Chapter 5: The more things change, they don't always stay the same.

Five months.

Five months since Naruto had left the village. Five months since he was taken off planet by the Galvan known as Merlin. Things had changed all over the place. First, we will be sending out vision towards Naruto and see how his training is coming.

On the elemental nation's moon, Merlin's secret base…

Naruto grunted as he pushed up a heavy set of dumbbells, weight a good amount greater than what a normal human could lift. He was currently shirtless with a good amount of sweat forming on his body, showing off the good amount of muscle his body had gained from both his life a as a ninja, and from his training with the banished Galvan.

In the five months that had passed, Naruto had undergone a strict diet, mostly consisting of those horrible nutrient bars, as well as a strict physical training, including weights, cardio, and all kinds of physical exercises. When Naruto wasn't training with his body, he was training with his mind. Naruto was put in front of a computer that would help train his strategic thinking, memory, and other parts of his brain. At times Merlin would combine these with a special training room that allowed him to combine the two. However, it was somewhat limited due to a lack of resources on Merlin's part. However, he had plenty of drones for Naruto to spar against.

Another change, was Naruto's training in chakra and jutsu. Using the same cameras used to spy on the trail of Danzo, Merlin used the to spy on the training of certain members of certain villages, using what they scanned for their training to add to Naruto's training. Naruto also managed to learn a few extra techniques from the hidden water, hidden sand, and hidden cloud villages.

There was also a slight problem that had come up with the whole…alien thing. Some of the technology went right over Naruto's head, and left him very confused. Naruto was also introduced to powerful weapons and tools that could rival certain jutsu and could cause a lot of damage. It also helped hammer home just how small in the universe that his species were.

Naruto let out a grunt as he let down.

Naruto set down his weights. Grabbing what looked like a canteen he drank the cold liquid, feeling the refreshing beverage go down his throat, quenching his thirst.

"Naruto," the voice of Merlin said, "over the intercom system. Come down to the lab, please. I have some things I want to show you."

Naruto stood up, dried himself off with a towel, and put on a shirt. He then exited the exercise room and walked down the corridor. After a few minutes, he arrived at the banished Galvan's lab. The former member of Konoha entered the lab.

The lab itself wasn't as impressive as some of the flashier ones around the universe. There were a few tables filled with different gadgets and experiments that the man had been working on. There were a few other things, including a refrigerator like-device, no doubt for storing chemicals and other things needed to be kept cool. There were also several warnings on the object, reading "Danger", and "Do Not Touch", and a more recently added one read, "This includes you, Naruto!"

Naruto rolled his eyes. He turned to the side and finally landed his eyes on Merlin. The banished Galvan was currently sitting at a computer, typing as fast as his tiny hands could, numbers, equations, and all kinds of technical mumbo jumbo reflected in his eyes. He was mumbling to himself, making sure that everything would go perfectly for what was about to transpire.

As the Galvan was completely entranced in his work, Naruto glanced around. Nearby the computer that the man was typing on, there was a type of bed, resembling, what looked like, a high tech tanning bed.

Naruto glanced in another direction and saw Merlin's workbench. There were several items and objects on it that looked incredibly sophisticated. Naruto saw a glass ball hooked up to was bunch of wires with a hand in it. Occasionally, the wires would flash with electricity and the hand would morph. First become covered in orange fur, with thick black claws, then turning rough and red, and then turning into sharp dark brown and covered in scales.

Naruto removed his eyes from the strange sight at a few other things. Naruto saw what looked like the beginning of a gauntlet, primarily black with a few pieces of orange here and there. There were also a few devices that resembled the grenades that he had seen used, a few high-tech guns, knives, and swords. They all looked half finished, however.

Before Naruto could finish his examination, the sound of a throat being cleared got his attention. He turned around to see Merlin looking at him with a quirked eyebrow.

"Are you done?" he asked.

Naruto shrugged and said, "Hey, excuse me if I'm a bit curious. I've never been allowed in your lab before."

Merlin sighed and said, "Those aren't finished. So, please, don't touch anything at all."

Naruto nodded. While in his stay, Merlin had shown him a few times when greatly advanced technology, wound up in the hands of species that were considered to have low level technology. He had seen people incinerated by their own weapons, and Naruto decided that it would be best to leave all the tinkering to the alien genius.

"So, what did you call me down for here, boss?" Naruto asked crossing his arms.

Merlin answered, "Naruto, over the past few months. You've improved a good amount, and you've adapted well to the technology I have here. As such, I believe it is time for the next step."

Merlin went over the computer and punched in a few keys. After a few moments, the image of a small machine appeared. It looked like a ball, glowing dark blue, with a few black pegs coming out of it.

"What is that?" Naruto asked, slightly confused, and in wonderment.

"These," Merlin answered, "are nanites, or if you want to use a different name, nanobots. These are microscopic machines, so small that even a huge colony of millions would be hard to see. It is these machines that will make you a greater warrior."

Naruto looked incredibly interested.

"How is that?" Naruto asked.

Merlin smiled and said, "These nanites shall be injected into your body. Once inside, they will begin the process of enhancing your body. Your strength will be greater, faster, it may even affect your chakra system, making it stronger, if I am correct. According to my numbers, it should even increase those regenerative powers of course."

Naruto looked excited for a moment, then he thought of something. What about the fox? What if it wound up becoming stronger? Naruto immediately flashed back to when Jiraiya tried messing with the seal during their training trip. His memories of what happened that day after the seal was loosened, but the outcome was clear as day. Jiraiya had multiple second-degree burns, some bordering on third degree burns, a few broken ones, and was suffering from chakra exhaustion. Naruto himself had suffered from several burns. Naruto remembered walking past the field where it happened. There were several knocked over trees, craters, and scorched earth.

Merlin saw his scared face and immediately added, "Judging by how the seal separates your chakra from the nine tails, they shouldn't be any effect on the nine tails."

Naruto let out a sigh of relief.

"However, there is another feature," Merlin said with a smile, "these nanites are connected to a special system that regulates the various DNA that I have connected over the years. With these, you will be able to transform yourself into various alien species."

Naruto whistled and said, "Wow. So how does this work? Do you just take a needle and inject me or something?"

Merlin lost his smile and answered, "Unfortunately, no. If you were a human of Earth this would be that easy. However, the nanites will need time to adjust to your body. They will need time to adjust your personal chakra network as well as your DNA. By my calculations, this process, while painless, will take a long time."

Naruto blinked and asked, "How long exactly?"

Merlin answered, "By my calculations, twelve hours."

Naruto blinked and asked, "Twelve hours? With all the advanced technology, I thought this wouldn't take so long."

Merlin answered, "Well, this may be advanced by your standards, however, by Galvan standards it is pretty behind."

Naruto sighed as he reminded, once again, that Merlin was not at the height of his technological prowess.

"So, what do I have to do?" Naruto asked, raising an eyebrow.

The diminutive genius smiled and said, "Well, all you have to do is lay down in the pod here."

He motioned to the machine that resembled a tanning bed.

He continued, "Once you lay down, the device will put you to sleep and the nanites will be injected into the body."

Naruto nodded and said, "Okay, let's do it."

The pod opened revealing an interior, with a spot hollowed out in the shape of a human body. The inside of it looked like circuitry, with a glowing green color, with black and gold lines running through it.

Naruto laid down into the pod. The lid shut, and a bright glow filled Naruto's vision. Outside of the pod, Merlin went over to his computer and began typing into the various numbers and commands. Inside the pod, Naruto felt his consciousness waver, and he finally fell asleep.

Merlin then continued typing. The screen showed a shape of a human body, outlined in green, and slowly filling up with a bright green color.

"Subject: Naruto Uzumaki. Consciousness diminishing. 80%, 50%...10%. Consciousness reduced. Beginning nanite infusion. Scanning systems. Probability of error, within permissible limits. Commencing nanite infusion."

As this was shown, it showed a timer, revealing a clock. 11:59:39, indicating eleven hours, fifty-nine minutes, and 39 seconds.

The diminutive scientist sighed and said, "Okay, now I just need to pass the time."

He walked over to another fridge, this one had a sticker with the word, "Food" written on it. He reached in and pulled out aa jar full of, what looked like, cockroaches, and canned drink, just the right size for him.

He walked over to his lab table. He sat up, popped open the can, taking a sip, and then munched on a roach before he began setting to work. He had twelve hours and he was going to use it.

On the planet's surface, Konoha…

Tsunade sighed as she finished up a set of paperwork. She leaned back in her chair, allowing the sense of accomplishment to wash over her. After a few moments, she turned and looked out the window over her village.

It had been five months since Naruto left the village, leaving behind his friends and comrades. To her, and several others, after Naruto left it was like there was a cloud over the village, like a large ray of sunshine had been blocked off. Despite the peaceful way the village looked, a lot of people looked like they were walking on eggshells, and for good reasons.

A reason that had happened, a few days after Naruto left.

Flashback begin, four months, and 29 days ago…

Tsunade stood above the bound form of Danzo. Nearby was Jiraiya, who stood nearby, glaring at the war hawk who had conspired against the village's resident prankster and diamond in the rough. They were currently in the arena that was normally used for the chuunin exam finals. The villagers were currently watching with rapt attention. The members of the shinobi clans had serious looks on their faces, especially the members of the konoha rookies, who had been under the old man's genjutsu. The civilians however, were confused as to why one of the hokage's personal advisors was currently in chains.

"People of Konoha," Tsuande announced, a small microphone on her ear, "We have gathered here today to witness to the execution of Danzo Shimura, for acts and conspiracy to commit treason against the village of Konoha."

Whispers of shock and surprise, ran through the villagers who weren't part of Danzo's trial.

Up in the stands, Kizashi Haruno feigned surprise. He had a feeling something was wrong when his wife was called in for a council meeting and he was not. Immediately, he began an operation, putting up a few people as patsies so that he would get off without being noticed. Thankfully, with all the other people being secretly taken down for crimes against Konoha it worked. He was currently sitting next to his wife and daughter, both of which seemed glad to hear the news.

Tsunade stood before the man and said, "Any last words before you meet your maker?"

Danzo spat and said, "Everything I have done was for the good of Konoha. The nine tails was meant to be our weapon, and you foolishly lost him because of your bleeding heart. You are just as pathetic as that fool, Hiruzen!"

Unfortunately, the statement about the village's resident Jinchuuriki was heard and a small uprising began in the village.

"This is all about the demon brat?!"

"The kid should have been given to Danzo years ago!"

"She's killing a patriot of the village because of some brat!"

Other such calls came up from those who were blinded by prejudice towards the boy, but were not part of the conspiracy. The only member of the conspiracy who wasn't talking was Kizashi, who knew it would be best to keep quiet. The shinobi members of the village were currently

Jiraiya stepped up, a microphone like Tsunade's on his head, and yelled, "SHUT UP!"

The sound of the shout, plus the enraged look on his face.

"You know over the past few days, I've gathered a lot of information on what has been going on around this village, and I am beyond sickened with how my village has fallen! Seeing as you all seem to live in your own personal bubbles when it comes to reality, it is time to finally pop it!"

Those listening were now surprised, and a sudden feeling of nervousness flooded the arena.

Jiraiya said, "The supposed failure, was sabotaged early on by teachers who wished to keep him weak and malleable. As for the potential to lose control, here is a little bit of information you should all know. The only way for a Jinchuuriki to be influenced by the beast sealed inside of him, is for his mind to break! In other words, if he had been given to Danzo like your all so blindly suggest, there was a good chance the little self-fulfilling prophecy you all made would come true!"

Many of the civilians all looked shocked at this information. In the stands, Iruka suddenly realized why many of his coworkers hadn't shown up for work the past couple of days. He also felt guilty as he realized he had allowed his own prejudice blind him when it

Jiraiya continued, "As for your precious Sasuke, he is being hauled off to prison. And before you say anything, we checked his mind, and he had no intention of ever returning to the village! There is also the fact that he suffered from severe PTSD, that resulted in his currently mentality. Something that the elders kept from the populace, so they could push forward their agendas."

Looks of absolute surprise went through the villagers. Many who were hoping to have the Uchiha wed their daughters, but weren't part of the conspiracy, were suddenly filled with dread, at the thought of Sasuke being anywhere near their daughters.

Jiraiya then decided to go ahead and pop the final bubble they had surrounding them. He glanced at Tsunade with a questioning expression. She nodded.

"As for Naruto being an orphan," he said, "He is no such thing. His full name, was Naruto Uzumaki Namikaze!"

Everyone in the village looked shocked upon hearing that. Everyone recognized the name of their beloved yondaime and many of them were now kicking themselves for not noticing it before.

Mebuki groaned in frustration as she now realized the name. She didn't associate Naruto with her old friend as he had blonde hair, and now she was kicking herself or not realizing it sooner. He even had the same verbal tick!

Down in the arena, Tsuande felt that Danzo's execution had been held off long enough and walked forward. Chakra formed around her fist as she raised it into the air. Without a moment of hesitation, she brought her fists down with earth shaking strength.

When the ground stopped shaking Danzo's body wasn't even recognizable. However, a gasp of shock ran through those present as his body faded into mist, leaving only the bindings that were used to hold him.

Jiraiya's danger sense went off, just in time as a large group of ANBU, all wearing blank masks.

Danzo growled as he stood up, flexing his crippled arm, causing the braces to fall off, revealing multiple eyes embedded into it, as well as some strange discoloration.

"I see now," Danzo said, unsheathing his cane, a slightly unhinged tone in his voice, "I see that I can't control things from the shadows anymore. If I wish to have what is owed to me, then I will take it!"

Flashback end…

Tsunade sighed to herself as she remembered the following fight. Danzo was much stronger than she originally believed. The man made incredible use of the implanted sharingan eyes, which acted like a big middle finger to the deceased Uchiha clan.

However, the fight didn't exactly go in his favor, having apparently underestimated how much the people would fight. In the end Danzo lost a good amount of his forces, and was forced to retreat. He wound up using a few of his root ANBU as meat shields to protect himself while he ran. Afterwards, the ANBU continued to fight until they were dead or captured.

Immediately afterwards, Tsunade sent a new file towards the daimyo to add a new criminal to the bingo book, Danzo Shimura. He was a high S-rank bounty with a kill on sight order. She also made sure to Danzo's crimes, thought she made sure to keep what knowledge he knew that could be used against them. She didn't want anyone taking the risk of Danzo taking over their village.

Naruto wasn't officially put into the bingo book himself. However, it was considered an ongoing mission to bring Naruto back. It was considered a high A-rank mission given his importance. If anyone were to ask, tey would respond that Naruto was a person of interest in a high-profile case.

To make things worse, nearly a day afterwards, Sasuke's transport to the blood prison was intercepted and attacked. She quickly dispatched a group of ANBU to deal with the problem. However, it seemed that I wasn't needed as when they arrived Sasuke was found tied up and ready to be imprisoned.

Tsunade smirked at she remembered that part of her and Jiraiya's plan. During the traing trip, Naruto had apparently mentioned how easy it was to steal the forbidden scroll. After that he and Naruto came up with a special seal to be used on it, dubbed the Cerberus lock seal. The seal was a special lock, which could only be opened using the distinct chakra of three people. In the case of the scroll, the hokage and her advisors. If someone tried to use their own chakra, it would turn against them resulting in a crippling injury and letting out a loud siren-like sound. After Inoichi, wiped all the ninja training, from advanced to academy lessons, from Sasuke's mind, Jiraiya applied a version of the seal that could only be opened by his, Inoichi's, and Tsunade's chakra. If someone tried to undo it, the seal would obliterate Sasuke's chakra network.

Tsuande smiled to herself, wishing she could have seen the look on the cycloptic war hawk's face when he found that all his manipulating for Sasuke's behalf had all but failed.

Soon after, Sasuke was escorted to the blood prison where he was locked up.

Even after all that there was still some hard work after that. It took Jiraiya nearly a month to crack the seals that were on the root member's tongues, and it took Inoichi nearly two to crack through the mental conditioning, or as she called it, brainwashing, on the root members. After that they group need to be assimilated into the village, which was rather difficult given how they were shut ins and weren't very social adapted, but they were adapting quickly.

With their brainwashing mostly undone, Danzo's bases were found and exposed. They found out about how Danzo had Itachi murder the Uchiha clan, and how he worked with Orochimaru. Tsuande had been furious when she found out that Danzo had transferred Sharingan eyes into his arms, but also cells from her grandfather! After that, Danzo's bounty almost double overnight.

Tsunade sighed once again before looking out over her village. After the truth of Naruto's parentage came out, several of the civilians were expressing remorse for their actions. Though a few were upset that they had missed out a potential cash cow, the greedier ones anyway, but they made sure not to say such thoughts out loud.

However, things got crazier when word of Naruto's burden spread out as well. The children who had mocked Naruto or listened to their parents to ostracize him, now looked at them with disdain for telling them something without getting all the facts. A lot of parents lost the respect of their kids that day.

Other groups that were affected was the main konoha shinobi.

Kakashi had gone into a depression, by not only not recognizing his sensei's son, but because he had failed so epically. He had officially become an outcast among some of his fellow shinobi and had been demoted to chuunin. And once he got his rank back, if he got it back, he was forbidden from teaching a team again.

Shino and Shikamaru were both upset that they hadn't seen the relationship between the two sooner.

Hinata became slightly depressed as he realized she could have done more when she was a child. It also hardened her reserve to come out of her shell more.

The others now respected Naruto even more, realizing what he went through trying to keep the great beast at bay.

However, out of all of them, the one who seemed to be taking things the hardest was Sakura. The rosette had here entire world shattered after learning of Sasuke's true nature, and of Naruto's burden and how it affected him throughout his life. Sakura regretted every time she punched Naruto just for asking her out, and every time she called him an idiot. Her own self-image as the top kunoichi of the year had always prevented her from seeing how Naruto had grown stronger and more mature, if only just barely, over the years.

Tsunade was pulled from her thoughts about the recent events by the sound of the window opening. Turning towards the noise she sawt he familiar sight of Jiraiya coming in through the window.

"Can't you ever use the door, pervert?" she asked, with a raised eyebrow.

Jiraiya smiled as he said, "And not be able to keep you on your toes, princess?"

Tsunade smiled to herself, glad that Jiraiya could keep up his attempts to cheer her up.

"So, any news from your spy network?" she asked.

Jiraiya's smile quickly became serious as he said, "Well, first off, Sasuke had just recently become a member of solitary confinement in the blood prison. So, I guess we won't be hearing anything about that for a while."

After Danzo's attempt to grab Sasuke from the prison transport, they decided it was best to keep an eye on the boy. Apparently, the harsh reality of prison and no chakra was not doing well for the boy.

"Now, moving on to more important matters," Jiraiya said, "The Akatasuki organization hasn't move in a while, since Naruto's disappearance. My guess is that they are wating for a concrete location on the boy before they make their move on the rest of the Jinchuuriki. My sources still haven't been able to confirm as to why they are after them, however."

Tsunade nodded.

"A man fitting Danzo's description was reported being spotted near the hidden rain village, but it has yet to be confirmed if it is in fact him."

Tsunade rubbed her chin in thought. What would Danzo want with the hidden rain village?

Jiraiya's look took on a somber tone, "And unfortunately, no one has seen hide nor hair of Naruto or the mysterious man who saved him from the retrieval team and the Akatsuki members."

Tsunade sighed, dejectedly. It had been almost five months and there had been no sign of the orange clad knucklehead anywhere. She was starting to wonder if he had been killed.

Jiraiya, seeing her upset, walked over and gave her a small hug.

"Don't worry, Tsunade," he said soothingly, "We'll find him."

Tsuande simply sighed and leaned into the hug, after making sure Jiraiya's hands were staying in the appropriate zones of course.

Meanwhile…in the hidden rain village…

Danzo was starting to curse himself for not planning so far ahead if his plans had been discovered. After escaping his execution, he ran for it. However, his assets were frozen in the village and only a handful of his root ANBU came with him.

His first act was to make sure Sasuke didn't get sent to jail, hoping to use the boy as a puppet. However, he quickly realized that was a mistake as Sasuke had his chakra sealed away and he couldn't undo it. If that wasn't enough, he had bounty hunters on his trail trying to collect the bounty put on his head.

Because of these attacks, Danzo had lost his remaining soldiers and he couldn't risk going near the village to get more. Not to mention, the money had had saved in case he need to move from the village was running low.

He couldn't risk going to the major villages, as they would no doubt be privy to his necessary actions back in Konoha. So, now he was in a village that would probably not know of his crimes. One that hadn't been a part of any alliances for a very long time.

So now, Danzo stood before the kage of the hidden rain village.

The orange haired man, with piercings in his nose, and strange eyes looked at him, with a blank expression.

"You wish for us to take you into the village?" Pain's deva path asked, as he looked at the man.

Unknown to Danzo, the Akatsuki's own spy network had found out about Danzo's crimes and they had no doubt that he would try to play the master manipulator here.

"Yes," Danzo answered, "I have knowledge that could be very useful to you."

The path looked at him for a moment and said, "I'm sorry, but I cannot allow an S-rank criminal into my village, or can I even begin to trust that one who is as manipulative as you to keep your word."

Danzo's visible eye narrowed. He activated the sharingan eye behind his bandages to try and control the man. This proved to be a huge mistake.

In puffs of smoke, the preta and naraka paths appeared.

The preta path grabbed Danzo's face tearing off the bandages covering his stolen eye. The chakra was ripped from his eye, ending the potential genjutsu. The Naraka path then grabbed Danzo by the neck and hauled him into the air.

Danzo found himself paralyzed. With a simple thought, the Naraka path performed a summoning, bringin gout a large pale head with bizarre eyes and surrounded by dark purple flames. The head opened its mouth and a tendril shot out, connecting with Danzo's back. Danzo's eyes, real and implanted became blank.

"Now then," the deva path said, "Tell us everything that you know."

Danzo proceeded to spill his guts about everything. How many he had, his money, his contact with Orochimaru, even the specialized dead man seal tha the had on his chest. Thanks to the Naraka path, nothing was kept secret.

With that done, the Deva path grew a black rod from his hand and proceed to swing, severing Danzo's head, from his body. The preta path then proceeded to drain every drop of chakra from the man, preventing the use of the powerful seal he had on his chest.

"Pain-sama," a voice said.

Everyone turned to see Zetsu standing on the windowsill, "I sensed something strange, what has…Oh."

The plant man calmed down upon seeing the dead form of Danzo. Then he cocked his head to the side and asked, "Who is that?"

The extension of Nagato's will answered, "Just a fool thinking he could manipulate a god. You may consume him if you want."

If Pain wasn't so good at hiding his emotions, he would have ripped Danzo apart. As it turns out, he had helped Hanzo the Salamander years ago during the shinobi war and had been perfectly fine with ruining the lives of several people. If he wasn't so good at hiding his emotions, he would have destroyed the man on the spot, with not even ashes being left. However, he felt more content to see man who thought himself untouchable being used as food for Zetsu.

The plant man got down from the window and walked over. He sniffed a bit and said, "Nah…too old. He'll be too chewy. Plus, insanity leaves a terrible aftertaste."

The paths had to suppress a shudder as the plant man said this.

"Throw the body away then," the deva path said, "I do not wish to dirty my office with such filth longer than necessary."

Zetsu leaned down and examined the body for a moment. Suddenly, a disturbing grin spread across the man's face, well the white half of it anyway.

"I think I might have an idea for that," Zetsu said, gaining the attention of the paths.

Cut! Okay, that was a little harder to write than I thought. Anyway, now Danzo is dead, the Akatsuki is biding their time, and Naruto is getting an upgrade. I hope you all enjoyed this chapter. What does Zetsu plan to do with the body of Danzo? What does this mean for the future? What else is going to happen? Well, just keep reading and you'll find out.

Merlin is now working on Naruto's nanite upgrade, while he works on some new tools and weapons for Naruto. If there is a particularly awesome sci-fi weapon or feature you think should be featured in the armor or if there is a specific weapon you want to see, please, let me know in the comments or PM me. Let me know what you think.

Criticism is welcome, flames will be ignored.