Disclaimer: I do not own Naruto or Mass Effect; they are properties of Masashi Kishimoto and Bioware respectively; but some theories in this story are my own.

Shadows

Chapter 1: A Mystery

"Talking"

"Thinking"

"Biju/VI/Geth/Reaper talking"

"Biju/VI/Geth/Reaper thinking"

The shiny warm rays of sunlight slowly advanced further in his room. Step by step they came closer until they were directly on his face, giving him their warmth and making him realize the beginning of a new day.

He slowly opened his cereluen blue eyes, and looked out of the window of his room.

The vast deep space always was a mystery to him, where did it start from, and where did it end?

Curiosity had always been a unique trait among humans, they were the most inquisitive creatures in the world. The desire to learn more, the need to achieve more could be seen in humans the most in comparison to any other species in the world.

It wasn't their fault either, human life span was one of the shortest in the galaxy. An average human lived up to a century at most, a few lucky survived for a few more years; but that was it.

Humans didn't have a thousand years to live like the Asari or the Krogan race, so they tried to accomplish as much as they could in their short lives.

His blue eyes gazed at the sun that glowed magnificently, this was a view he always liked.

Looking at the sun, that was hundreds of miles away from ship brought back memories from the past.

Memories that he cherished till this day...his eyes looked around in his small room.

It was just a small room on a ship, but it was his home. A small bed, a few electronic devices, a bathroom, and a small desk where he used to work.

Yep, his life was not exactly what people would say as exciting.

A tired sigh escaped from Naruto's lips, he slowly got up from his bed...and the cool air of his room hit his bare chest; he stretched his muscles a little earning a few small cracked voices coming from his body...as it got ready for another day.

"Another day in paradise..." thought Naruto with a chuckle

He put on a his dark blue pants and stepped in front of the mirror, looking at the reflection in the mirror showed him that time had indeed past quickly; even though it just seemed like a flash sometimes.

Naruto Namikaze?

Who was he?

Well, if one could say he was a 19 year old boy, 6ft tall, average weight. He was quite handsome...all due to the good looks he received from his parents. He had silky blonde hair that reached up to his neck, cereluen blue eyes...an angular face that was just like his father, some people had even called him a clone of his father due to their almost identical looks.

However the most beautiful thing was his smile...that he inherited from his mother.

He looked at a small picture on his desk, it was a picture of a couple. The man had spiky blonde hair that reached up to his neck...and his face was the same as Naruto's; beside him was a woman with dark red hair and a very beautiful face, but her violet eyes still amazed Naruto.

The coupe had one thing in common...they both were wearing alliance uniform.

They were none other than Minato Namikaze and Kushina Uzumaki, his parents. To him, they were the most wonderful people in the world.

19 years...

It had been 19 years since the First Contact war, a war that marked humanity's entrance to the galactic community.

He still couldn't understand why had the turians started firing at humans...when they had tried to activate the Relay 314, they could have just tried to warn the humans as they were unaware of the laws that the Citadel had made after the Rachini wars.

Activating mass relays was forbidden...and the humans didn't know that. Hell they didn't even know any other life form existed in the universe apart from them; they had just developed space technology and were making new exploits to find out more about their world.

He still remembered the times when his mother told him...about the days when she was deployed at Mars as a Lieutenant.

Kushina Uzumaki was a Lieutenant in the 103rd Marine Division of the Alliance Navy; a brave marine...she had served humanity all her life, even now after all these years...

A sudden voice interrupted Naruto from his thoughts...

"Naruto...there is an incoming transmission for you,"

The voice of his VI made him realize that, someone wished to talk to him. He put on a small white tshirt and went towards his desk.

"Who's it from, glyph?" asked Naruto curiously

He had named his VI as glyph, as he liked that name.

"It's your mother...Commander Kushina Uzumaki, 5th fleet, Alliance Navy," said the VI named "glyph"

"Of course, she would call today..." thought Naruto calmly

It was his father's death anniversary today...and was the saddest day in the entire year for him.

Minato Namikaze, Commander of "SSV Storm", Alliance Exploration Flotilla. His father was one of the most skilled leaders in the Alliance Navy...it was him who discovered the first mass relay.

While his mother Kushina was a soldier, his father was a great commander...his intelligence and skills were unparalleled.

However...when Minato was trying to activate the Relay 314 along with his small convoy...they were attacked by patrolling ships of the Turian Fleet; the Exploration Flotilla didn't have advanced weapons like the Turian patrol ships...and as a result his father was killed in action along with most of his convoy.

But a single ship from his father's convoy made it back to Alliance Command, and relayed this news; and thus started the First Contact War between the Humans and the Turians.

A war which took a thousand humans and Turian lives...a war which could have been avoided, only if the Turians had tried to negotiate this bloodshed would have been avoided.

Naruto never met his father...his mother was pregnant at the time of the war; and as a result she was forbidden to participate due to medical reasons.

He hated aliens...most of all he disliked Turians the most. They considered humans as second class citizens, just because they are a little more developed...but they still forget that humans had given the turians a tough fight despite all the odds.

"She's waiting for your answer. Would you like to receive it?" asked Glyph again

"Yes...patch it through," said Naruto quickly, he knew his mother was a bit impatient.

A Hologram appeared on his terminal; and the image of his mother quickly flashed in front of him. She was in her Alliance uniform, her hair were tied in a small ponytail that reached up to her shoulders.

"So...finally got some time to speak to your mother," said Kushina in a playful tone

Naruto was a little surprised by this, it was actually the opposite...Kushina was always on active duty, and had less time to speak with him. After his father's death, she had struggled a lot...but despite her pain, she loved him with all her heart and raised him as well as she could.

He moved constantly from one ship to another, he went wherever she got transferred until he became 15 and went to a flight school in order to become a pilot.

Like his parents, he was also a skilled person...and the Alliance had also offered him to join their forces like his parents...but he had refused. He could not stand to work with Turians, they reminded him of the past, the father he lost.

He was comfortable in dealing with other races mostly...the Asari and the Hanar. They were peaceful races, which intrigued him a lot.

After his graduation he became a freelancer, who transported goods and people from one system to another. The income was decent and he was living a peaceful life.

Kushina had offered to come with him, but he knew the Alliance was her life. It meant everything to her, it was her career in Alliance that had helped her deal with her husband's death; she was a brave woman and had saved an entire human colony on her own by fighting off against an army of pirates.

She was a war hero...and if what he had heard was true, she was one of the most likely candidates to be made the first Human spectre.

And Naruto was proud of his mother, and he did not want her to abandon everything for him. He loved her more than anything.

"Well...you seem a lot busy these days, so I try not to bother you" said Naruto sheepishly

A sad look appeared on Kushina's face, as she knew she had not talked with him in weeks. Even though most families today stayed apart, they constantly kept in contact via the extranet...but the Alliance wanted her to become a spectre and she had been so much busy with her work, that she had forgotten about her son for some time.

Naruto sensed his mother's feelings, and decided to ease her pain.

"Its alright mom, you probably should not waste your time on me...I'm just a normal person, but you are humanity's face in the galactic community these days...so its ok if you get busy," said Naruto comfortingly

A small tear slipped from Kushina's eyes, her son was so kind to her.

"No...its not ok. I'm sorry, I should have been there for you more," said Kushina sadly

"Hey...I'm an adult you know...I can take care of myself," said Naruto confidently

A smirk appeared on Kushina's face as she looked at his room...a few reports were spread everywhere. Some of his clothes were still lying on the bed...but she frowned a little when she saw many bottles of alcohol on his shelf.

He had forgotten to hide them...any other person would have missed them, but not Kushina. She was not a commander for nothing.

"Have you been drinking lately?" asked Kushina sternly, even though he was an adult...and had a right to live his own life; she still felt he was her little boy and she had every right to scold him.

Naruto looked back...and noticed he had forgotten to hide the bottles, he was caught now.

"Well...you see...my friends kind of came here, so.." said Naruto sheepishly, trying his best to lie.

Kushina put a hand on her hips, a small smile came on her lips as she saw her son fumble over what to say. It was a trait he inherited from his father...and Kushina sometimes saw her husband in Naruto.

"Naruto...you need to tell me if you have any problem. I'm always there for you," said Kushina comfortingly

She knew despite her son's calm personality, he was a troubled boy. She had seen how much Naruto was affected due to Minato's absence in his life, she had seen the look in his eyes...when he saw other kids with their fathers, and due to her constant transfers to different posts his life had not been stable...and he did not have much friends.

"I know...its just this week's been a little rough," said Naruto silently

"It'll be alright," said Kushina comfortingly, usually her son would be fine...but on Minato's death anniversary he would always be like a lost person.

She decided to change topics, to take of his attention from more depressing thoughts.

"How's your work going?" asked Kushina curiously

Being a commercial pilot was a fairly easy job, customers contacted you if they wanted to send their belongings to other systems. The more dangerous the system, the more you got paid for delivering the packages safely.

Sometimes even people were asked to be smuggled secretly to other worlds.

The most dangerous was the Terminus System, which was filled with pirates; that looted almost any ship that passed through their territory. Even the Alliance and other races were helpless against these pirates, their network was strong, and if war was waged against them; then several different colonies of different species which were in Terminus System would be destroyed due to the conflict.

Many companies like Nos Astra, Elkoss Combine and others had difficulty in delivering their products to the customers in such systems. They could take the help of the Citadel Fleet...but there were some places where even they could not reach.

So they hired freelancers like Naruto...who transported their products to such worlds, the job was risky because if caught the freelancers would be executed, while their ship would be seized along with the products on it.

But Naruto didn't care, it was a better job in comparison to his mother's, where she had to bear with the Citadel Council and their partial behavior towards humanity every day.

"It's going fine actually...I recently purchased a UT-47 Kodiak from the black markets," said Naruto happily

Kushina seemed shocked to hear this, the Kodiak was extensively used by the Alliance and to find that it was now available through black market dealers was quite a surprise. But she knew in their world, they could get anything they want, drugs, weapons, ships...everything was available if you had the credits.

"Naruto...why do you do such dangerous jobs?" asked Kushina worriedly

"It helps me make a living...and its kinda fun," said Naruto with a smile

"You idiot, with your skills you can easily join the Alliance Navy as a fighter pilot, its a safe job and the credits you get are much more," argued Kushina in protest.

She was a little sad that her son had not joined the Alliance like her husband, she really hoped that he would fight for humanity too; but as soon as he turned 15 he left her home, and joined flight school. At first she had thought that he had enlisted in the Alliance Navy, but he had lied to her and had actually went on to become a commercial pilot. He did not even try to remain in much contact with her for the next 3 years, and then after some time he disappeared from his flight school at the age of 18.

Only she knew how worried she had been, those years had been like hell, she didn't even know whether he was alive or not. Kushina had searched everywhere for him, but he was no where to be found.

It was just a few months back, that he had contacted her...and said he was a freelance pilot now, he never told her where he had been despite her attempts he never told her anything.

Ultimately she stopped pestering him, because he was the most important person in her life, and she believed some day he would open up to her fully.

"It's because I cannot lick the Citadel Council's shoes like the Alliance...they treat us as trash, despite humanity's achievements in all these years, we still have not received a seat on the Council," said Naruto angrily

"It's not that simple...it takes time to earn someone's trust Naruto, and we are new to the galaxy...it has just been 20 years since we discovered that there were other species in the universe," said Kushina calmly

"I know...but the Turians-" said Naruto sadly

"You need to let go Naruto...it was an accident, a bad accident that led to war, and both sides lost soldiers in it. You should not judge an entire species on basis of actions of a few patrolling scouts," said Kushina patiently

"Is that what the Alliance told you?" asked Naruto sarcastically

"Naruto...I know how you feel, Minato was my husband too. A part of me died when he was killed, but we have to move on. I want you to consider joining the Alliance, I could use your help on the Normandy, I need a skilled shuttle pilot like you...but more than that I need my son back," said Kushina gently

Naruto thought about the offer, he could easily join the Alliance...and his mother had great contacts within the top brass, especially Admiral Hackett and Captain Anderson, and he could get a position on the Normandy.

He didn't know much about the ship, but it was said to be one of the finest ship in the galaxy which the Turians and Humans had created with combined efforts; but...

"I can't...I'm sorry," said Naruto apologetically

A sad look appeared on Kushina's face but she quickly hid it and replaced it with her vibrant smile, his mother did love him the most in the world despite how much of a disappointment he had been to her.

"I understand, and no matter what happens I'm always with you...next time you are on the Citadel contact me, if I'm there I would like to meet you. It has been 3 months since we last met," said Kushina cheerfully,

"Thank you...I know I have been nothing but a disappointment-" said Naruto but was cut off

"You are not a disappointment..." said Kushina quickly

"No...I failed you and dad, both of you have done a great service to humanity. You saved an entire human colony on your own, and now you are on the road on becoming a Spectre, Dad was one of the most skilled commander in the Alliance Fleet...and it was due to his efforts that humanity could explore deeper into space and make discoveries...and yet I failed all your hopes," said Naruto sadly

Kushina smiled a little on seeing that her son respected her and Minato so much, but it seemed he felt very guilty about not being a good soldier like them.

"You know...Minato never wanted you to join the Alliance," said Kushina softly

"What?" asked Naruto in shock,

"Yes, your father always used to say...he wanted his child to make his own choices. Naruto, each of us decide our own paths and create our own destiny...and I believe one day you will be seen as a great hero too," said Kushina with a warm smile

"I'll make him proud one day," said Naruto truthfully

"I'm sure you will," said Kushina confidently

Both mother and son looked at each other calmly for a few moments, a lot had changed in their lives. Kushina was now on the road on becoming the first human spectre, and was going to be humanity's face in the galactic community.

While her son, Naruto was living his life as a mercenary pilot...away from all the fame and glory of the Alliance Navy.

Now that Kushina thought about it, her son had always been a strange child. There were times when she felt, he was hiding something from her, something big.

And she would find out about it soon enough.

"Well, I've got to go...duty calls," said Kushina with a smile

"Keep up the good work...I love you, mom" said Naruto with a warm smile

"I love you too.." said Kushina happily

The hologram vanished and Kushina's face disappeared, but she missed the change in Naruto's eyes.

Instead of being calm and innocent they were now replaced by a pair of cold blue eyes; that could send shiver down people's spines.

"Thank you, mother"

A figure walked into a dark room, the sound of his footsteps activated the lights in the room; and soon instead of a dark room there was a Combat Information Center(CIC) in its place.

Various digital screens could be seen on the wall of the room, showing various types of information with the help of pictures, graphs and various other types of figures.

In the center of the room was a large digital mainframe device that was displaying the entire galaxy map, it showed all the various systems known in the universe, along with some certain other information attached to it.

On the left side of the room was a comm terminal, while the right side had an entire digital library with majority of information about various species, mass relays, different myths...and many other classified data.

The person was wearing a black metallic armor over his entire body; it had faint shades of blue color on some places; his hands were covered by synthetic gloves that were specially made to protect a person's hands during gun fire.

His blonde hair were hanging freely and the look in his eyes was of a combat soldier.

There was a shining sniper rifle hanging on the person's back and a diamond shaped marked on his chestplate that was surrounded by two curved arrows on both sides. The mark was yellow in color.

Looking at the galaxy map in front of him made him remember his mission, his quest.

The galaxy was heading towards dark times, and an ancient threat that had existed since ages was making a comeback with the aim of wiping out life from the face of the galaxy.

He knew he had to do something, the world leaders were busy playing politics and were not at all concerned about the safety of the galaxy. Even the Alliance was busy playing politics with the Citadel Council, instead of focusing on protecting humanity.

Nevertheless, he would make sure that the task his father had assigned him was completed, no matter the costs. He would stop the enemy at all costs, even at the expense of his soul.

He had worked for years in order to achieve his objectives, and had come a long way from being a emotionally troubled boy to a deadly special ops soldier, whose only aim was to protect humanity from the shadows.

"EDI, patch me through Cerebrus Command now"

The person's voice was cold and confident, yet it had an authoritative tone to it too.

"One moment please...Logging you in Captain," said the Aritifical Intelligence(AI) named "EDI"

The person moved towards the comm terminal and a voice was heard across the communication channel.

"Welcome to Cerberus Network...please state your Codename Operative," said the VI

"Operative Shadow, Captain of Special Ops Divison," said the person firmly

"Verify your ID number, name and code word while we confirm your identity," said the VI

"ID: 655401, Naruto Namikaze...Codeword: Reapers"