Welcome to another fanfiction of mine, this is Difference of Shadows except done differently, I felt that the plot was being messy, I mean, would it actually make sense to end up time-travelling into Konohagakure and then asking a boy who you don't even know to be his apprentice?

That was a joke.

Disclaimer: I do not own the characters in the fanfiction, Naturo will become more mature eventually, but still keeping his cheery personality, Sasuke will mostly stay the same, however there could be changes about that.

Difference of Shadows

Chapter 1: Sins of the Forsaken

(Arlington National Cemetery, September 19th)

There had been graves, graves full on the land, where flowers had surrounded the place, and the forest dimmed with the whistling leaves that flew off the branches, stones and stones with every name on them, specifically a few related to the patriots, there was a man with half of his entire face burned, and as he had looked

The most saddening thing of all was that reality was never good, and eventually, the light had shined slightly more, due to the wind currents getting some of the leaves out-of-the-way, the man had held a pistol in both of his hands, pointing it up to his face, as he had memories flash through him, He remembered some of his missions, he remembered the first time when he had gotten to Shadow Moses, he felt all cold, lonely and several other emotions, and last, hatred.

That was what he had felt, when he had done his assignment.

When Snake was called back to the U.S. military in February 2005 when he got deployed by his former commander Roy Campbell to Shadow Moses Island, he had doubts about several things, questioning of his need to fight, and his purpose, he always got reminded several times that he may have returned because of enjoying war, he had denied it at times, though.

However, he wasn't too happy with Campbell for how he decided to call him back into service, since he sent armed soldiers to his doorstep in a way that seemed like they wanted to capture him and they stripped, and searched for things as well taking all his weapons away from him.

There, a rebellion had taken place by the members of FOXHOUND, his former unit, who were threatening the U.S. with a nuclear strike. The task fell on Snake, a former operative and expert, to stop them. Although he wasn't willing to get out of retirement, he ultimately accepted the mission under two conditions: that he be given full disclosure from Campbell on what was going on in the mission, and that he answer to no one besides Campbell, with no cutoffs involved.

His mission, however, was a cleverly woven plot, prepared by the Pentagon. Through the secret, Pentagon-guided efforts of genetic engineer Naomi Hunter, Snake's body became host to the artificial virus FOXDIE. Snake was outraged to hear that his mission was a government conspiracy, and that he was merely sent as a carrier of the virus, which was programmed to kill Baker (for knowing too much about the project), and the FOXHOUND operatives just to make sure that the bodies of the Genome Soldiers and Metal Gear REX could be recovered undamaged. He was also reminded of the possibility that he had willingly returned to the battlefield because he enjoyed war, as commented upon by Meryl, Psycho Mantis, and Liquid Snake, and echoing Big Boss's words in Zanzibar Land.

And after everything he went through, he had now stood at the graveyard where his suicide would be committed to end the suffering, of the son of the Legendary Soldier, Big Boss.

Solid Snake visited the grave of Big Boss once again. Collapsing in front of the grave, he vowed that the last thing for him to do - his last mission - was to take his own life, thereby erasing his genes from the Earth, and removing the threat of the mutated FOXDIE strain. Finishing his last cigarette he put his gun in his mouth and fired, only to drop it out of his mouth at the last second.

Snake couldn't go through with it, and had fired into the air at the last second. The stress of nearly dying had apparently taken its toll, as Snake remained on his hands and knees, panting and sweating profusely. In that moment, Snake heard a voice.

"That's right. Good. No need for you to go just yet. It's been a long time Snake."

Solid pondered frantically, mostly how unexpected it had been, he hoped it was just some random voice in his head that was just trying to make him stop from ending his life. 'Whose' voice was that?'

He had turned, and then at Big Boss himself with Zero in his wheelchair, the Major dependent on the life support that is the only thing protecting him from his death, Big Boss's light brown coat moved along with the wind, like a pattern, as his black eye-patch on his right eye was staring along his left eye at not just a soldier, but a son who he never acknowledged, though the eye-patch did not see through, as his grey tie and grey/white hairs swayed along with the whistling grass.

Solid Snake, surprised to see him, though he stood up limping, as he had frowned at the man who had Liquid Snake and Solidus Snake's parts, as he had been rebuilt, Solid was not aware of this however, but he was still furious at his father, he could not acknowledge him as his father anymore.

He had looked at him with his voice having the tone of surprise, "Big Boss?"

He had said, as several birds flew from the trees in the despairing forest that was once peaceful, and the both of them were on their respective sides, staring at each other,

But he couldn't think and make conclusions after that.

Big Boss, was also brandishing the Patriot Assault rifle. Surprised, Snake quickly reloaded his gun, but after a few moments of holding each other at gunpoint, Big Boss dropped his gun, and disarmed him as he overpowered him, and then embraced him, assuring his son that he wasn't there to battle for their lives, Solid had frozen as he didn't know how to respond to his father.

"Let it go. I'm not here to fight. Or should I call you brother?"

"What?" As his eyes were burning in water, as his face had jerked up in movement and his body stood still, and his father had moved his hand on to the gun, taking it slowly and removing every bullet from the gun and dropped it on the ground.

"It's over, It's time to put aside the gun and live." He had said, as his son stood still in place, and doves had flown from the trees, and the sun shone in the luxurious clouds and the illuminating sky, he slowly sighed, and then stared sadly at his son.

"It started with a bunch of old fools. Now.." He paused for a few seconds, and then started talking in a normal vibe of voice.

As he had turned to the right direction in his eyes, as the muscles in his face jerked slightly, and in a rough voice he had resumed explaining about the thing.

"They've all passed away. Their era of folly is over. I'm the only one left, and soon.." He paused, as Solid Snake stared.

"I'll be gone too.." He muttered quickly, as Solid Snake then quickly walked a few steps forward in an urgent speed, having to wanting to say something.

"How can you still be alive?" He questioned, he couldn't understand it, the whole thing was that he died, and his body, conserved, and then asked to be brought to another clone of Snake, he knew that his body was still around somehow due to the fact that was said earlier, but how could he have been alive? He died, he knew! It was too strange and it was impossible to be revived so easily.

Big Boss had turned to him, as he stared for what seemed like longer than it should have, he had to do this quickly as possible without making it rushed otherwise the entire era of the Patriots wouldn't be explained, he had to be quick, but not too quick.

"That body, that Liquid burned on the Volta... Wasn't mine. That was the body.. Of a Clone.. Solidus." Solid Snake had frowned, as he had still remained quiet, he was jumping to conclusions as quick as possible, wondering about the entirety of everything involved, it was another problematic situation that he wounded up in, only it was the aftermath, that was once what he thought, but it wasn't just a problematic thing. It was something that worried him off.

as Big Boss started to explain, knowing of the fact that his son was questioning about things.

"He was a perfect clone, Zero, and the proxy AIs that came after him, were convinced that Solidus was me.. I was implanted with nano-machines, kept in a state of eternal sleep.. By JD the Proxy AI. They had me sealed away completely.. Not just my physical body, but my will, too. The technology was similar to what they used to restrain the B&B Members you encountered." He had paused, as several images in Solid Snake's imaginations had begun to exist, and most importantly, the history of the Patriots that had been told to him.

"For me to wake up again.. The System had to be destroyed... One way or another. Ocelot and EVA wanted two things... To bring me back to life, and to end the Patriots. That meant destroying the AI and killing the man..."

"JD and Zero... " He had paused in his words, as he looked at Zero, who was sleeping soundly with his life support, as Zero wheezed slightly, and Big Boss begun explaining the thing again.

"Right before you uploaded the virus into GW.. The way to JD opened, but only through the physical manifestation of GW. That's when we finally had learned the location of this man. Zero. For me and for them.. For Naomi.. Nothing was more important. And it was for that they put their grand scheme into motion. EVA stole by body from them and reconstructed it with pieces from Liquid and Solidus. And Ocelot.."

And that's it for now, the prologue for the remade DOS complete, thank god for that, I was more into getting a break than people could have thought with their imaginations, constructive criticism, appreciated, as long as it isn't involved with many flames, but go right ahead and be honest, as long as it doesn't end up not making sense or having no reason at all, if that happens, I will count the review as a troll.