Disclaimer: I do now own Naruto or Mass Effect as they are respective properties of Masashi Kishimoto and Bioware, but this story is my own creation.

Shadows

Chapter 2: The Past

"Talking"

"Thinking"

"Biju/VI/Geth/Reaper talking"

"Biju/VI/Geth/Reaper thinking

Cold blue eyes stared at the vibrant screen in front of him as a picture of man slowly appeared on the glowing screen.

The man was currently sitting in a comfortable chair, he was wearing a stylish grey suit and dark black pants. He had croppy silver colored hair and the same cold blue eyes as Naruto himself.

However instead of being focused like Naruto's eyes...those eyes appeared to be calm and calculative as the person carefully smoked the cigar in his hand.

"Illusive Man" said Naruto curtly, there was no emotion in his voice...well except for the tiny bit of respect he had for this man.

For the few years that Naruto had known him, he was one of the few people in the galaxy that Naruto respected the most. He had the guts to do what was right, even if the so called "righteous" masses of different races considered people like him as terrorists...Naruto considered him a patriot.

A human who would do anything to protect his race. A man who would not turn a blind eye to threats to his race and had the balls to make harsh decisions.

A small apprehensive look came on the old man's face as his eyes bore into Naruto's very own soul, as if searching for any kind of deception or betrayal.

"Captain Namikaze, I'm glad you received my message and decided to contact me immediately. There are things we need to discuss," said the Cerberus Head flatly, he was not a person who talked in riddles.

If he wanted to say something, he would say it flat out. And most of all he considered the cause to be greater than the personal feelings of a person.

He knew today was Minato's Death Anniversary, and under normal circumstances he would have left the boy alone today. But he had received information which he could not turn a blind eye too.

What he really liked about Naruto was that the boy shared his ideals, he was willing to take risks to protect his race...well, not his race to be precise.

"Is it something about the Reapers?" asked Naruto seriously, "Reaper" the word his father mentioned just before his death...

(Flashback: 4 Years Ago)

Location: Flight School Nemisis, Tarian System

A 15 year old Naruto currently sat on the observation deck of the small space station he was currently in. It was early in the morning and most of the cadets were currently asleep in their dorms, however he had a habit of waking up early.

Or Maybe he just liked to see the magnificent sun that stood thousands of miles away from his space station. The interesting thing about the celestial thing was- that it was not yellow in color, instead it was a dark red which reminded him of his mother's beautiful red hair.

He idly wondered what it would have been like if he had red hair just like his mother?

"It's just like you...to be up so early in the morning," said a melodious voice, and a small smile came on Naruto's face.

He turned around and was greeted by the sight of one of the most beautiful women he had ever seen in his life. She had jet black hair that reached up to her waist, and had a angular shape. Her bust had quite appealing C-cup breasts, however the most fascinating thing about her were her dark black eyes.

Yes, 36 year old Mikoto Uchiha had all the traits to be called a MILF.

She was one of the instructors in the flight school and possibly one of the best eye candy young boys like him had ever seen.

"Not to mention a pervert too!" said Mikoto naughtily, as she gently flicked his forehead that instantly brought him out of his perverted state.

His cheeks turned a little red on being caught providing Mikoto a heartful laughter.

"Boys are so silly at this age..." thought Mikoto bemusedly, as she gently ruffled his silky blonde hair making him more embarrassed.

"Why are you up so early? Last I heard, you liked to enjoy your beauty sleep" said Naruto quickly, he just wanted to stop her from embarrassing him further.

The older women got the hint, and decided to call it off. He had been teased enough for one morning...

"Well I do like to watch the beautiful sun...and besides I like to company I have right now," said Mikoto honestly, and this brought a small smile on Naruto's face.

For a moment a sad look appeared in Mikoto's eyes which Naruto completely missed.

"You are so much like him...you truly are-"

"Mikoto, do you think Humans can one day gain equal importance in the galaxy?" asked Naruto curiously, and an inquisitive look appeared in her eyes.

"I have a feeling that time is going to come soon, the galaxy cannot ignore us like pieces of trash. We have achieved so much on our own, despite constant roadblocks the Citadel sets for our race...we are advancing faster than any other species in the world" said Mikoto passionately, and Naruto was really surprised by her belief in her race.

"Wow, I didn't know you believed so much in humanity," commented Naruto curiously, as she just gave him a gentle smile in return.

"We all have to believe in something," said Mikoto with determination, she had to get her message through to his heart.

This was what he wanted...and it was the last wish he had requested from her. There was no way in hell, she could let this young boy slip away into the Alliance.

Those Bastards...how dare they!

Despite knowing everything, they chose to ignore it. They were the same as the Turians, those monsters that took away all those whom she held dear.

"Mikoto your eyes are red," commented Naruto in shock, as her calm black eyes were currently red and had 3 small black tomoes in it as she tightly gripped her hand on her jeans.

Now that Naruto thought about, there were some things that were really strange about Mikoto. She joined the Flight School the exact same time as him, she only talked business with most of the students...except for him.

She would always be there to support him, cheer him up if he failed in class...but the most interesting thing about her was that she would never leave him alone on his father's death anniversary. She would stay with him the entire day and make sure that he didn't get too depressed.

He was not an idiot, so many things about her looked fishy. Yet he couldn't just ask her flatly, as he feared she would run away like most of his classmates.

He didn't know why but they always gave him a scared look, okay maybe he could run faster than any other person in the flight school. He could endure lack of gravity like it was nothing, his reflexes were tested to be far more superior than a special ops soldiers.

Just what the hell was all this mess?

"I'm sorry, I have some work to do...I'll see you in class," said Mikoto fleetingly, and before he could even protest she quickly ran away.

One thing was certain to Naruto...he utterly hated mysteries.

"I need answers..."

He stealthily pressed the numbers on the electronic screen as his eyes alertly scanned the surroundings for any presence. After a few moments the screen turned green as the door to the room slowly opened.

"I have to thank Murphy for teaching me how to break these codes..." thought Naruto proudly, as he currently stood on the entrance of Mikoto's room.

He knew what he was doing was trespassing and if caught he would be expelled from the school, but after thinking about these mysteries for all day had made him anxious.

His life was full of unanswered questions, and even his mother Kushina didn't have the answers he desperately seeked.

The reason he ran away from home was not because of his emotional turmoil but his desire to find answers. Ever since he could clearly understand the happenings around him, he had noticed he was a lot more stronger than most boys his age.

His IQ level while far from perfect was still higher than most average humans. He would have agreed that those symptoms could be enhanced genetics some humans had.

However there was something inside his body...a power that he always felt. A mysterious power waiting to be unlocked...

And Mikoto was probably the closest person he thought would have these answers. She was the most intelligent person in the entire staff, and he had clearly noticed her physical strength and endurance capacities were far greater than any female her age.

Plus, there was the fact of those weird red eyes that he would rarely see when she was really pissed.

All in all...Mikoto Uchiha was just another mystery like him. A mystery he wanted to solve.

He quickly started searching the desk of her room, he didn't know what he was looking for. But he had to start somewhere...he kept on searching but found nothing of significant importance.

Next he went towards her wardrobe and searched it thoroughly...however this time again he was disappointed.

"I guess there's nothing-" said Naruto defeatedly but was stopped when his eyes landed on a small picture that was currently placed carefully right beside her bed.

He gently edged towards her bed and quickly picked up the small device, and his eyes widened in shock when he saw the picture of a small group of soldiers.

Specifically he was looking at the picture of a tall blond man in "Commander" Uniform. He had spiky blonde hair that reached up to his neck and there was a vibrant smile visible on his handsome face.

"Father.."

Yes, there stood Minato Namikaze proudly in his alliance uniform and right beside him was a very young Mikoto Uchiha, if one could say she had just passed her teens, there were a couple of more soldiers around them as all of them were giving a happy pose.

"Beautiful, isn't it?" asked a sad voice, and Naruto immediately became alert as someone slowly started coming out of the shadows.

He was further shocked when it was none other than Mikoto herself.

"Who are you?" asked Naruto sternly, and a tired sigh escaped from the pretty lady's mouth.

"My real name is Lieutenant Mikoto Uchiha, Ex-Alliance Exploration Flotilla. And a friend of your father," said Mikoto truthfully, as she saw the shock deepen in his azure eyes.

"Bullshit, the entire flotilla was wiped out by the turians, even the one survivor that made it back to Alliance command died a few days later!" said Naruto angrily,

"That is the official story, Naruto...what do you know about your father?" asked Mikoto gently, she knew the boy just had a huge bomb dropped on him and it was her job to be patient with him.

"He was the Commander of "SSV Storm" and was killed in action when the attack started" said Naruto seriously, just what did she know?

"Yes, that is the truth. Your father was killed that day...however he was more than just a commander of a flotilla, he was something far more different," said Mikoto mysteriously,

"Cut the riddles and get to the fucking point!" said Naruto impatiently, as a small "Tch" escaped from her lips.

"He has definitely inherited some of your traits Kushina," thought Mikoto tiredly, as an image of a fuming red head appeared in her mind.

"You are not human"

"Excuse me?" asked a bewildered Naruto, did she just say he was not human?

"I know it sounds crazy...but that's the truth. In fact, even I, your father, and your mother are not humans. At least not totally," said Mikoto seriously and to make her point clear she activated those weird red eyes again, and Naruto quickly came towards her and looked her straight in the eye.

"What are you talking about?" asked Naruto worriedly, it seemed he was finally getting some answers today.

"I'll explain everything I know...but only if you listen to me," said Mikoto strictly, and he gave her a hesitant nod.

"Talk"

"It all started 16 years ago, when I joined the Alliance Navy as a science team leader. I specialized in biology, studying of artifacts and conducting research. I had also received additional training as a co-pilot of a small shuttle," started Mikoto slowly,

"That's a pretty interesting profile...I must say," said Naruto with a small smile, and she gave him a acknowledging nod.

"My first posting was on Mars under the leadership of your father in the Alliance Flotilla. I was assigned the task of studying the ancient ruins on Mars...in order to find clues to properly activate the Mass Relay 314. That was the time I met your father..." said Mikoto happily, and Naruto saw she truly had good memories about his old man.

"What kind of person was he?" asked Naruto curiously, and he saw a happy smile appear on her face.

"He was one of the finest men I ever met, he was kind, gentle and at times even silly like you. But more than that he was a great friend, and a damn good leader. Also he was the strongest soldier in that flotilla," said Mikoto proudly,

Naruto was really happy on hearing this, he was getting to know his deceased father more and more. He never tried to ask his mother about Minato, as he knew it would only cause her more pain.

But now he had a chance to get to know how his old man was,

Mikoto pointed a finger on his chest which made him look at her curiously.

"You feel a power in yourself, don't you?" asked Mikoto sharply, and he didn't know how she just read his mind.

"How do you-"

"I have the same power in myself...and I have something that belongs to you" said Mikoto sadly, as she gently took out a small letter from from one of the drawers and handed it to him.

"It's for you..." said Mikoto hesitantly as the young boy shakily opened the letter in his hands.

Dear Son,

It's me, your father. I know I'm not good at writing these...so please forgive your old man if I make some mistakes. I'm embarking on a historical mission tomorrow and if successful it can change the destiny of mankind. I know, your nagging mother would have told you about me...but if you are reading this letter, then I am no longer in this world.

Hey, don't be sad. You're better of with Kushina than me...and I know you'll become a fine man one day. I want you to know, that no matter what path you choose...know this that your father always loves you.

I also want you to know this...during my time at Mars I discovered a strange archive. It was in a language which none of my soldiers had seen before, not even the best linguistic experts could decrypt it. Strangely I and Mikoto (My Research Team Head) were able to decipher certain parts of it...but the archive was in a really bad shape, so we could only decipher two words.

Shinobi, Reapers.

We couldn't find much, but I have a feeling it has a real dark mystery behind it and is something which we cannot ignore. I presented the alliance with this information but they were more interested in the Prothean data that was proving more helpful in our study of the Mass Relay.

Your mother is too much loyal to the Alliance to look into something that the Alliance has deemed as classified. So, if by the time you read this...if there is no inquiry done by the Alliance in this matter, then I want you to look into it.

Please do it as a favor to your old man.

I'm sorry for not being there for you and I have no excuses for that. But I am sure you will understand the choices I made was for our future, and if you don't agree with me and are mad at me for not being there for you, then I totally understand and I am sorry.

Well, I've rambled on long enough...(Kushina's really rubbing off on me, you know?).

Take care of your mother and find a girl that will love you for what you are (PS: Find a sexy one like your mother!)

Your loving father,

Minato Namikaze

Tears freely slipped from his eyes as he read those precious words his father had written only for HIM. This was the only thing he had of his father besides a few photographs and he was really grateful that he was able to find it.

Mikoto was hugging him tightly and was trying to comfort him as best as he could. However his emotional turmoil soon died down as he looked at her gratefully.

"Thank you for giving me this...you don't know what this means for me," said Naruto happily, and the women just gave him a motherly smile.

"It's alright...it was meant for you anyway. Minato was my friend and mentor, he had asked me to look after you in case Alliance tried to do something funny...although I doubt anyone could harm you if you had someone like Kushina protecting you," said Mikoto jokingly,

"You know my mother?" asked Naruto curiously, however this time Mikoto shook her head in negative.

"No, I don't know her...but I did hear many of her stories from your father. She also is a great soldier and has talent..." said Mikoto honestly,

"But if the Flotilla was destroyed...how did you survive that day?" asked Naruto suspiciously,

"Well, it was by pure luck. Just a few days prior to that mission, I broke my leg during a Cave visit and was hospitalized on Mars. Minato gave me this letter just in case he didn't make it back..." said Mikoto sadly, and Naruto understood her completely.

"But if you knew about this information...then why did you not present it before the Alliance again?" asked Naruto flatly, and he saw her anger flaring again.

"I did present that case multiple times, but no one listened to me. They were more interested in their war against turians than some mysterious information about an ancient race...however Minato wouldn't deem it important, if he didn't think it was so crucial. I tried to go public, and the Alliance court martial-led me and destroyed all the data, claiming they didn't need myths to spread fear among people." said Mikoto angrily,

Naruto put a comforting hand on her shoulder and she calmed down a little.

"I kept tabs on you and waited for the right moment to contact you. Kushina would have never let me meet you, as she hates anyone who opposes the alliance...and I was dismissed from service, so you know how it would have turned out," said Mikoto sheepishly,

Naruto gave her a nod as she was right, his mother vehemently supported the Alliance and if a dismissed officer like Mikoto would show up on her door, then the only thing she would have gotten from Kushina was a solid punch and a fair warning never to come near her family again.

"So, you used your degree as a co-pilot and entered as a faculty in this school. You contacted me and became my friend...and slowly gave me hints that you were somehow connected to my family. The only question that remains is what you want from me now?" asked Naruto sharply, and Mikoto was really taken aback by his intelligence and how quickly he put "Two and Two" together.

He was indeed Minato's son.

"I want you to join Cereberus" said Mikoto firmly and looked at him straight in the eye.

"What is Cereberus?" asked Naruto sarcastically,

"It's a pro-human group that aims to protect humanity at all costs, they are willing to look into minute things that can endanger our people. When I presented this information to them, they started investigating the case immediately and discovered that I was no ordinary human. I was far more advanced than human biotics...and we believe it has a connection with "Shinobi, as the word "Reaper" means death and destruction," explained Mikoto briefly,

"And why should I join you? I can join the Alliance and try to find the truth without joining some mysterious organization" said Naruto sarcastically, and a loud snort escaped from her lips.

"Yeah, go ahead and work with those pussies who cannot hear the truth. You'll have a good career because of your skills, but just like your father and me, you will be ignored if you try to show this case. Work with us, and fulfill the last wish of your father!" said Mikoto emotionally, and she knew she hit the right spot as his eyes softened a little as he remembered his father's request.

"How can I trust you and Cerberus? For all I know, you could be terrorists" said Naruto harshly,

"The line between patriotism and terrorism is very thin. Only you can judge what is right for you...live a life of submission in the Alliance or Join us in our fight against Reapers..."

Naruto was really taken aback by those words and Mikoto slowly stood up and offered him her hand.

"What is your choice?"

(Flashback end)

A choice he made that changed his life. At the age of 15 he joined Cereberus under Mikoto and came to know about the Illusive man. He trained day and night in order to fulfill his father's last wish and now it was finally time to make it a reality.

Mikoto was easily able to get him out of flight school...and Naruto later discovered that it was due to her eyes that she wiped the memory of most of the people there. They knew nothing about him...and for the next 4 years he had no contact with his mother.

It was painful...but it was necessary.

In a few years he saw the Alliance bending over their knees to get a seat on the Council, and the Turians were still the arrogant bastards and treated humans like dirt.

His mother was playing politics, even if she didn't want it...she was being used. And he HATED it.

That was why, he loved Cerberus...they were willing to discover the mysteries and do whatever it takes to get the job done.

No stupid rules, No political bullshit, just the mission alone.

"Not exactly, but I have some disturbing news that Saren Arterius, the Turian Spectre is working with the Geths...and my sources inform me it has to do something with destruction of humans," said Illusive Man seriously, and he saw Naruto's hands clenching.

"Orders?" asked Naruto quickly, if the Geth wanted the massacre humans he had to stop them at all costs.

"I want you to head to Illuim...and find quarian there named Tali Zorah. You'll be briefed in detail as you reach there," ordered Illusive man strictly,

"What does this Quarian know?" asked Naruto curiously,

"We have to take harsh decisions Captain...the Council are a bunch of fools, they won't care if our colonies get destroyed. That is why they need to be taken care of...the galaxy has to accept humans as equals from now," said Illusive man with utmost conviction in his voice,

Naruto prepared himself for the mission...if it meant protecting humanity, then anything was fare to him. Illusive Man looked at his most trusted soldier and told him a few words that would change the future.

"I want you to assassinate the council..."