenten. Your orders?"

Hanzou thought long and hard for a moment. "They are of no consequence to us. Our mission is accomplished. Consider this a mercy to the remnants. However, should they try to kill me, I will be more than willing to send them to meet their family and friends."

"Sir!" Another ninja appeared. "Word from the Fire Capital! The Fire Lord was found in his office. He's dead, General."

Hanzou nodded. "Withdraw our forces from the capital. We are returning to Amegakure."

It all returns to nothing, I just keep

Letting me down, letting me down,

Letting me down

By the end of the week, the news would spread throughout the Elemental Countries. Konoha had fallen to Ame and Iwa.

Most of the people's reactions outside of Fire Country came up to just two words: "Good riddance."

The destruction of Konoha had not left a power vacuum as expected. Konoha had long since lost its status as the powerful of the Shinobi villages. Neo Uzushiogakure was now the most powerful, Suna and Iwa tied for second place. The people of Fire Country – their pride was broken with the loss of their village and of their wealth. Even Wave Country under Gato's rule was better off than Fire Country.

The old saying was indeed true. Pride does come before the fall.

Neo Uzushiogakure – three days after Konoha's destruction

The message from the ANBU was brief, yet satisfying.

Konohagakure destroyed. Fire Lord committed suicide. Tsunade Senju – confirmed K.I.A. Jiraiya – confirmed K.I.A. Hanabi Hyuuga – confirmed K.I.A. Nara, Yamanaka, Akamichi and Tenten confirmed missing. Amegakure and Iwagakure forces returned back to their villages.

Naruto read it once again before setting the slip of paper down. Konoha was gone. Out of the entire Shinobi force, only four known survivors. The assault had taken place during the Whirlpool Taijutsu Tournament. In a way, it was justice. A long time coming, but it was justice.

He shared the news with Hinata as they sat over lunch inside his office within the Neo Uzu Compound.

"It's finally over," Hinata said. "Konoha is gone."

Naruto nodded. He could have destroyed Konoha any time. But he chose not to, deciding to let Konoha dig their own grave.

"For Fire Country, the destruction of the Leaf and the suicide of their leader will probably be the most important day of their lives," Naruto mused.

"Really?" his wife rebuked. "So what was it for the both of us?"

Naruto smiled at his wife. "For us...it was Tuesday."

Hinata chuckled and the couple resumed eating. "Maru asked me to relay a message to you. He wants to lead a group of ninja to the ruins to recover the ashes of the first four Hokages."

Naruto grunted. "The idea does have merit. They deserve a better resting place than in the ruins of a soon-to-be forgotten city. Tell Maru that I will accompany him. We will leave for Konoha by the end of the week. Besides...I always wanted to piss on the ashes of the Leaf."

Hinata shook her head. "Honestly...why do I even bother with you?" she said in a teasing tone.

"Because you've been nuts over me since our genin days..."

"Whatever. I'll tell Moegi, and she will relay the message to Maru."