Silence in the Skies

by greyblueflames98

Torn from his world, altered against his will by a motionless machine only to be saved by another, Naruto finds himself a stranger on a new world where he blends in perfectly. Not one to sit by, he joins his savior in the fight to save his new home from the Decepticons. Rated T for now. Cover by Koniak007

3. Chapter 3: Project Reprisal

Silence In the Skies

"Speech"/ " Thoughts"

"Tailed-Beast speech/ " Thoughts"

AN at bottom.

Japanese will be between ] and Cybertronian between { } to differentiate between "English."

Going to answer the guest reviews here.

1st guest: Yes, Naruto was taken after he fought Sasuke for the first time at vote.

2nd guest: Yes, a million solar cycles is the Cybertronian equivalent to a year. Chapter three will show what happened to Naruto's world. It ain't pretty.

TRIGGER WARNING: ATTEMPTED SUICIDE IN THIS CHAPTER. WARNING WILL BE GIVEN BEFORE IT OCCURS.

Chapter 3: Project Reprisal

Ratchet stood off to the side, facing his leader and longtime friend, who turned back while he slowly read the contents of a datapad. This device contained all the recently-decrypted files stolen from Shockwave, organized chronologically for ease of examination. The medic watched as the last Prime stood still as a statue, datapad in one hand, the other clenched tightly at his side. Optimus possessed an amazing amount of control over his emotions, but for Ratchet, this stillness was actually the only sign needed for him to know his Commander's emotional state.

Put simply: Optimus Prime was angry. Very angry.

His mood had started off calm when he began reading, Ratchet placed contextual information regarding Naruto's world, which had been dubbed 'Elementia' by other species in the galactic sector before Shockwave's notes on the experiment. This planet possessed a unique energy known as 'chakra', which served as the life-force and internal energy of all organisms and the world itself. Civilization there seemed to be incredibly young—its history only going back a thousand solar revolutions, and almost entirely filled with war, much to the Prime's disappointment.

Of course, he knew he was in no position to judge, given his species had engaged in a multi-million year long Civil War which had destroyed not only their own world Cybertron, but also countless others. Despite those undeniable facts, the leader couldn't help but feel disappointed such a young civilization turned to violence so often. His frown lessened as he went through supplemental videos and pictures, showing these humans controlling the elements through their mastery of their internal energy. Optimus was reminded of how his own kind used their own lifeblood—Energon—for ammunition, fuel, and currency at times, even sharing the risk of ceasing to function if they ran out.

Unfortunately, these visual aids and minor text were the only information salvageable regarding Naruto's world, with the only information on the boy so far being his birthplace: 'Konohagakure', or Village Hidden in the Leaves. Prime saw an image taken from orbit, showing a small city surrounded by a sea of green and a mountain with four faces carved into it. The sight reminded Optimus of Mount Rushmore, a monument with the intent to honor four important figures from their main human ally's—the military of the United States of America—history. Briefly wondering if the purpose was the same, Prime steeled himself as he started to delve into how Shockwave captured and processed the inhabitants of Elementia.

The Decepticon scientist relied on stasis technology to freeze large groups in place, special care taken not to turn off the beam until each individual had their hands removed to prevent use of elemental manipulation through chakra via the "hand seals" they relied on. A ruthlessly logical method to ensure no one could resist from within—typical of Shockwave. After removing their hands, the prisoners possessing the highest amount of chakra were immediately taken to have their chakra drained entirely, whereas the others were essentially put in a pen until a spot in the processing chamber opened. Until then, they were fed small, flavorless cubes filled with enough nutrients to prevent premature death, but kept the prisoners too weak to resist.

Not like they could without their hands…

{Pink alchemy usually requires thousands of organics just to make a single cube of Energon, yet the chakra of these humans cuts the amount down to between one-hundred to one-hundred-fifty needed, with noticeable individuals possessing enough chakra to fill half a cube by themselves…} Optimus read directly from Shockwave's notes, fist clenched tight enough to dent his plating. Further reading increased his indignation when he learned drained husks were callously thrown into an airlock until full, then simply jettisoned into space without a thought. Oddly, there were numerous individuals Shockwave refused to abduct, instead choosing to monitor their locations from orbit despite their immense chakra capacity—one such individual being deemed too hazardous to even exist, prompting Shockwave to unleash an antimatter charge, followed by an oxygen bomb, on top of continuous orbital bombardment to ensure his death along with the surrounding village.

{How powerful was this 'Pain' for Shockwave to respond so drastically?} Optimus questioned. Unfortunately, this was the last bit of information available on the Decepticon scientist's harvesting of the population of Elementia, the rest of the data lost to corruption. Moving on, Optimus now read into the strange red spacebridge Windblade told him of during their prior conversation. This spacebridge was designed to run on chakra from a powerful secondary source found within Naruto—known as C4-621 "Reprisal" in the notes.

{Just what was Shockwave attempting to harness?} Optimus wondered, recalling the immense energy signature which emanated from Naruto as he slept in the pod. Putting this aside for now, Optimus learned this secondary chakra possessed a highly corrosive nature, wear on instruments and their components noticeably accelerated along with random glitches, yet those same devices operated with a fifty percent increase in output. As such, Shockwave heavily modified the nearby spacebridge to withstand the strain, curious to see if there were any improvements or unexpected effects to be found.

Shockwave wouldn't learn anything, as before proper testing could be done, he would lose the source of energy. Given Windblade's testimony and the data from her ship, it stood to reason Shockwave was about to discover a method for time travel… Optimus dared not even consider what he would do with such power, let alone Megatron. Resuming his reading, Optimus now reached the information he wanted to know most: Exactly what did Shockwave do to Naruto—and if possible, could they reverse it?

The first of many modifications which had forced been upon Naruto was a pair of mechanical hands to replace the ones severed upon his capture. These prosthetics were specifically designed to allow chakra to flow through them, but a failsafe had been installed which would cause them to lock up if Naruto attempted to form any hand seals. Second, Shockwave implanted a device meant to translate the chemicals and electrical signals deep inside Naruto's brain, and transfer the data via cable connection from a port installed at the back of Naruto's skull. Thirdly, Shockwave placed Energon filters in key locations throughout Naruto's body, such as his major arteries, heart, and bone marrow centers. All of these filters were surgically placed inside the young human at the same time, their effectiveness already tested on less fortunate subjects while, Shockwave waited until he had everything prepared for his desired specimen.

So far, everything was meant to monitor Naruto's body and provide signs if any implant started to have a negative effect on him. Shockwave planned to start genetic modification, when Naruto acted in defiance of his situation right after he awoke from the third surgery.

(AN: TRIGGER WARNING. SKIP TO NEXT AN)

{He attempted self-termination?!}

Optimus read with wide optics, as Shockwave described Naruto thrust the replacement hands into his ribcage, weak bone easily splintered by superior Cybertronian metal. He directly pierced both his lungs and heart, messily yanked both hands out with middle digits raised, directing a bloody grin at Shockwave as he choked on his own life fluid. It was a brazen move, done directly in front of his tormentor as an insult. Shockwave admitted he had not expected such an action to be done in his presence; however, Naruto's timing actually worked against him.

(AN: ITS SAFE TO CONTINUE READING)

Hardly a stranger to such attempts occurring, surrounded by medical equipment and disturbingly familiar with the human body, Shockwave had already gotten to work on fixing Naruto before he even lost consciousness. Aided by the secondary chakra within Naruto, the logic-driven scientist managed to prevent his death at the expense of a loss of sixty percent organ efficiency. This would have complicated further modification, but Shockwave was unfazed, deciding instead to replace all three organs with far superior mechanical copies unimpeded by the limits of plain flesh. Of course, Shockwave knew Naruto was likely to attempt to tear those out as well, which led to another so-called 'upgrade' to the boy's body.

Tapping on a video taken from Shockwave's perspective, Optimus saw the foreboding sight of Naruto, stasis-cuffed to a slab of metal, lowered into a rectangular tank of water slightly bigger than him. Multiple instruments, including a breathing tube, were attached to his immobile form. A horrific device bearing multiple arms tipped with thin drills loomed above the submerged youth, tubes connected the drills to an ominous metal canister. Shockwave's gaze drifted to a monitor showing a feed of Naruto's skeleton, then went to another screen displaying the canister, the temperature of what was inside and a percentage of its capacity.

Optimus paused the video and gave the frozen image a hard stare for a few moments to read the listed contents, before he turned to Ratchet with dim optics and a deep frown. {Please- tell me I'm reading this wrong.}

A somewhat uncomfortable feeling crept into Ratchet's tank as he stepped forward, looked at the screen and froze immediately. He double-, then triple-checked to make sure his optics weren't malfunctioning.

{…play the video. It's entirely possible this is nothing more than a threat to keep the organic in line,} Ratchet suggested, unable to believe the scene developing. No organic could survive such a… Ratchet wasn't even sure what to call this insanity Shockwave was about to conduct!

Optimus resumed the video, Shockwave's deep monotone voice heard through the datapad's speakers.

{Previously-injected nanites have arrived inside the braincase, spinal column and long bones—beginning complete transmutation of calcium-based skeletal system to one of comprised of Sparked/chakra-Metal alloy.}

Shockwave's optic went to the multi-armed machine as it hummed to life, arms moving into position as Shockwave continued speaking, drills slowly descending into the cold liquid.

{Metal temperature well-within acceptable levels… nanites ready to protect brain and spinal cord… Commence injection.}

The drills slowly pierced Naruto's skin, speeding up as they churned though meat until they met bone, tunneling deep inside before releasing the molten metal. Shockwave turned to a monitor displaying multiple feeds from within Naruto's body, swarms of nanites performing one of four tasks. A vast majority spread the metal evenly throughout the skeleton, except for the bone marrow centers responsible for the creation of red blood cells. Some protected the brain from overheating by cooling the surrounding blood, while other nanites altered the structure of the vertebrae to better protect the spinal cord. Lastly, the nanites reinforced Naruto's ribcage, covering the gaps with a strong network of overlapping plates meant not to hamper mobility, while completely protecting his vital organs. The entire process finished within a few minutes, monitors showed the canister empty, bones once a pearly white quickly cooled to a dull metallic gray with nanite assistance.

Shockwave lazily glanced at Naruto's failing vitals turning completely flat for an entire minute, the sight causing both Autobots optics to widen as they knew this meant a human had perished. Shockwave did nothing, however, merely adjusting his helm to watch the deathly still body. A red aura, small at first, began to leech out from Naruto's lifeless body, spreading like an unrestricted fire.

Shockwave noticed a twitch, followed by a single beep from the prior monitor. Shockwave went back to the monitor, watching each vital quickly return to normal levels. The aura soon faded away, the water steaming from the intensity.

{As expected, the Kyūbi won't let the host die if the body hasn't been gutted or decapitated. This will be useful in the coming muscle fiber and genetic modifications. A month's worth of monitoring will be-}

{Shockwave! What blasphemy against Primus have you created this time?!}

The feed cut after Shockwave turned to see two heavy-framed Decepticons fliers, recognizing them as Dreadwing and Skyquake, approach with optics blazing indignation and disgust. Both Autobots were in stunned silence at the end of the video, Ratchet in particular felt a swarm of questions buzz around his processor. Where did Shockwave get Sparked-Metal? Were the nanites still inside the organic? Why was Shockwave investing so much in a single individual when he planned on cloning him? Wouldn't they all possess that strange red energy?

{None of it is reversible, is it?}

Lost in thought, Ratchet nearly failed to hear Optimus, momentarily swallowed his shock and disgust at the video to confirm Prime's inquiry.

{There's nothing I can do which wouldn't kill him, even if I had my lab from before the war,} the medic admitted, adding, {And I'm only talking about the chips in his head. His internals and skeleton? Only the ancients could hope to reverse that.}

Optimus gave a solemn nod in response before he resumed reading, Ratchet doing the same at his own pace. Now digging into the genetic half of the modifications, they were surprised to learn the governments of Naruto world possessed a rather impressive understanding of their species' genetics, given their lack of advanced technology. Their various experiments on transplanting genetic anomalies known as 'Kekkei Genkai' to other individuals, allowing them to use rather unique abilities—one granting creation of crystals at will.

{Well, that explains how Shockwave mapped out their genome so fast—they did the foundational work for him!} Ratchet commented with an annoyed huff.

{And gave him the idea in the first place.} Optimus pointed out as he showed his friend pictures and a report of a largely failed attempt to infuse a group of sixty individuals with the power to control wood, resulting in a single survivor. Shockwave deduced it was their inadequate level of technology and the chosen subjects lacking compatibility with the introduced genes which was responsible for their failure. Utilizing far superior Cybertronian technology and his own vast understanding of genetics, Shockwave quickly figured out how to pass on these genetic anomalies to whomever possessed a moderate compatibility, with minimal risk to the recipient. The Kekkei Genkai known as 'Crystal Release' proved easy to modify, requiring a mere cycle to splice the needed CNA in to allow future test subjects bodies the ability to recognize, produce and manipulate Energon.

It was here when Energon's high toxicity to organics quickly became a big problem, as subjects died within weeks of implantation of the modified Crystal Release, even with the previously mentioned filters installed.

{Scrap, the rest of this section is corrupted,} Ratchet swore in irritation as he stared at an illegible mess of symbols. Cutting ahead to the next section, the pair were disappointed to find no information on further modifications, only reports on Naruto's ability to create Energon, notes on how to properly care for his unique needs, and some personal information.

{He needs approximately a cup of Energon a day to maintain his implants, and must have his filters cleaned at least once a lunar cycle or as needed depending, on the level of Energon in his body…} Ratchet read, groaning as he realized he'd need to learn human anatomy and figure out how to service his mechanical components. Optimus, despite the situation, felt the smallest tinge of amusement at seeing his long-time friend gripe over now having to care for an artificial techno-organic, before it vanished as he looked at Naruto's information.

{Only fourteen years old, yet you've survived events which would've broken even the hardiest soldiers I've served with…} Optimus somberly observed when he learned Naruto's exact age, idly taking note of the Cybertronian date on the log, so they could give Fowler an accurate date of birth to help form the boy's new identity later. He also saw multiple images of Naruto from before he was abducted, the person in the last seeming much happier from the one he saw earlier. His vibrant blond hair was a wild mane made of numerous spikes, skin a healthy shade of pink, and a broad smile full of brilliant white teeth.

Optimus paused as his optics went to Naruto's previously sky-blue eyes, noticing a glint of loneliness in his gaze, followed by realizing his smile didn't quite reach his eyes. The other pictures had not given Prime a clear view of his face, mainly showing the boy engaged in some kind of training, the rest being corrupted from an incomplete download. Still, he saw enough to want to know more about who Naruto was before Shockwave.

{Optimus, I'm going to see if I can restore any of the corrupted files; we need more information, and I doubt he'll submit to a scan.}

Optimus gave a curt nod in response, wishing Ratchet success before departing to where the subject of their study sat. Fowler and Windblade seemed to have made some progress with Naruto as he was out of the bodysuit Shockwave dressed him in, now wearing socks, black pajama pants, and a red shirt with sleeves reaching halfway down his hands. His attention was currently occupied by the video playing on Fowler's tablet, the agent sat next to the boy as they watched what sounded like an Earth "cartoon". Windblade rose to give Prime a respectful bow, before approaching her Commander.

{Welcome back, Sir, did you find the information you seek?}

"While we learned much of what Shockwave did to Naruto, I'm afraid too much is still unclear, and nothing is reversible," Optimus shared, speaking in English so Fowler would also hear the latest information.

"Ratchet is attempting to restore some of the corrupted files, but I fear we still will not know everything Shockwave changed, nor how he planned on mass production of the clones."

Windblade nodded in understanding, apologizing for the situation with a regretful smile.

"My team and I just didn't have enough time."

"There is nothing to apologize for. It is thanks to their sacrifice the boy is free, and not a Decepticon slave." Optimus Prime reminded Windblade with a gentle smile, which she returned with a nod. Both turned to the smaller beings, Optimus inquired how Naruto was while he was with Ratchet. The femme faced the taller mech before answering, wings lowered nervously.

"I took him outside," Windblade admitted without hesitance, stating she was entirely prepared to be reprimanded for this unauthorized action.

"How was he?" Optimus inquired, slight concern in his optics.

"He initially refused my offer to carry him, but relented when the walk up proved too strenuous for him," Windblade began to summarize her time in the sun with Naruto, starting with his immediate tearing of the bodysuit to allow more of his body to soak up the life-giving rays. She then told Optimus of the multitude of scars he possessed.

"The majority were surgical, but a number were definitely combat-related, and micro-scars circle his wrists, leading me to be believe Shockwave replaced his hands with prosthetics."

"You are unfortunately correct," Optimus confirmed, before he informed her Naruto's species' primary way of manipulating their internal energy, revealing it was called 'chakra', was through their hands. Windblade's optics widened in horror as Optimus told her Shockwave's method of eliminating the danger this posed to him.

"You and the others will receive datapads containing all the information we have on Project Reprisal sometime later today. Steel yourself, as there are images which are… disturbing." Optimus finished with a warning, his own processor going back to Naruto being in the tank as the needles plunged into his flesh. Mentally shaking that particular scene out of focus, Optimus asked if anything else of note occurred while they were topside.

"Naruto admitted he planned on fleeing, but realized he had nowhere to go, and his body couldn't make the trip. I told him we only want to help, but he thinks we just want to take advantage of the Energon he can produce." Her wings dipped a bit, saddened to be seen with the same lens as the Decepticons.

"I have no desire to use the suffering of another to aid this team in any way or form, nor will I allow any attempt to be made. It is not the Autobot way." Prime firmly denied the possibility of such thought.

"I told him as much when I said we'd earn his trust."

Windblade received a nod of agreement from the larger Cybertronian, unaware he told Naruto the same words earlier. He then told Windblade there would be no discipline for her actions, but to tell him next time Naruto wanted to be outside, switching to their language for the remainder of the conversation.

{I am pleased to see you have taken the first step towards a more amiable relationship with Naruto, one I hope helps him on the path towards healing.}

{You would too, if you found him how I did,} Windblade stated with a wince at the memory. Stasis-cuffed and chained to a table with multiple straps, keeping his head and body still as clamps held his eyes open was the scene she walked into, only Primus knew what Shockwave planned to do. The sheer terror she saw embedded in his expression would haunt her processor for vorns.

{It would be wrong of me to get him out of there, then just leave him on his own.}

Optimus remained silent for a moment. {Then I suppose you wouldn't mind if I ask you to be his guardian?}

Windblade's optics held a questioning gaze, silently asking for an explanation.

{Given how unfamiliar this world is to Naruto, and the Decepticons will undoubtedly detect his energy-signature, I feel it would be best if he had an Autobot with him when he eventually is able to interact with the natives.}

{I understand the assignment, but I have no knowledge of this world or its customs. Would not one of the others be a better choice?} Windblade respectfully suggested. Optimus, however, shook his head negatively, agreeing with her first point but explained she was the best option for this task.

{You have already laid a small foundation on which trust can be built and deepened. Naruto accepts your presence, and—to a degree—is comfortable speaking to you. As the humans would say, you've already got the ball rolling.}

{You aren't wrong,} Windblade agreed with a browplate raised at the alien expression Prime used. She turned to the subject of their conversation. He didn't appear too interested in what Fowler showed him, but seemed to be humoring the man's attempt at entertaining him, a rather convincing smile on his face, yet the emotions in his eyes hadn't changed from before. Hurt and loneliness ringed with a cold defiance. The gaze of one bent beyond the breaking point, yet somehow holding on for a reason only they knew.

It was almost as impressive as it was sad, especially considering his youth.

{I guess it was already decided when I found him, he's my responsibility,} Windblade stated in acceptance of her new role. Optimus gave her a small smile, before he called Fowler over to him, the agent offering Naruto his device to which he declined, expression stagnant until Fowler stood, turned his back and walked away. Naruto let out a deep sigh as he dropped the smile, slight pain in his facial muscles from holding them in a long unused expression for an extended period. A part of him wondered why he even bothered faking it while the rest was just glad for the stimulation and distraction.

Meanwhile, Fowler had reached the two Autobots and climbed up a ladder leading to a raised area more level with the larger beings, though they still needed to tilt their helms down to look at him. Optimus quickly filled the agent in on Windblade's new role as Naruto's guardian, and told him he would receive a copy of the information they recovered from Shockwave before long.

"I will warn you, it's contents are rather disturbing," Optimus advised his human ally with a grim expression and tone.

"If it's got you upset, then I'll be sure to prep myself," Fowler replied with a pinch of his nose. Turning to Windblade, he gave her his contact information to use whenever she needed.

"Let me know whenever you need money for food, clothes, toiletries and I'll pick it up until he is ready to get them himself," Fowler explained, adding, "I'll try to help out where I can when the trauma starts manifesting, but I doubt even an expert will be much help given his situation…"

Windblade nodded in thanks at his support with a half-Sparked smile, entirely aware her new assignment entailed much more than just bodyguard work. She didn't mind. After millions of years of war, helping to restore someone was a welcome change of pace. Their planning continued for almost half an hour, until Fowler was contacted to deal with an unrelated matter to the Autobots. Before leaving, the agent returned to Naruto, taking a sleeping bag out of a duffel bag, then showed him which bag held a toothbrush and some toothpaste. Lastly, Naruto was shown the location of a few bathrooms, most placed on the upper-level Fowler used to stay off the ground and level with the Autobots sight, the boy moving up there to roost.

A few hours had passed following Fowler's departure, Ratchet having little success in restoring the corrupted files. That wasn't to say what he did recovered was irrelevant. On the contrary, possessing the schematics for the mechanical organs, prosthetic hands and Energon filters were invaluable assets, allowing the medic to study their design to familiarize himself with how they worked, tolerances, make replicas he could practice on, and create replacement parts should the need arise. The schematics aside, nothing answered any questions they had.

After getting everything he could, Ratchet proceeded to add this new information to the data already collected and edited the contents into a clear, easy-to-understand record of everything Shockwave had done to Naruto and the people of his world. Ratchet reworded quite a few sections which contained too much graphic detail, leaving enough for what happened to be recognized. A select few images and videos remained in as they best represented what occurred. Despite his edits, Ratchet knew some of his fellows would be rather disturbed by the contents even he, a seasoned medic who has seen the absolute worst of their war, was appalled to view.

{But they have to know,} Ratchet told himself as he transferred the finished product into multiple datapads. {Because this boy—this artificial techno-organic—can quite easily threaten us. I get the feeling Shockwave's endgame wasn't just a source of Energon, but a weapon we'd never see coming.}

Kyūbi. That was the name Shockwave referred to the red energy as… It meant 'Nine-Tails' in the English language.

Stacking the datapads in his manipulator, Ratchet went to pass them out to the others so they would be well-informed about the new addition to their headquarters. The medic found his comrades easily enough, advising they read in private before handing each individual a pad. On his way back to the medical office, Ratchet entered the command center, optics zeroing in on Naruto's shifting form tucked into the sleeping bag. Turning up the sensitivity of his audio receptors, Ratchet picked up unfocused muttering from him.

[Coward… too afraid… should be… your fault…]

At first, Ratchet figured the techno-organic was simply talking during recharge, but his next words were of immediate interest.

[Bastard Nine-Tails…]

There was that phrase again! Shockwave had earlier credited the energy he called "Kyūbi" for reviving Naruto, who now cursed it.

{I'm being to think this Kyūbi is something we need to know about.}

Casting an uncertain look at Naruto, Ratchet returned his hearing to normal before leaving with an uneasy feeling growing in his Spark. Too much was unknown about this individual, restoring those files now high on Ratchet's to-do list.

CHAPTER OVER!

I told you guys the next chapter would come sooner! It's admittedly shorter than what I usually write but I don't mind given it's contents.

Speaking of, Shockwave really went and turned the people of Naruto's world into cattle. I know some may dislike how this was done but I think it's what Shockwave would do. No hands means no jutsu for the overwhelming majority of shinobi. Of course there are exceptions like those Shockwave only monitored and then you have Pain who got the "Screw you and everything around you" treatment.

Also pink alchemy is actually a thing in the IDW Transformers comics which I am taking quite a bit from. Nasty process, if I remember correctly it was also called "Bleeding the meat."

Poor Naruto! He got the wolverine treatment with a few extra steps thrown in! Those of you wanting him to be a techno-organic must be happy. Now if only Ratchet can fix those files… you guys might be able to see Shockwave's final plan for Naruto but alas! Guess you'll have to wait to find out.

Oh, and TFcon was great! My wallet hates me right now but at least it's not as bad as last year!

Anyway, read and review! Tell which Bots and Cons you guys are hoping show up cause I'm adding quite a few from multiple different continuities.

Greyblueflames burning out!