Episode 1: Hidden Command
Colonel John Sheppard was extremely nervous. He had woken up that morning relaxed and ready for what was coming but now he was in a deep panic. Today was the day that Atlantis would be inspected and scrutinized to decide if it was ready for duty. Since Richard Woolsey had left Atlantis, Colonel Sheppard had been left in charge, which he was particularly good at. But today, for the first time in a very long time, he was nervous. If this inspection went wrong, Atlantis would be taken over by the IOA with the rest of Atlantis booted back to the SGC. This was not a day to make any mistakes.
Sheppard watched out over the beautiful ocean as the waves slowly followed the currents of the water. It was beautiful, almost as beautiful as the seas in the Pegasus galaxy were. Atlantis had been almost immediately moved away from where it had originally landed on Earth to a new location where it would not be found: somewhere in the Pacific Ocean. It meant Atlantis was rarely disturbed, although occasionally it was. On one occasion, a small fishing ship had arrived near the station and the Colonel had been left battling to active the ship cloak so that it would not be found.
The moment of peace Sheppard was enjoying was immediately interfered by Chuck (the gate controller) as he called the Colonel to the gate room. "The guests have arrived, sir." Chuck told the Colonel over the radio. Sheppard reacted as soon as he heard this; he was sprinting down the Atlantis corridors to get to the gate room as fast as he could.
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General Paul Clark and Dr Liam Johnson stood in the gate room with Chuck, waiting for Colonel Sheppard to arrive. The pair had been given the job of evaluating Atlantis, much to their disliking. General Clark and Dr Johnson were good people and so didn't enjoy pointing at the problems with everything but when a job called, the pair would follow the description. And evaluating Atlantis for the IOA clearly had the description of pointing out everything wrong with what the Colonel was doing. They stood straight, ready to confront the Colonel. Minutes past and the Colonel still hadn't arrived, much to Chuck's disliking. He already had the feeling that this evaluation wasn't going so well.
When the Colonel finally arrived, Chuck to the excuse of dismissing himself. Colonel Sheppard was extremely pleased to discover that his inspectors would be General Clark and Dr Johnson; he had encountered the pair before. In fact, he had even served on a couple of missions with them whilst Atlantis had been on Earth (and Woolsey had been in charge). The General and the Colonel had always got on very well which meant that a great weight had now been lifted off of the Colonel's shoulders. Everything was going to be okay, wasn't it?
"Colonel Sheppard, how are you?" Asked the General. He seemed very pleased to see Sheppard today.
"Very good, thanks, sir." The Colonel replied in a very unenthusiastic way. As much as Sheppard like General Clark, he didn't want to have this 'stupid' inspection or evaluation as the IOA called it.
"You don't seem pleased to see us, sir." Dr Johnson said, with a large smile spread across his face. The Dr's smile was contagious and soon the Colonel also found himself smiling.
"Any way, to the evaluation..." begin the General, "I need to meet your staff before I do anything else. Do you mind introducing us to them?" The Colonel's face lit up when the General said this; the others could deal with this evaluation now...
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Dr Rodney McKay was worried. His experiment had gone completely wrong and now he had accidentally knocked out Dr Zelenka because of it. He sat by the Dr, shaking him viciously with the hopes of waking him up. "For flip sake," he began, "get up. It was just an accident." When Zelenka did not respond, he suddenly felt terrified. What if Zelenka was dead? What would happen to Rodney? McKay was showered in relied when Zelenka slowly lifted his body off of the ground and looked at him.
"What did you do?" Zelenka asked. McKay didn't want to answer, which resulted in a moment of silence. This silence was interfered by Zelenka swearing in his Czech Republican language. "What did you do?" Zelenka asked again.
"I stunned you, that's all. Unless you were pregnant, the stun will have had no physical affect on your body at all." Rodney informed the Doctor. Zelenka was still not that sure on Rodney's explanation.
"You thought that you'd killed me, didn't you?" This was less of a question and more of a statement. "Didn't you Rodney?" Zelenka was desperate for Dr McKay to respond to him.
The conversation between the pair halted immediately when General Clark and Dr Johnson entered the room, closely followed by Colonel Sheppard. General Clark smiled as he went to shake Dr McKay's hand.
"Hi, I'm General Clark." The General told him. Dr McKay did not seem amused.
"Yes, I know who you are." Rodney said, pretending to be bored. He hated inspections and hated being disturbed. The General was both inspecting him and disturbing him at the same time, which left the McKay feeling mad. McKay unhappily accepted the hand shake from the General but did not do so without showing how annoyed he was. Dr Zelenka was more positive about seeing the General and Dr Johnson.
"Sir, it's an honor to meet you." Zelenka said with a cheeky grin on his face. He wanted to make a good impression. He wanted to make a better impression than Rodney, anyway.
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Teyla Emmagan and Ronon Dex were sparing. Both of them were skilled fighters which meant that these sparing sessions usually went on for hours on end. They had already been fighting for one hour. Ronon, being a man, was more talented with using his strength but Teyla was far more skilled with her fighting skills. This made both of them an even match in ability. The battle had began with Teyla giving Ronon a strike to the head. This was no normal strike to the head: it was bad enough to knock out most humans. This had affected Ronon's fighting ability slightly but a few strikes to Teyla's waste had made the fight even again.
Now the pair were both tired and injured. They both knew that they would need to go to the medical wing after this but that fact did not stop them from fighting like they had taken no damage. The fought strongly, and as a result stained the room around them with their blood. Ronon took a lucky strike at Teyla, hitting her in the ankle and tripping her over. She screamed in pain as she crashed to the floor.
"I win." Ronon said, simply. A big smile was spread across his bloody face, even though he was going through immense pain. Winning was extremely important for Ronon; even if it made him feel terrible.
The two were disturbed when General Clark and Dr Johnson entered the room. They seemed to both look annoyed, which made Teyla think that they had already talked to Rodney. She lifted herself onto her feat, ignoring the pain in her ankle, and slowly approached the General. He smiled as he shook her hand; she was allot more positive than Dr McKay had been. Ronon was less positive however. Like McKay, Ronon hated being disturbed unless it was somebody telling him that he was needed to go and kill some Wraith. After some massive encouragement from Teyla, Ronon reluctantly talked to the General. Ronon had known that this would happen today but he had not expected it to be so boring.
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Dr Rodney McKay sat alone in the cafeteria when Ronon and Teyla entered the room. Both of them looked bored out of their minds which suggested to McKay that they had already been evaluated. He watched as they took up their trays and joined him on his table. McKay's usual look of arrogance stretched across his face. "So I guess you had General So-and-so scrutinizing you?" McKay asked the pair. Ronon and Teyla looked at each other before Teyla decided to talk. Her voice was firm and showed that she was not in the mood to be messed about with.
"Yes, we did. I didn't find the men to bad to talk to but the questions were... tiring." It was clear that she didn't want to talk about it but Rodney couldn't pick up her hints.
"They dropped in just after I'd stunned Radek, lucky me! And guess what, they liked him more! Can you believe that?" It was clear that McKay had been desperate to get this out of his system.
"I don't like them." Ronon said, simply. He wasn't joking, he was just being blunt.
"No, I like them, I just found them extremely annoying." Teyla told Ronon, in a way which sounded like she was correcting him. There was a moment of silence again before Ronon talked.
"I don't like them." And with that, Ronon tucked into his food.
The group sat at the table for half an hour, eating the food which sat on their trays. Ronon was finished first; he ate like a wolf which had been deprived of food for the last five years. When he was done, he simply got up and left. That was when McKay noticed how many injuries Ronon had. McKay looked at Teyla before he asked:
"You been fighting?" Teyla gave McKay an evil stare and so Rodney backed down. She was clearly quite annoyed which meant that when she got up to leave, Rodney felt a bit relieved. Limping away, Teyla vanished from the room, leaving Rodney alone once more. Still hungry, Rodney launched himself to his feat and grabbed himself a new tray of food. "Much better, some piece and quiet." He told himself. Really, he wanted the company but he wasn't very good at showing this. He liked having friends... But he didn't like having friends when they had just been scrutinized by inspectors.
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Far away, in the Pegasus galaxy, a fleet of massive space ships sat calmly in the middle of the sky. They were gold and bronze; standing like the strongest statues that had ever been made. At first, they were alone, but after time, a new space ship appeared. It was scrap, covered in green and brown, and looked like the sort of thing you would find in a junk yard. The junk ship stopped when it met the other better designed ones and tried to hail it. This resulted in a warning shot from the gold and bronze ships. This other ship wasn't going anywhere near these good ones... Everything was tense, like a fight could start out at any moment.
Inside one of the gold and bronze ship, the Thorne commanders sat ready for war. The Thorne were massive, the size of two men put together, and were a dark brown. Big teeth sat in their mouths and their eyes shone out like the night sky. Each Thorne wore metal Armour, like the sort a knight would wear, but instead the Armour was gold. The Thorne leader, Quantec, sat at the head of the table; preparing to talk to his fellow commanders. He looked firm, ready for war. "Can you confirm that the ship approaching us belongs to the Genii?" Quantec asked his fellow commanders. One of the smaller, weaker commanders looked at a computer panel before he turned back to face Quantec.
"Yes, it is the Genii." The commander told Quantec.
"Good. You are to send them a message," he began, "telling them that their development in our space has drove us to the brink of war. If they do not back down, we will have to execute them all!" The commander did exactly as Quantec asked.
Minutes later, the computer screen started flashing red. The weak commander stormed towards the screen to find that a new message had been sent by the Genii. WE WILL NOT BACK DOWN. That was what the Genii had told them. And so the Thorne ships began fire on the Genii ship, taking down the ship's shield and eventually destroying it. As the scrap pieces of the Genii ship scattered into deep space, the Thorne prepared for their plan to destroy the Genii once and for all. It involved a city, a city which had vanished years ago, it involved Atlantis...
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Colonel John Sheppard, General Paul Clark and Doctor Liam Johnson were striding down the left wing of Atlantis when the Colonel got a radio call from Chuck. Chuck was clearly in a panic so the Colonel took it upon himself to go and see him. Leaving General Clark and Dr Johnson with Rodney McKay, Colonel Sheppard went to see the gate watcher.
When Sheppard finally reached the gate room, he found Chuck disturbed and nervous. He had clearly been shaking out of fear and it appeared that he had been nervous for quite a while. "Chuck, what's up?" The Colonel asked him. Chuck simply showed the Colonel his laptop screen for Sheppard to understand. The laptop was telling them that 1000 miles away sat a massive space ship. It also sat in the sea, but instead of being in the middle of it, it was right next to the shore. "How long's it been there for?" Colonel Sheppard asked Chuck.
"Ten minutes," Chuck began, "it's already made itself into the news. The Air force is telling them that the ship is one of theirs but they've already messaged me to say that it isn't." Colonel Sheppard turned to leave but stopped last minute, turning to look at Chuck.
"I can't leave, I've got visitors," declared the Colonel, "get Major Lorne to assemble a team."
Colonel Sheppard was now running. He had left the inspectors waiting for far too long and he needed them to continue the inspection so that it would finish in time for him to be able to get rid of this strange space ship 1000 miles away. When he finally caught up with the General, he apologized for being late and told them the situation. Not to worried any more, the Colonel, the General and the Dr continued the inspection.
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Major Lorne had assembled his team and they were now approaching the ship in a cloaked Puddle Jumper. He had bought with him Dr Zelenka, Lieutenant Jessica Haywood and Sergeant William Greel. They were all in the traditional Atlantis battle uniform and all held small P90's. They didn't know what to expect as they approached the ship but knew that being careful was the best option. "Zelenka, where's the best place to park the jumper without being detected?" Lorne asked the Doctor. Lorne was the only one who could fly the Puddle Jumper in his team as he was the only person who had the Ancient gene.
"I would say that parking the Puddle Jumper on top of the ship would decrease the chances of being picked up by any of the ships scanners. I would think they wouldn't be expecting that." Zelenka told the Major.
"Okay, I'll park the Jumper on the roof." The Major said.
When Major Lorne finally parked the Jumper, the team explored the roof of the ship; looking for an entrance. Just when they were about to give up hope of finding it, they checked under a random metal panel and found it. Lowering themselves through the entrance, they found themselves in a large golden corridor. It looked very similar to the corridors you would find in a Goa'uld ship. Slowly the team delved deeper into the ship yet they still hadn't come across any aliens yet. A panel on one of the doors confirmed the name of the aliens who owned this ship: the Thorne. They must have been massive because the corridors were! It was just strange that there was no Thorne in this ship.
After a long time of exploration, Zelenka was able to find signs of technology... but he didn't like what he saw. He saw a picture of Atlantis being sent to another Thorne ship! Zelenka began to study the picture and the more he found out, the more disturbed he became. This Thorne ship had been sent to the sea to take control of Atlantis and now the control was being passed onto a more powerful ship! The Thorne had to be stopped before it was too late... If they got away with this, Atlantis could be used as a weapon against the Earth.
Zelenka told the Major about this and the team launched themselves towards the Puddle Jumper. Once inside, the Major flew the Puddle Jumper blast distance away from the Thorne ship. They then began to litter the ship with massive drones. The drones dropped like rocks in water; they had a massive amount of success when they hit the ship. The ship was launched into the sky and engulfed in flames. People who stood by the shore were shocked by the sight and terrified as well. They had been told that this ship was an air force ship so they were convinced that this ship had been destroyed by a terrorist attack. The Air force did nothing to change this view.
Major Lorne was too late, any way... The control of Atlantis had already been handed to a much more powerful ship in the Pegasus galaxy. There was nothing that Major Lorne and his team could do about, Atlantis was out of his control!
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General Clark was shocked when Atlantis began its flight. Everybody was shocked when Atlantis began its flight. Dr McKay said that some unknown force was dragging Atlantis into the sky and their was nothing that him or anybody could do about it. As Atlantis left the Earth, everybody realized that there was no solution. There was no way to fight this, there was no way to survive. This was the end, for everybody.
Atlantis left the beautiful ocean which had surrounded it with a burst of bright light and powerful energy, resulting in the sea being slightly unsettled. The waves which crashed into the shore that day were bigger than what had been expected. The news said that this was a sign of change, and it definitely was for everyone.
To Be Continued...