Disclaimer: I (very obviously) do not own the Stargate franchise, or any of its characters, settings,...yada yada yada...
Summary: Just a missing scene about McKay from SGA Season 4 episode "The Last Man" that popped into my head.
It was…surreal, stepping through the gate and back onto Atlantis again. Everything looked exactly as it had the day he and Jennifer had left. For a moment, he could almost believe that he was back there, before everything went wrong, and that the past 27 years had just been a terrible nightmare. But then his arthritis, a by-product of decades of scribbling on white boards, flared up, reminding him that no, this wasn't the past, and everything really was all wrong.
The current leader of Atlantis greeted him, but he couldn't be bothered to listen to what the ignorant little whelp was saying. Another snivelling IOA representative, some hot-shot bureaucrat who couldn't make a moral decision if his life depended on it. He doubted if the idiot could make any kind of decision himself. He was obviously just a figurehead, a puppet the IOA placed there to make it seem as though there was actually someone in control. Ever since Sam had…well, it was obvious that the standards around here had fallen drastically since he had resigned. This halfwit made Richard Woolsey look competent. Which, of course, he hadn't been. Elizabeth – and Sam – had been more than competent. They had both excelled at being the head of the expedition. They had been everything that defined a leader – strong, intelligent, kind…But no use dwelling on the past. It would be different soon anyways.
An offer to see him to his room so that he might "rest after such a taxing trip" was extended, but he refused, saying that he wanted to get started on his work immediately. General Lorne had told the IOA some cock-and-bull story about a project on improving the city sensors, or some other such nonsense. He didn't care what the people in charge had been told so long as he was able to finish what he came here to do.
He recruited a handful of young Marines to transport his equipment and accompanied them to the appropriate lab. He had chosen a vacant one on the lowest floor of a particularly sturdy tower on the northern pier to ensure privacy while he worked and, once he was finished, a measure of protection for his program to withstand the years until it was needed. He didn't know whether the city would survive long enough, but he had to make sure that if it did, his simulation survived with it. It had to remain intact if it was going to be of help to any of them.
The Marines almost dropped the naquahdah generator when they arrived in the lab, and he spent a good five minutes expounding upon the reasons why they were incompetent imbeciles who had very nearly blown everyone to bits before sending them away. He spent the next hour or so carefully unpacking his equipment and making sure all the essential parts were still intact and functional. With the oafs that worked here now, who knew what state it could have been in. Thankfully, everything was in order, and he got started with the real work.
As he whiled away the hours, he found himself reminiscing about all the time he had spent like this in his younger years, back when the expedition was still new to this galaxy, Zelenka sitting close by with his own laptop and Sheppard stopping by to pester them. God, he missed them. All of them. Radek had stayed on with the expedition as the new head of the science department after he and Jennifer had resigned their positions, only to be killed a few years later by exposure to radiation. At least they'd had a body to bury. Not like so many of the others…
He worked diligently over the next few days, writing the complex base code for the simulation, entering multiple solutions for as many possible situations as he could fathom, integrating the latest version of the Asgard hologram technology. He'd had a basic outline for the program written before he'd come here, but had needed access to more sophisticated technology in order to really get things accomplished. Now that he had that access, things were going much faster. He took a room a short distance from the lab so that he could rest somewhere close by when he needed to, and regularly called for food to be brought to him as he worked. He had no time to walk all the way to the mess hall, and besides, he was an old man, not to mention the one who was going to save the galaxy (again).
He wrote in a few improvements for the sensors since that was what he was supposed to have been working on anyhow – besides, it wouldn't hurt his plan at all for the city to be better at detecting things. In fact, it would probably help in the end. Once he'd finally finished writing the program, he had a few of the expedition's scientists pry open the floor panels so that he had access to the space below. With a little rearranging, there was plenty of room for everything he needed to connect. He set the core drive, along with the naquahdah generator and various other key components, into the space in the floor and linked it to the city's main systems. The generator would ensure that his simulation had enough power to operate, even if Atlantis itself did not, and the core drive would allow it to function should the city's systems be shut down or destroyed for whatever reason.
He'd been careful to hide the program so that no one would notice it and try to remove it. Of course, everyone who looked would be able to see that some slight modifications had been made to the sensors, but his true contribution was buried so deep that it was unlikely to be noticed. It would run quietly in the background, tapping into the sensors to monitor everything that was going on, waiting for the moment it would be needed. He'd designed the simulation to activate when it sensed Sheppard's bio-signature in the city once more.
He made sure everything was sitting snugly and turned on the Mark-12 generator. It took him more time than he was willing to admit to stand up again, and the familiar aches and pains of old age intensified. He wasn't used to this kind of work anymore. If only his team could see him now…
Memories flashed through his mind at light speed…watching Sheppard walk through the gate to M4S-587 with Lorne's team only to never return…seeing Teyla lying dead on the floor of Michael's laboratory, still managing to look graceful somehow…finding the wreckage of Sam's ship floating in space surrounded by the remains of three hive ships…listening to Ronon's strike force relay the news of his sacrifice in order to destroy the Wraith lab…sitting next to Carson's bedside as his internal organs failed because no cure for the degeneration had been found…and Jennifer…oh god, Jennifer…
Tears rose unbidden to his eyes, and he fought to regain control of his emotions. His work wasn't quite finished yet. He shuffled over to the last container, and pulled out a small device. It was an adaptation of one of the many technologies SG-1 had encountered in their travels, and would allow him to put the final touches on his program. He turned it on and waited as it scanned his body from all directions, watching as a 3D representation of himself appeared on the display screen. When the scan was complete, he attached the device to the rest of the components in the crawlspace. He'd designed the program to mimic his own personality and responses, and now with a simulation of his physical appearance, it was complete.
The floor panels were fused back into place to make the compartment airtight, and the empty containers cleared away. He checked via the console in the room that everything was working properly, and then locked the doors as he left. His one last attempt to protect his work was to seal the lab against anyone but himself or Sheppard.
As the technician dialled Earth, he looked around one last time, absorbing every detail he could. He knew he would never return to this city, but hoped that he'd done enough to change the timeline in order to prevent all the horrible things that had happened since Sheppard's disappearance.
Two weeks later, the obituary section of a Canadian newspaper announced the death of a Dr. Rodney McKay who had passed peacefully in his sleep.