This story came about because there are so few Naruto/Hulk crossovers and so I decided to increase the number slightly.
However, after getting into Chapter 2, I realized I had essentially trodden the same path with Kitsune's Power, so I stopped and placed it here in the hopes it would inspire others.
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Prologue
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-SHIELD report H-559150
-Subject: Bruce Banner/Hulk
-Location: Goodnews Bay (Alaska, USA, 59.07N 161.34E)
Subject Banner has been tracked to the city of Goodnews Bay where he purchased the house of a recently-deceased local (see file Z-151990 for details on individual in question).
Subject Banner proceeded to introduce himself as Doctor Bruce and proved his medical credentials by diagnosing one local who had an illness that the local doctor was unable to identify. Subject Banner then aided local doctor in procuring required medicine, exchanging medical knowledge in the process. Since local doctor was near retirement age, Subject Banner was recruited as new local doctor.
Subject Banner utilised basement of new house as lab, constructing equipment of designs previously not encountered by observer (see attached picture file BM1 for details). Power levels into house were noted as averaging 192% of normal power level for single-occupant.
After three months, power readings spiked briefly to 385% of normal usage, then dropped to 105%. At the time of the spike, sensors created by Reed Richards of the Fantastic Four and covertly placed around Subject Banner's home detected the brief formation of a Portal. Analysis of readings indicates the Portal was of a sort only capable of transporting energy, not matter. The purpose of the portal remains unknown.
-Special Notes
Asset Reed Richards has identified one of the unknown machines as being superficially similar to the de-powering device he constructed during the early days of the Fantastic Four (for the use of Ben Grimm/The Thing). Said device overloaded beyond repair after two uses and Ben Grimm has since requested the machine not be rebuilt. It is unknown if or how Subject Banner gained access to the blueprints of the machine.
The sensors deployed around the house confirm that Subject Banner no longer possesses the internal gamma-ray circulatory system that he had possessed prior to the energy spike. Observers have noted Banner becoming angry on several occasions, in each case the transformation did not occur.
-Conclusion
Subject Banner is no longer capable of transformation into the Hulk.
Subject Banner's active usefulness is now only as a scientist.
Due to advances in scientific departments of SHIELD, Subject Banner's status as an asset is rated only 2.4.
-Suggestions
To make General Thaddeus Ross better disposed to SHIELD, Subject Banner's location could be divulged to him. Without the ability to transform into the Hulk, Subject Banner will be unable to escape or successfully resist. Once Subject Banner has been captured by General Ross, General Ross will be more capable of focussing on other potential threats, thus allowing him to be utilized in suppressing the insurgency led by Steve Rogers.
Once in captivity, Subject Banner can be interrogated for details of the machines he constructed including their purpose and whether or not they can be used to generate Gamma-enhanced operatives.
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-Internal Memo
-SHIELD Headquarters
Banner is to be arrested and charged with treason for destroying a valuable asset (the Hulk).
Upon conviction, he is to be transported to Black-Lab 7 for full debriefing and interrogation prior to neurological re-calibration to instill total loyalty to SHIELD.
Special focus during interrogation is to be directed towards the utilization of Gamma Rays to induce meta-human capabilities.
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-Internal Memo
-SHIELD Headquarters
Banner was captured as planned, but was removed from custody during transit by forces loyal to the traitor Steve Rogers.
At present, Banner's location remains unknown.
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The Sealing
The rampaging monster howled, the sound echoing through the woodlands and causing many of the shinobi semi-concealed in the braches to wince or even briefly cover their ears.
"Hold the line!" Sarutobi shouted as he motioned for the fifteenth squad to move left. "I want walls to trip it up and check for any civilians still in the area! Where the hell are the Uchiha? We need the Sharingan users, one of them might be able to control it like Madara did!"
The ground shattered as the Kyuubi slammed its paw down and Sarutobi rode the resulting groundwave, using it to power himself into the waving trees and anchoring himself with a reflexive use of chakra.
"Where's Minato?" He asked the Anbu who had materialized by his side.
"He's getting his equipment."
Sarutobi leapt off the branch just as another howl from the Kyuubi caused it to shatter.
"He'd better hurry, we're losing too many of our shinobi!"
The nearby impact of one of the Akamichi clan who had tried to use his expansion-jutsu to uppercut the Kyuubi and received a tail-slam that knocked him off his feet went almost un-noticed except as a mental note that the Konoha forces had suffered yet another casualty.
"Kunai barrage!" Sarutobi commanded and a veritable wall of pointy metal hurtled towards the Kyuubi's head, only to be harmlessly deflected by yet another roar.
"Where the hell are you, Minato?" Sarutobi whispered, then his question was answered by the appearance of a gigantic toad, almost as large as the nine-tailled monster. Perched atop its head was the familiar figure of the Hokage and from his position, Sarutobi could see that he was holding something in his arms.
"Minato… what are you doing?"
His answer came an instant later when space seemed to warp and twist before snapping back showing that Minato, Gamabunta and the Kyuubi had all vanished.
"Start evacuating the wounded and get sentries posted!" Sarutobi ordered, then he looked at the shattered wreckage that marked where a healthy forest had been mere hours previously.
"I hope you have a plan, Minato." He whispered, then a net of chakra chains lashed out from a distant cave just as the Kyuubi appeared in exactly the right position to be caught. A glow of white light built up, engulfing the restrained Biju, then it suddenly flared green before it faded to reveal that the Kyuubi was no longer there.
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Fuuinjutsu is one of the least-practiced skills of the Shinobi.
A skilled Fuuinjutsu Master is almost unbeatable on the battlefield if he has had time to prepare. Seals can, with enough preparation, do almost anything. They can create pocket dimensions to store things in. They can siphon off chakra, store it and then use it to replenish a person's chakra resevoirs. Anchoring genjutsus, changing battlefields, summoning, explosions… the only true limit is the imagination.
But Fuuinjutsu is notoriously difficult to understand.
At the basic levels, it is easy. Storage scrolls, explosive tags, these can be created by anyone who has a steady hand and training in calligraphy.
The more complex seals, though, are an entirely different level of difficulty. At the level of Master, the seals warp space, time and reality itself to perform their designed tasks. The interaction between different Seals can range from unnoticeable to a localized reality-storm where anyone who enters may not be the same shape if they actually manage to leave.
The act of twisting reality can cause other effects. The Seal that imprisoned the Kyuubi into the body of the Fourth Hokage's Son was a work of art, even by Seal standards. Every brush stroke had been perfect. Every line of ink placed exactly right.
But the Seal had acted in other dimensions as well. And part of it had existed at exactly the right time and place in the realm between realities to intercept a bolt of energy.
The Seal did its job and the energy was contained.
But the effects would shake the world.
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Feeling every single year of his age (and then more besides), Sarutobi Hiruzen slowly sat down behind the desk that he had once happily handed responsibility for to his successor and now was forced to reclaim. Glancing across, his gaze came to rest on the small basket that held the only living being found in the cave. Discovered cradled in the arms of his deceased parents and with the corpse of Hiruzen's wife Biwako near the entrance, Namikaze Naruto lay quietly, only the occasional soft murmer showing that he was asleep and not dead.
"What can I do?" Hiruzen sighed sadly, looking at the innocent child.
Silence was his only answer and Hiruzen looked at the pile of papers that had been placed on his desk, the papers holding the list of the injured or slain.
"Is that the new vessel?" A voice intruded and Hiruzen looked up to see Utatane Koharu entering, her gaze fixed on Naruto. Behind her, Mitokado Homura finished cleaning his glasses and donned them once more.
"We need you to take the Hat." He stated calmly. "Our enemies will be moving against us, we need you back as Hokage."
"I know." Hiruzen sighed. "I had hoped that… yes. I will hold the Hat… for now."
Homura followed Hiruzen's glance and his eyebrows lifted.
"Is that…?"
"Namikaze Naruto." Hiruzen confirmed.
"Are you trying to get him killed?" Koharu snapped, spinning to scowl at him. "You let him have his father's name, he won't live to see his first birthday!"
"He needs a clan name." Hiruzen protested. "Without one, he'll never be allowed to follow in his father's footsteps."
"You see him as a future Hokage? Already?" Homura asked curiously and Hiruzen started to answer, only to be interrupted.
"Uzumaki Naruto." Koharu declared. "While his mother was a troublemaker, prankster and not capable of being quiet, she was still the last true Uzumaki and since he doesn't have her red hair, everyone outside Konoha will decide that we simply named him that to honor the Uzumaki clan."
Hiruzen sighed again, but slowly nodded in agreement.
"We need to keep him hidden." Homura mused. "Obscurity would be the best bet. Treat him like any other orphan, but keep a few ANBU nearby to ensure that no-one attempts to harm him."
"Or I can hide him for you." A new voice spoke and all three adults turned to see the one-eyed leader of ROOT entering. "I can have him raised as the perfect weapon, using the power of the Kyuubi for the good of Konoha."
"How did you know of the beast sealed within him?" Hiruzen demanded, his insides congealing as the magnitude of the potential disaster looming ahead of him registered.
"The news is all over the village." Danzo countered. "I heard it from three different people on my way here."
"Then I have no choice." Hiruzen declared. "As Hokage, I hereby declare that as from dawn tomorrow, it shall be treason for anyone to discuss Naruto's burden with one who does not know. The only exceptions to this law shall be myself as Hokage, or whosoever takes the position after myself, and Naruto himself. ANBU! Spread the word that I shall make an announcement at sunset… and that everyone should be there!"
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The Hokage's Law prevented parents from telling their children about the burden placed on young Uzumaki Naruto, but it did not stop them from warning their offspring to avoid the blond orphan.
In an attempt to try and give the Fourth's son a chance at a decent life, Hiruzen arranged for Naruto to receive his own apartment and a regular stipend. Hiruzen's old friend Teuchi and his daughter Ayame agreed to keep an eye out for Naruto and in return, Hiruzen gave them the deeds to the property they were renting for their Ramen stand as well as a regular infusion of cash towards the food that they gave Naruto, food that Teuchi often covertly slipped powdered ANBU vitamin-pills into to help Naruto remain healthy.
And so Naruto grew over the years, doing his utmost to remain cheerful despite how often people turned away from him or simply ignored him and he never once lost his temper.
Until the events after his failure to graduate from the Academy once again…