Hey guys Fanboy913 here, I hop you enjoy my newest story, if you are currently reading my other story Ichigo the new school arc know that I have not under any circumstances abandoned it a new chapter will be out soon.

I hope you will like my story and by all means tell me of any flaws you find, any glaring plot holes you see. I will try my best to explain or fix what ever you point out. Thank you and enjoy the Story of Mass Effect A New Beginning

Mass Effect A New Beginning

"Captain! We may have a problem" said the ships watch officer.

Captain Zaal'Garlar vas Defrahnz Nar Epsilon pressed his hand against his face mask, "First the Engines then the Weapons and to top it all off that idiot of Sergeant we have manage to get himself sick by doing Ancestors knows what. What could possibly be wrong now?"

The Watch Officer never flinched "There is an unidentified ship that is entering the our space. It seems to be a rather small freighter our first scan of it shows no engine activity and our attempts at contact have been met with silence."

Zaal absorbed this information in silence, standing fleet orders stated that any ship that did not give a good reason for being near the Fleet were to be destroyed. However there was also orders that if any ship was found abandoned that recon would be sent to asses its potential to be added to the fleet.

Really he could give the order to destroy this ship and be done with it but with the death of his wife and unborn child the only thing he had left was the fleet and if he could make it stronger then he would do it.

"Send in our Marines to bored it" Zaal stood up "and tell the commander I will be joining him."

The watch officer seeming to want to say something but held his tongue the actions of his captain while not protocol were increasingly common since his wife had died. Thought everyone on the ship would have preferred the Captain to stay safe and in his chair, they also knew that this was his way of dealing with grief. Of coarse if he believed this ship to be truly dangerous they would have tied there captain down kicking and screaming and court martial be damned, there captain had earned that much from them.

The Migrant Fleet marinas moved down the air lock in row's of two, there weapons were out and loaded ready for whatever was behind that door. The only thing that made them nervous about this satiation was the fact that Captain Zaal had decide to help lead them. And by help lead them they meant stand at the front and let their Sergeant, the good sergeant not the sick one give the orders. Their Captain was smart enough to know when to let others give the orders, except when it came to his personal safety. Which annoyed the Marinas to no end their thoughts could be summed up in the same thought that entered every soldier's mind everywhere from every race ever.

"Why did the good commanders the ones who acutely knew how to lead always insist on doing it from the front?"

They reached the door and the tech expert of their group a Corporal who went by the nickname Gadget went over to the panel and began to work. He had a habit of talking to himself as he worked but they bore that oddity because he was the best at what he did.

"*Hum* circuits burned out, and someone has not been updating their security this tech went out of date several years ago." Gadget's hand fiddled with the computer "So if I connect this wire here and that wire there, ah got it" half of the holographic interface sprang to life, Gadget reached into his pouch and took out a single capsule of Omni gel he placed it somewhere in the interface and the door opened.

And the moment it opened they all whished it hadn't, the stench of blood and death filled there suits. Each marine flicked a switch to filter the smell from the air entering there suits but nothing could stop a small bit of the smell from making its way through.

Captain Zaal took the lead following the ship's corridor, a glance in the two forward rooms showed several human bodies, all male all killed by a single shot to the head. He noted his marines had there weapons aimed and ready to kill now. He opened the door to the main cargo bay.

There were more bodies, several women and children their deaths had been violent several seemed to have had their throats slit while others strangled. Anger flickered across Zaal's face these looked more like revenge killing than anything else. A small part of him hoped that whoever did this was still alive, just long enough for him to send the bastard on a one way trip to hell.

Thankful his tinted visor gave him a stone faced appearance he walked through the room of horror trying not to look at the victims of such senseless violence. In the middle of the room lie a body this one however was not human, half of its face was missing but the two eyes it had left showed it to be Batarian. His clothes were well made but covered with blood much lighter than his own, and the bloody knife in his hand sealed the fact that this was the monster that killed all these people.

Zaal noted a seal on the batarian's vest and bent down to look at it, the action saved his life. Shielded or not a shotgun blast at a range of less then ten feet was almost certainly a kill as it was the blast went over his head scattering uselessly against the hull.

Every single marine reacted at once assault rifles sprang to life twenty at once spraying the area around the crates with lead and death. Zaal however noted something different, perhaps because he was lying on the ground having been pushed their by an overzealous marine, the moment before the shot had fired he noticed a small figure out the corner of his eye.

"Cease fire!" he yelled

The now confused marines complied with his order nervously, rifles at the ready and to confuse them even more Zaal handed the Sergeant beside him his fire arm "Do not fire unless I order it" he said with a tone the brooked no decent.

"But sir."

Zaal ignored his sergeant and took several steps forward turning around the creates that hid the shooter. The first thing he noted was the shotgun lying on the ground, the second thing he noticed was it shooter.

It was a boy, a child he had black curly hair and piercing blue eyes he was a shade under three feet tall and wore clothes that were in tatters. He was breathing hard obviously in pain and from the way he held his shoulder Zaal guessed that it was dislocated. Considering the child had just fired a shotgun it made sense, several Marines approached behind him weapons ready "Get those pointed somewhere else!" he snapped.

The boy seemed to look at him for the first time, his eyes were like that of a wounded animal scared, angry, and desperate for survival. He was holding his shoulder tightly his face a mask of pain.

Zaal knelt down bringing his visor to the boys face level, he spoke quietly and calmly as one would to a spooked Medelorn. "Boy are you hurt?"

The kid flinched away hissing in pain as the movement caused his shoulder of bump a crate.

"I'm not going to hurt you, I am here to help."

The animal light faded from the boy's eyes, a sad aching glow filled them, his body language said he wanted to believe him but even still he tried to back away.

Considering where they had found him and what had happened to him it made his actions made sense. Still Zaal did not give up, "Come boy lets get you out of this nightmare, I swear by all my ancestors no harm will come to you as long as I am alive."

The boy stared at him for a long moment before slowly making his way over, when he was just within arms reach his eyes rolled back into his head and he collapsed the pain overwhelming his small system.

Zaal caught him and picked him up, "Sergeant secure the rest of this ship search for survivors, I need to get to the doctor."

The Sergeant nodded and began to issues out orders in a steady steam as their captain carried the strange boy out of this hell hole and to the safety of the Epsilon.

Zaal walked towards the medical area, it had been three hours since the finding of the nameless ship he had sent his repot off to the admiral board and had left he bridge to his watch officer.

The doctor was waiting for him Doctor Shamo'Shaanah nar Leli vas Epsilon was a godsend to his ship. Her knowledge and skills had saved the life's of his crew more times than he could count, her altitude towards her profession was a no nonsense one. However when off duty her kindness and selfless love had every non married male Quarian on this ship wanting a date with her. He himself would admit that he enjoyed her presents but for ancestors sake he was ten years older than the girl and he still was not over his wife, and mostly likely never would be.

She was not smiling when her entered which was strange, a glance around the room showed him the boy currently sleeping on one of the beds their he had been washed and cleaned his black hair almost shining in the wan light of the room.

"How is he Doctor?"

This was the part were she normally insisted he call her Shamo but that did not come "He is resting, I reset his shoulder and attended to his injuries so he will be fine at least in terms of the body." She frowned "His mind on the other hand I'm not so sure about, I read your report and." For a moment anger seemed to make her suit glow "And I'm not sure what kind of effects that will have on a child this young."

"Did you find out anything about him?"

The doctor wordlessly handed him a small locket, it was opened to a picture of a small family, a mother , a farther, a daughter and a small boy. "The names were written on the back of his picture, the says his name is John, John Shepherd"

It was almost time for his chance to sleep, normally he would gratefully entered the world of his dreams where he could see his wife and child, where he could relive his happiness. But instead he was sitting by the bed in the infirmly. This boy was a beautiful child his face calm and pure as he slept in the dreamless sleep brought on by the sedatives. Zaal had no idea why he was here, he had done his duty the Board would probably contact the alliance and this boy would be pick up by them.

But he still found himself drawn to this boy, though the marines believed it unlikely Zaal was sure this boy had killed the Batarian they had found. The bodies they had found in the ship two of them were a match to the picture found the locket and since they were adults it was assumed they were his parents, his sister was no where to be found. So his entire family was dead or missing, Zaal could not began to imagine the strength of will it must of taken for a child to aim and use a shotgun.

His own child would have been this age by now, Zaal mused would that child have been a boy or girl? What awaited this boy when her was returned to the alliance, did he have any other relatives?

What he would have given for his wife to be with him right now, she would have know what to do.

And then he heard her voice in his head, clear as the day they were married she told him a very simple solution. He stared at the boy even harder, could it work? It might if he called in the right favors. Was this a chance for him? Or just a cruel trick of fate.? But what ever he had in store .

He left the doctors office and walked over to the commutations center, as he entered the room came to attention. "I need this room for ten minuets" he said, with a collective nod they complied with his request.

He togged the controls and a Quarian face appeared on his screen "Get me Admiral Rael'Zorah and tell him that I want to call in that favor."

It took much longer that ten minuets for him to finish "Are you sure this is what you want Zaal, you do realize what could happen if this goes south?"

"In the same way that you know what will happen If your experiments go south" Zaal was not threatening the Admiral, after all he had helped at first until his wife managed to talk him out of it.

There was silence on the other end of the line for a long moment before the Admiral spoke again "You saved my family, so because of that I will do this for you, but be warned this is all I can do."

Zaal nodded what he had in mind was crazy anyway Rael sighed "Approved Zaal keelah se'lai"

"keelah se'lai and tell Tali I said hi" he answered back before turning off the comm link.

He had just put himself in the position for a world of hurt but some how he had not felt this happy since his wife died.

Doctor Shamo just stared at him in shock "Your going to adopt him?"

Zaal nodded "Yes I am."

"Why?"

Zaal smiled under his visor "Because I want to, because I have been given a chance and I'm going to take it."

The Doctor turned to look at the sleeping child and after a few heartbeats "I think I under stand." She turned back to him "How will you take care of him? You have a ship to run, paperwork to do and people to train. How do you plan on getting enough supplies to feed him, human bodies are not designed to "

Zaal shrugged sheepishly "I haven't thought that far ahead yet."

Doctor Shamo glared at him form under her visor "Shouldn't you?"

Zaal set down and finally thought about those important questions beyond how can I keep him, how to take care of him should have been top of the list.

After a few minuets an idea came to mind "During my pilgrimage, I met and saw many things, one of them was pulling a helping a scientists escape from pirates. Though one could note that they captured me as well and I was just escaping myself and dragged him along. As it turned out he was the son of the current CEO of Exogeni. Maybe I can call him up and see what he could do."

The Doctor stared at him "You were captured by pirates?"

Zaal shrugged "I was young and stupid and convinced of my own prowess, not the best frame of mind to be in at nineteen."

Shamo spoke again "Well that might work, however you are still missing something."

"And that would be?"

"A child like this will need a mother, and you will need the help as well."

Zaal was silent for a long moment "I, I sometimes thought about but I never, I never really considered that someone could ever replace her."

Shamo reached out a hand to touch his shoulder, "It been four years Zaal, she would want you to be happy." Her voice hardened "She would not want you charging in first through the breech with the other Marines, you are our Captain not a teen ten days away form pilgrimage."

Zaal turned his head away from her "I, I guess somewhere in my head I wanted to follow her, I wanted to be with her again so bad. But after the first year it became a habit, fighting head to head with boarders, taking on pirates. I earned the respect of my crew all the while I was just trying to get myself killed."

"Respect? Zaal'Garlarvas Defrahnz nar Epsilon, they love you, they are one and all willing to die for you. And in answer to you unspoken fears they will support you in what ever you do. Even this plan of yours, she leaned closer wrapping her arms around him and I will to if you will have me."

Zaal gaped at her thought you could not see it through his visor, but his mind restarted itself "But I'm teen hears older than you, and I will always still love her, could you stand that. Knowing I will always love someone else."

She smiled a clearly visible change under her visor, "You would not be the man I fell in love with if you told me any different. As long as you love me too I will be fine,"

Two weeks later they were married at a privet ceremony, though by prevent it meant the whole ship knew was were cheering for the new couple while pretending to be surprised when they were told.

Though they were truly surprised, no the better word is stunned when the couple introduced they son John Sheperd vas Defrahnz and his new life began.

Two Years Later

Zaal entered his quarters to find his son curled up in a corner reading as always, if he was not reading he was watching and copying the exercises of the Marines. Zaal truly wished his son would join the play of the other children, but as he suspected while the adults were more tolerant, the children did not want anything to do with the human. Zaal suspected there was some Jealousy on there part as Shepherd needed noenviro suit to live in. Had not his wife made sure through use of what she called a germ pod which exposed his son to the many things he would have been experiencing as a normal human child, he might have had some complications with his immune system.

His son, he never lost pride in saying that or thinking that, his son was amazing, in six months he had mastered the Quarian language, three months after that he mastered the reading and writing aspect. Zaal at first was ecstatic and proud of his son, he still was but he had failed to realize at the time what the reason for it was.

It was only after hearing first hand accounts of John's interactions with the other children of the ship that he realized its source. He was starved for attention, the other children had constantly teased and pranked him when he attempted to play with them. And after awhile he started finding solace in books. Zaal quickly found his library ever expanding filling with new books both Quarian and Human.

This had continued tell his sixth birthday, which was when his wife came up with the idea of having him interact with other adults. It was not the solution that would have been preferable but he was desperate for his son to experience kindness among his people.

The first true friend that John would call his own was the Sergeant of all people, Shamo had arranged for John to spend time with the Sarge calling in several of her own favors with the old man.

After several hours with John the Sarge had given her the favors right back and asked to have more time with the kid.

When Zaal had asked why Sarge gave him a straight answer "Because he listens and asks good questions."

The next sort of friend he made was with Gadget, the resident tech expert, the man was a bit eccentric but kind enough in his own way. And Shepherd was a good listener, the boy soaked up there stories like a sponge, always asking for more when they were done always with new questions.

He was a good Son to Zaal and Shamo it hat taken him a while but he had grown to love them as only children could. The thing that worried them about him was his aptitude towards trouble, with any thing that happened to him he never said a word. Only the fact that his wife was a Doctor allowed her to notice a slight limp which had turned out to be the result of oil on the stair case. When he had asked why he never said a word the boy had answered "Because I did not want to bother you."

Zaal felt real pain at those words, a child should not force himself to act like an adult but how could he tell his son that it was all right to share you burden with others? Because the words John had answered with had come out of his own mouth many times before.

As he looked at his son with a mixture of pride and sorrow, he happened to glance at the book he was reading "When did I buy him Sun Tzu's Art of war?"

Three Years Later

Zaal watched as John was flipped to the ground with a heavy thump, Sarge stood above him watching as the boy pulled himself back to his feet. "You need to use your own movement to create even more power, use the enemy's own power against him and add it to your own." Said the Sarge, there was iron in his tone as the spoke to the child. "If you really want to learn this than make sure I don't have to show you again, because you have a long way to go." His son nodded saying nothing.

"Now try again."

A droid that simulated an opponent roughly Johns own size and weight it rushed at his back and wrapped its arm around the boy's neck. Shepherd reacted like a coiled spring using his shoulder to push up, pushing his body forward using the power the droid had put behind the rush as power to completely flip the bot over his head and slam him into the mat.

Zaal noted that even Sarge seemed shocked that his son got it right on the first try.

The Captian mused on the past several years as he watched his son repeat his pervious feat. When he reached seven that ran out of books for him to read, so John had with the help of his wife taught himself the Asari dialect, he was almost good enough to listen in on a conversation in that tongue and understand it all.

Zaal and his wife were quite convinced they had a genius for a son and no one who spent time with the boy would tell them any different. To keep him form reading books all day they had upped his education. His wife homeschooled him in Math, Science, History, Medicine any thing she could to keep him occupied.

Gadget of all people took it upon himself to give John real world education and started to teach and show the boy the aspects of hacking, decrypting, repairing, repurposing, anything he was working on at the moment.

And if that was not enough John had grown board of just watching and copying the Marians exercises, so he took it upon himself to ask Sarge to teach him the Quarian Self Defense style. The Sarge had complied telling anyone who asked "The boy had earned that much."

There were two levels to the style of fighting the Quarians employed the first being Self Defense, it had no other name but was quite similar to Akido the human fighting art, its strength revolved around circular movement and using the enemies power against him. The second level was simply called Assault it was a more brutal style that focused on the fact that the user was armed and gun's cause more damage than fist's. The entire point of it was simply to get the users gun into action, any thing that would lead to this event was allowed in this art.

His son was though his hard work and kindness had gained the respect of most of the adults on his ship, even his marines which was no mean feat. The children while not welcoming him had grown tolerant of John an attitude that he seemed perfectly content with. Another good thing was the fact that his nightmare which had plagued the boy for years were dying down, the sharp edges of the memory dulling in time.

His wife grasped his arm drawing his attention away form his son's lesson, she seemed a bit uneasy watching Sarge throw their son around like that.

"Its all right" Zaal said "He will not hurt him that badly, he had been doing this for years."

"I know" Shamo said "But I don't like watching my baby get hurt."

Zaal completely sympathized with that emotion but said nothing, it's a guy thing.

"What will we do with him?" she asked "I have never seen such a bright mind, I can only shutter in wonder at the thought of him growing up like this."

Zaal hugged his wife close "We will think of something I'm sure of it."

Five Years later

Zaal stared at he board in front of him, it black and white pieces poised to smash against each other. Chess the human game was one of the few things nearly every race in the galaxy had picked up on when their kind emerged. It had so many uses in teaching minds to grow that even Batarian commandeers were required to learn the game, if only to know the mind of their human enemy better. The current galactic champion was an Asari Matriarch who had nearly fallen in love with the game. Her current mate was the second best a human who turned out to be the only one who could really challenge her any more.

Zaal himself had picked it up on his pilgrimage and had decide to teach it to his son.

He glanced at his now fourteen year old son a five foot thee inch tall boy with a body of whip cord and muscle. He had an intense expression on his face as he and moved a knight to a position that threatened Zaal's king. That sounded normal but John had used biotics to do so.

The boy had figured out he had the gift at around twelve, that's when Zaal had started to come home and find glowing coins and marbles floating around his room. At first he had been surprised then ecstatic, no Quarian alive had the power of biotics that would make his son valuable to the fleet.

That was his thoughts until his wife had called him for a privet talk, "We cannot tell anyone about this Zaal"

"Why not this is amazing is it not?"

"Yes thought you don't quite understand how, Zaal he has not amps implanted in him, I checked."

"So what does that have to do with anything?"

"Only the Asari have the ability to use biotics without amp's the fact that he is human and has that power is nothing short of amazing. It also explains his large appetite, and might have something to do with his insane immune system. Every virus I introduced into his body so that he could gain the antibodies needed was killed before it caused any symptoms. He had never been sick in his life, that even for humans in nothing short of amazing."

His wife stared at him fear conveyed in body "If any body figures that out, he would become a target, by any number of races and organizations."

With that in mind Zaal had made sure to have his son keep his abilities out of sight, though John practiced his power with the same energy he did everything else. And as evidenced by his ability to move the chess piece with out disturbing the others his control was growing.

In terms of his studies, John was finished he had passed all the exams required never scoring less that an ninety nine. Through sheer willpower and hard work he had become quite fluent in Asari dialect. A visiting Asari who had passed through fleet had commented that he was almost as good as an Asari himself. That had only spurred him to try and make himself as good as an Asari, a strange goal for a human raised by Quarians but the boy was always trying to be different, different and better.

As for his social life one an all every adult on this ship licked him or at least respected him. He had proved himself second only to Gadget in tech, something the Quarian race as a whole respected. He now not only trained with the Sarge, but also the Marines of the Epsilon who all enjoyed his company respecting his tenacity and willpower, hell many were impressed at how in a short amount of time he managed to become a decent shot with the assault rifle.

The Quarian Children now in their teens were finally staring to interact with John though now it was far to late for this son to develop any sort of real friendship with them, he was simply too mature. But at the very least there was some warmth between his son and the others.

His son's voice brought him back to the real world "Its you move dad" Zaal nodded and stared down at his sons move. Studying it for a moment, considering what it ment.

"Why did you make that move? If you had put the pawn up one space instead the game would have been yours."

His son answered easily "Yes I could of, but that pawn would have been lost, I don't like sacrifices."

Zaal nodded gravely; "But sometimes it takes sacrifices to win, now we will have a much longer game in which more pieces will be lost."

Shepherd paused for a moment: "That is why I will never be a good chess player, I would much rather be one of the pieces."

Zaal curious asked, "Which one?"

"The knight"

"Why?"

"Because it is the only piece not bound by limits, it moves where ever it wills no matter where it is. If it is surrounded it goes over, if it attacks it attacks in a manner outside the box. And it protects the other more important pieces."

Zaal contemplated that as the game stretched on long in to the night.

Two Years later

Zaal watched as his son received a simple iron medal from Sarge, there was not ceremony to it, one day the Sarge had come into the training room where Shepherd waited and handed him it saying "I have noting left to teach you, and I appoint you a Master of Self Defense and Assault." Then the Sarge nodded at the boy and said now all that's left for me to do is watch you and the other young Marians duke it out and point out all your flaws as loudly as I can."

Shepherd laughed at that saying " Sir I am still willing to listen to your stories."

Zaal could have sworn that the Sarge chocked up at the but passed it off as an optical illusion created by the man's visor.

Words could not begin to describe what his son had accomplished in the past two years, at Sixteen he was a master of Self Defense and Assault, he was the best tech expert this ship had, Gadget giving him that title after Shepherd had out hacked him a cyber duel that lasted five hours. His biotics were growing stronger and more controlled thought it was getting harder and harder for him to keep it hidden. He was finally on friendly terms with the other people his age, as they had finally learned what the adults know since he was a boy. He was a good listener and a better advisor that most would give him credit for.

The Marines even the new ones were all to the point were they considered themselves surrogate older brothers to Shepherd, his marksmanship was almost to the level of the Marines themselves and they worked all the time to help him get better, showing him the tricks they had pick up over the years on how to get the most out of their weapons and armor.

Zaal could now say he had a fully functional and diverse library on his ship, having made use of a store room to house his collection.

And best of all his son's nightmares were gone for the most part, no longer did he wake up screaming in the middle of night.

Zaal considered the fact that his son would be old enough for pilgrimage in two years, the though frightened and elated him, his son was amazing at every thing he did, what he could do on his pilgrimage well if it was anything like life so far it would be incredible.

And the final change in his son was the smile, his son had began to smile more often Zaal was pleased every time he came home to find his home empty of his son, not that he wanted his son gone it just meant the boy was not reading in a corner hiding from the world.

So as Zaal watched his smiling son move through one of Self Defense and Assault's eight main forms he thanked the God that watched over the universe that he had allowed him the best son a farther could hope for.

But alas the ways of the universe, pride, cruelty, vengeance and hate one could never truly avoid them forever. And this is were we truly start the story, the story of John Shepherd vas Defrahnz the future hero of the galaxy. And this tale starts just like in prologue with tragedy.