Title: Return Of The Phoenix: Beginnings

Series: Atlantis: The New Order

Summary: A Little Girl who had been prophesised… A City with a hidden past… The Return Of An Ancient Race… A Family who will battle the odds in the hope of normalcy… The Fight Begins…

Genre(s): Action/Adventure; Hurt/Comfort; Future Fic; Angst; Drama;

Warnings: Violence; Character Death;

Disclaimer: SGA is not mine, and neither are Sheppard, Weir or the rest of the team. I do own any original characters though, and i'm only playing in Robert Cooper and Brad Wright's Sandbox. So this is all for fun :)

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Author's Note: Okay, this is a re-post of this story, after suffering MAJOR writer's block and losing the chapters i've already written, i've just found them and so i'm going to slowly post the chapters i have and hopefully, i can get some more of the story done- i hand wrote up to chapter ten but i've changed my idea slightly for the plot and so i'm going wherever the story may take me. This was written pre- season three so i'm going with that, so sorry if your looking for Sam Carter as the Atlantis Team Leader- and look out for an old nemesis coming back seemingly from the dead much later in the story...

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Chapter One: Punishment

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"Elizabeth, your pregnant."

Carson Beckett's word's echoed in Elizabeth's mind as she watched John Sheppard's dirt covered shirt being ripped off of him as he was held tightly by the arms as the two men holding him thrust his arms up into shackles above his head as he involuntarily yelped as his right shoulder was dislocated as the guard pulled his arm- John making a futile attempt to resist- A large man came up behind him, holding a cat-o-nine tails, patting the faded whip which had small metal balls on the end of each piece of leather.

Elizabeth's punishment was to watch him suffer because of their failed attempt to escape the prison planet- The two Atlantean leaders had been taken from a mission almost three weeks ago and just a few days before John had put his escape plan into action; They had almost made it to the gate. Almost- when they had been caught. They had been put in a prison cell after giving John a beating when he tried to fight back at the gate but now it was time for both of their punishments.

As Elizabeth was held firmly, a tall dark haired woman dressed solely in Black came to watch. Her name was Beta; An Avatar of immense power, Beta had been known to use her powers to torture a person by using their worst fears against them. Elizabeth watched as she calmly strode around the wooden structure that John was bound to- still standing- before coming to stand in front of him, her back to the crowd as she wrenched John's head back by his dirt covered hair and whispered something in his ear before roughly releasing him and turning back to the crowd who encircled the area.

"This is the punishment for all those who attempt escape and fail- Now this human man who has been so resilient to our preventions will pay the price for both he and his fellow escapee, whose punishment is to watch the man she loves suffer for both of their foolishness… let us see how much fight he has left once his punishment has been given."

The crowd murmured as Beta left the crowded arena- even though Elizabeth knew she would probably be watching- as John and one of the guards standing near him challenged each other as Elizabeth felt hot tears on her cheeks as they escaped involuntarily as the larger man raised the whip high before bringing it down on John's back which caught John unawares as he let out a yell in pain; His legs giving away beneath him at the shock of the metal balls ripping into his flesh.

The large man took his time delivering the blows knowing that it would prolong the prisoners pain.

As John tried to catch his breath, he stole a quick glance at Elizabeth, whose pale face was becoming more tear stained every moment. His face and torso were covered in a thin layer of sweat as his back felt increasingly wet as blood ran down through his pants and to the dirt. As John fought his pain, he gave Elizabeth- who was in the front row of the crowd- a weak attempt at a smile. As his glazed Blue-Grey eyes made contact with her hazel coloured, he silently told her "I love you," As he mouthed those words, the large man lifted the whip over his head. Johnwas unprepared for the blow which caused him to yell once more as the lashed criss crossed his back as more blood seeped from the now deep lashes left by the blood stained metal balls and staind leather of the whips.

"I love you, too," Elizabeth whispered as more blows caused John to grunt in pain- mostly on his back but at least one slashed his front which caused the soldier so much pain that he passed out as his right shoulder began to bleed as one slash went so deep as to reveal his collar bone.

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It was early evening by the time the punishment was completed. After a while of the feared cat-o-nine tails, the whip had been switched with and ordinary one used on animals but John remained in a pattern of passing out after every few blows and had to be startled awake by buckets of ice-cold water being splashed over him.

When his arms were released from the shackles, John collapsed in a heap in the dirt as Elizabeth rushed over to him and turned the injured man over which caused John to whimper as she placed his head on her lap as she cried openly as the crowd dissolved until there was only a trickle of people, mostly guards, and kissed his forehead reverently as John lay with his right arm across his stomach as he whimpered from the dirt entering his mass of wounds on his back as well as his dislocated shoulder and revealed collar bone.

"Oh, God…John… I'm so sorry…" Elizabeth cried as Beta approached the couple with the cover of four members of her personal guard. Elizabeth looked up to them as John now lay unconscious on the dirt ground, with his damp head on Elizabeth's lap.

As they stopped, Beta turned to one of the guards around John and Elizabeth and spoke tonelessly, "Dial the Atlantis Stargate,"

Elizabeth looked up, and sniffed. "What?"

"The Colonel is to be returned home- he is of no use to me or my people any longer so he will return to your world where he may or may not recover; It depends on how good your doctors are."

Elizabeth gripped John's limp hand in hers and swallowed. "And what about me?"

"I am afraid you must stay a little longer but you shall not be harmed; you have a few moments to say goodbye to him before he returns to the city of your ancestors."

Beta nodded to two of her guards as she turned and stalked back to her mansion which was situated at the edge of the encampment- the two guards remaining to take John away.

Elizabeth sniffed and brushed her hand through his damp hair as she spoke to him in a quiet voice, "John… I love you… Please, don't give up… Just hold on and Carson will make everything right… I'll see you soon…"

"'Lizabeth…" John murmured weakly as he attempted faintly to grip her hand in return as he swallowed, opening his eyes open slightly. "'give me… Love you..."

"There is nothing for you to be sorry for," Elizabeth replied, trying to put as much strength behind her words as possible, as the guards came over and bent down to grab John's arms, pulling the Lt. Colonel upright which caused him to yelp and pass out as the combined pain became unbearable, releasing Elizabeth's hand as two more guards who had been standing nearby came to hold her back as she fought to get to John as the two guards roughly dragged him to the gate.

"No," she cried. "John, No!!"

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The two guards dragged John's unconscious and broken form to the now active Stargate. One guards forcing John's limp fingers to put in his IDC Code that would lower the Atlantis shield, before going up to steps and shoving the injured man through to the ancient city and to a shocked gate room….