Episode Tag: Ghost in the Machine
Several Months Later:
He still couldn't sleep. Despite countless hours alone in his quarters, or running through the city, or even on "their" balcony, the pursuit of dreams always eluded him. It seemed as if his mind would not shut off for more than the required amount of time to repair his body, which wasn't much these days. Thoughts of the past year, indeed the past five years ran through his mind at lightning speed, only slowing fractionally when she appeared, as if taunting him. His emotions, while still hidden to the vast majority of the city's inhabitants, ran just below the surface, threatening to erupt fully in every situation that arose. He had cut back on his off-world missions, finished all his backlogged paperwork, even taken on some science projects that had McKay speechless with his ability. Nothing worked, for she remained, like some permanent bastion in his thoughts, refusing to even mention the possibility of leaving. He only had himself to blame.
It all started coming back from a planet that really could have been Oz, flying monkeys and all. Their jumper hadn't sustained any damage and the planet looked suitable to be an Alpha site, not to mention the tourism that would come from said flying monkeys. Unbelievably, they had completed a routine reconnaissance mission without a run-in with Wraith, Asurans, or Genii. He knew it was too good to last. On their final approach to the spacegate, McKay detected an energy spike that changed to an energy surge, that shut down the jumper, only miles from the gate. With the autopilot shutdown, and the controls unresponsive, the jumper had drifted slightly off course and instead of flying smoothly through the gate, it veered slightly and hit it. Then it got worse.
Everyone came back in one piece, and even the jumper was unharmed, but faulty. The real incident occurred when random power spikes began happening throughout the city, culminating in everything shutting down except for McKay's laptop. He knew then that whatever was about to happen, would not be a good thing, and more than likely, cause someone close to him pain and suffering. Fate, it seems, is not without a sense of irony. One entity, for that is what had effected the operation of the jumper, and now Atlantis, tried to contact them. Countless billions lived in some form within the Pegasus Galaxy, and it had to be her. One single name that was his brightest hope, and his worst nightmare, the living bane of his recent existence.
Elizabeth Weir
She had finally come back to her city, the city she loved and was loved from in return. Thus began a series of events that would lead to her once again proving who she really was, sacrificing herself for the good of the Atlantis Expedition. It was at that moment, seconds before she readily walked to her own death, that she looked back. She did not speak, did not gesture in any way, shape or form, yet her message crossed the distance between her and one other instantaneously. It was a message of repressed affection, love, longing, and the final goodbye of the knowingly departed. It was a message from Elizabeth Weir to John Sheppard.
Since that moment had confirmed what he had suspected and amplified his own feelings, he had been haunted by the possibilities that might have occurred. It started simply enough, a small amount of sleep lost here, an extra vigorous run there, until he was barely able to function in his role as military commander-in-chief. He was thankful, those days he spared a thought to comprehend it, that Major Lorne had taken up the slack without much hassle, proving once again that Atlantis was closer to a large family than a military outpost. It made his plans concerning the future that much easier.
While he was affected by the lack of sleep, it only served as a fuel to his ever burning desire to rescue her. He had failed once with Lieutenant Ford, and never wished to repeat that experience again. His mind was constantly working, always drawing up new plans, pointing out flaws or revisions needed, then storing them for later perusal or deleting them. His withdrawal from the city was not noticed, and he proceeded with extreme caution to continue in that fashion. One off-world assignment dismissed here, a shift in responsibility to Lorne there, willingly joining McKay on Puddle Jumper research, finishing up paperwork and delaying it's publishing, all steps in his ultimate goal, the culmination of his plans. He, John Sheppard, was going to rescue her, Elizabeth Weir, and his plan to do so was flawless. It just needed the perfect time to be implemented.
It came about one afternoon. He had just been cleared, again, for active duty by the good doctors in the infirmary. After his recent adventure with a memory of Kolya, and his previous habits of not sleeping and emotional repression, something inside of him had snapped, breaking the metaphorical dam, and he became obsessed with Elizabeth's rescue. He quietly thanked the resident psychologist for his clearance and proceeded to his quarters, unhindered. He passed no one on his way, years of military experience and the occasional observation had imprinted upon his brain, automatically taking him along the least used paths. He gathered up his few meager belongings, his clothes and an ancient device that seemed to be the equivalent of a lava lamp. It always helped him to both clear his mind when stressed and focus when performing complicated mathematical equations. When he left his quarters, it looked just like the other unoccupied places of the city, except for the note on the bed.
His trip to the jumper bay was not as unnoticed as his earlier escapade. He ran into several people whom he knew, and all of them inquired as to his destination with such a large and full duffle. He responded that one of the tenets of his release to active duty was the instigation of a retreat, to be taken at his earliest convenience, to one of the abandoned parts of the city. He was met with understanding and sympathy, which almost crumbled his resolve to carry through with his plan. In the end however even the large, loving Atlantean family was nothing without her, could never be anything more than a temporary solution to a permanent problem. He continued on his way, reaching the deserted jumper bay.
Part of the research he had been working on had been a way to shut off the jumper's automatic notification system to the city's central computer in the event that another enemy should gain control of the city systems. He had reported the program a failure to McKay, citing a conflict between the city's sensor logs and the Puddle Jumper's Unique Frequency Identifier, which would cause a glitch that would be highlighted in the Operations Tower. In truth, he had written the required program in two and a half hours, math based programming was just like he had remembered at McMurdo, and saved the compiled program to a memory stick. He then wiped the system and it's redundancy of all his work and proceeded to tweak an uploadable jumper operating system, adding such features as a cloak/shield switch, the necessary components for hyperspace travel, and an experimental method of assisted power generation utilizing replicator cells.
Everything was ready, the pieces all in place, the only thing left to do was rescue her.