Disclaimer: I do not own the Stargate franchise. Wish I did, cause then SGA would still be running! I do this for pure entertainment value and seek no monetary compensation, borrowing from the series because it still is my fave show!

Summary: Sheppard is having nightmares and second guessing his actions.

IT WAS

(Sheppard grasped the controls so tight his hands hurt as he mentally begged the jumper to go faster. But it seemed the faster he willed the flying ship to go, the slower it felt like it was going. Frustration caused beads of sweat to form on his brow. He afforded a quick swipe of his jacketed arm to wipe the annoying dampness from his forehead. The damp dark hair that was swept out of his eyes still managed to defy gravity.

The remnants of a village came into view. Smoke and fire dominated most of the buildings that had once been a thriving community. John's heart fell. He was too late.

He landed the jumper in a clearing near the edge of the village. The jumper hatch was barely down as he set off, jumping off the end of the still descending hatch. The hopes of finding survivors was unlikely, but that didn't dampen the urgency pounding in his veins.

Exiting the jumper at a full run, John pushed himself further into an all out sprint. Skidding to a halt next to the first emaciated corpse he encountered, he crouched down and shook his head in sadness. Dying by a Wraith feeding was a terrifyingly horrible death.

He heard sounds from further into the village. Raising his P90 to the ready position, he set off, more cautiously. It wasn't like the Wraith to hang around wreaking havoc after a culling, they had more of a "snatch and go" Modus Operandi. As he got closer, the sounds were more discernible. The moans and cries of many suffering humans filled the air.

He stayed close to the wall of a building, peeking around the corner to evaluate the situation. He was surprised to see a squadron of his men, all kneeling and tending to the half-fed-on villagers.

(Where did his men come from? He had come alone...how were they here?!)

The sight was like a vision from hell. Burning buildings, smoke thick and swirling in the acrid breeze and the bodies. Oh God! The bodies! There were so many! No one had been spared...and here, in the center of town, no one had been fed upon completely. The damned Wraith had left them-barely hanging onto what life they had left. The cries and pleas were deafening.

(But why would the Wraith do that?!)

John made his way forward, in a daze. Looking at everything, but seeing nothing. Each of the dying villagers struggled to hold their frail, skeletal-boned arms out towards him as he passed. Their eyes pleading for mercy. He became aware of the silence then. All eyes were on him. His men's...as well as each of the decimated-but still alive villagers.

(How were they still alive?!).

He stopped and suddenly Ford appeared at his side.

"What should we do, sir?! These people cannot be saved, they are too far gone! What do you want us to do?!" John looked around, stunned. Stunned and sickened. There were dying children among those ravaged.

(Why? The Wraith had always left the children alone before...as future stock!)

He became aware of the deafening sounds now. The pleas of the dying made him cringe. The sight his eyes took in, made his muscles tense so tight he couldn't move. Chaos incarnate.

"Sir! What would you have us do?!" Ford's desperate need for an answer barely registered with his commanding officer. "Sir, the men are willing to end the adults sufferings, but as commanding officer, I'm sorry to say that the lives of the children lay in your hands. The men refuse to take the life of any child, despite it being merciful."

Major John Sheppard came out of his fugue then. He understood. Well aware of what he needed to do. He swallowed hard and gave the order for his men to mercifully end the suffering of the adults. His men seemed rooted to their spots...no one moved...all eyes were on him.

He swallowed hard as he unclipped his P90 and walked slowly to the nearest child. Her sunken eyes begged for mercy or pleaded for help. He couldn't tell. Her skeletal arms reached out to him. Tears streamed down his face as he raised his rifle.)

John gasped as he fell off the bed. He couldn't breathe. Life-saving air couldn't get passed his spasming lungs. He felt sick, nauseous as he raced for the bathroom. Barely making it in time before he lost whatever was left in his stomach. Dry heaves followed.

Exhausted from being sick, John slumped against the bathroom wall next to the toilet. His limbs felt like lead and he was covered in sweat. He sat there, shaking. Too tired to move even an inch. Still too shaken to think about the nightmare. This was the fifth night he had woken from a nightmare, escalating from his revisiting the mercy killing of Colonel Sumner to this latest-a horrific culling with more pleading eyes begging for an end to their suffering. He shuddered with how real it had felt, the impossible decisions he was faced to make.

As reality slowly set in, his heart rate returned to normal. The sweat dried on his skin, but much had soaked into his Tshirt causing it to stick to his back and chest. The first night he had remained sitting in the very spot he now occupied, shaken and sick from the reality of that nightmare. Shivering in his sweat-slicked bedclothes, he had been unable to muster enough energy to move at all, until his alarm clock blared unrelentingly when morning came.

He knew a nice hot shower would do him good. The previous four nights' experiences had proven that. Luckily the shower activated by using the ATA gene. By the time he finally got moving, the room was steaming up, which reminded him of the smoke in the village. He shuddered and forced that thought from his head.

Once inside the shower, John slumped against the shower wall, letting the hot water cascade over him, refusing to let any thoughts through as he numbly stood there. He wasn't sure how long he stayed like that but the pruning of his fingers told him it had been quite a while. He shampooed his hair and washed quickly.

Dried and in fresh Tshirt and sweatpants, he decided to get some fresh air and made his way to the east pier. It was early, only near three in the morning so it was quiet, the only sound was that of the ocean waves lapping again the base structure. He stood staring out over the moonlit ocean.

It had been just four weeks since he had inadvertently sat in that very special chair, which ultimately decided his fate and changed his life forever. He still hadn't come to terms with where he was.

Another galaxy, in the lost legendary city of Atlantis. Atlantis! It was absolutely amazing! Stepping through the Stargate had been like stepping into his home, after being gone for a long time. It amazed him at how he had instantly felt at home here, like the city had been waiting for his arrival. Crazy thoughts, he knew he wasnt that special, despite supposedly having the strongest ATA gene found yet. But... he had been happy for a second chance.

That Dr Weir had insisted he accept the transfer to her expedition had not been lost on him. Oh, she had given him a choice, but what choice did he really have. McMurdo wasn't too bad,as far as he was concerned. He kind of liked the isolation, but the black mark on his record would haunt his every day, his chances for advancement long gone.

Coming here hadnt been too hard of a decision. Despite the fact that he may never be able to return to Earth, he really didnt have any real ties holding him back. His thinking was that maybe with this gene thing, things might be a little different. He hadn't really known what to expect. He certainly hadn't expected what they had faced so far!

So he had taken the turn of fate, hoping for a new start. Only...Colonel Sumner knew his record contained the black mark. Waiting at the Stargate, Sumner had made that point clear. John had decided at that moment that he would be the best soldier he could and change Sumner's pre-conceived notions about him. He never got the chance.

John cursed outloud. To no one in particular.

Nothing...nothing...changed his life more than going on that rescue mission. Not even coming to this galaxy-to Atlantis. That one second had changed everything. Pulling the trigger to end the life of his commanding officer filled him with guilt and a fair amount of doubt. He hadnt had time to weigh the options. It all happened so fast. Colonel Sumner had obvioisly been beyond saving. The life physically and literally sucked from him by the Wraith Queen left the dried husk of the man, alive only enough to lock eyes with him. He knew instantly what the Colonel wanted, there was no other choice. John knew he had done the only thing he could have but still he wasn't able to come to terms with what he had done.

He stood on the east pier watching his CO. Finding the Major here meant he wasnt the only one who had found this spot seeking solace. The Major's stance showcased the weariness and uncertainty that was hidden behind the stoic soldier persona. He was uncertain whether to approach the solitary man or leave him to his ponderings.

Something made him move forward. He was pretty sure what had brought the man from his sleep. He was sure that if he himself was suffering nightmares, then the Major most definitely was, in spades. The rescue had been deemed successful, bringing back all but two. He was sure the Major felt differently.

The loss of Colonel Sumner was shocking in itself. The man was an accomplished, well-respected leader that had been lost during their very first mission to their very first alien planet. He had seen the decimated corspe that had been his commanding officer. Shock and grief gave way to fear that he may face the same kind of death one day. The thought made him shudder.

He knew it took extraordinary courage to do what the Major had done. Not many men could have pulled the trigger. He knew instantly after seeing the Colonel's body that Major Sheppard had done the most merciful, humane thing possible and he respected the man for having the guts to go through with it.

Lt Aidan Ford decided to ease his own troubled mind as well as the new commander, who had earned his respect by taking the first tentative step out onto the pier.

Though lost in thought, the soldier in him was always alert, Major John Sheppard turned halfway.

"Having trouble sleeping, Lieutenant?"

"No more than you, sir."

The Major turned back to gaze at the open water. Ford joined him at the rail.

"Beautiful, isnt it? So much like Earth."

Yeah...except its not. Earth may have its share of scary bastards, but they have nothing on life-sucking aliens."

"Ain't that the truth, Lieutenant." Sheppard sighed with a sarcastic chuckle.

"What you did, sir?...it was the right thing to do."

"I dont know, Lieutenant. It felt...like the only thing I could do. Now, I'm not so sure." He found a loose piece of rubble, picked it up and flung it as hard as he could, out to sea. Both men watched the trajectory and splash.

Ford didnt know what to say, nothing seemed adequate. But he felt he needed to say...something. So he kept it simple.

"It was the right thing to do, sir."

Lieutenant Ford took his leave then, but not before he turned to his new CO and gave him the best salute he could.

Major Sheppard gave the soldier a slight smile. His eyes followed the soldier's retreat. His thoughts turned back towards the doubts he had harbored, seeking any other solutions. Not finding one, he turned back to gaze at the moonlit ocean, finally coming to terms with what he had done.

"Yeah...it was."

Fin.

Forgive me as I have tried many things to use italics, which was needed for the nightmare sequence, but I have not been able to figure out how to do it on only part of the story. I put the nightmare section in paratheses to differentiate it. Hope it wasnt too confusing!