Originally conceived as an alternate ending to Even In The Distance, but I think this stands on its own.
Salve Regina
(Or, Ever in the Distance)
By Reyclou
In twenty years, the city of Atlantis hadn't changed much – the fine towers still soared into the heavens, the piers still stretched into the ocean, and the stars of Pegasus still loomed bright overhead. Yet, so very much had changed. Faces come and gone, joyful triumphs and sorrowed losses, alliance and vengence. Life, death, and happiness.
But one thing, in twenty years, had remained very much the same. The gleaming clear desk in the office off the control room belonged to one woman and to one woman alone – Elizabeth Weir.
Sure, there were a few times where she was not in "official" command of the city. Carter's reign had been necessary, to be sure, and even in the years following Elizabeth's eventful return to power, there'd been extenuating circumstances – sickness, leave, investigations and the like. But in the end, the city always came back to her, and in the meantime the inhabitants within always tipped their hats to the true head of the Expedition. The Expedition that had now become the Embassy.
In those twenty years, she had overseen the downfall of the Wraith, weathered the Replicators and their savage onslaught, and seen the rebirth of an entire galaxy.
She stared into the face of death. And life. Happiness and betrayal. And yet, in fifteen years, she had not stared into the eyes of Colonel John Sheppard who, along with Teyla Emmagan, had been dead since shortly after she was reinstated as head of the city. A brushfire on a prairie world had scorched the two so dark and raw the search teams had thought them dead on sight. Only Teyla had been so lucky. It took John days to die.
Days of watching him lie in an infirmary bed, a miserable mess of melted flesh and shattered dreams, and Elizabeth had not known whether to cry or nod a silent prayer of thanks that it was finally over. But, of course, John Sheppard could never be over – there was no end to a soul born to the sky. Nor could the city accept an end to the first son of the New Atlantis. And thus, a little sensor spurred by desperation of his dying thoughts quietly mapped his mind, importing it into the city's database.
There the new John Sheppard was born, capable of whispering through the city's crystalline circuitry like the wind through her hair.
It was unusual at first, to hear a voice long buried in the Earth, to see his influence on a city he had died to truly command. The newer folk took him for granted, a novelty of a mechanized miracle, and the expanse of his presence flustered Caldwell until the day he retired.
In theory Rodney had stunted the program so that he could not wrestle control from a breathing human, but John still found his ways around. The door to her office had been a particularly hard fought battle. John insisted a gentleman should open the door for a lady, even from the grave. Still, there was a certain attitude with which the doors opened wide for guests of loving honor, or shut tight and firm on the heels of men he "just didn't like."
He opened and slammed it at insistent intervals when she stayed too late in her office, and, upon her leaving, refused to open again for eight solid hours.
The night someone inadvertently 'let it slip' about her engagement, he'd slammed the doors shut on her office and fired the stardrive so fiercely it had her shouting before a group of terrified dignitaries: "You're a big city now, John. Act like one!"
She still went out to the balcony to talk to him, though he was no longer a physical man but a shadow of a being. She still called him Colonel and he still called her Boss. The closest they could get to a face-to-face was the horribly inefficient avatar program in the hologram room. They'd really only tried it a handful of times but, truth be told, facing the young and flawless Sheppard with the depth of her own wrinkles was just a little more than she could handle. He could not see her, she knew, but the intangible reincarnation of the lost and dead suddenly made the window from life to afterlife a little clearer.
The day she called off the engagement, she swore he was channeling "I Still Miss Someone" over the citywide.
Regardless, that was ages ago, and she now stood at the doors of the bright, glass-lined room that had been her seat of power for the greatest years of her life. Her tenure in Atlantis was now coming to an end. Elizabeth could still do her job, she knew. But she was also old now. Horribly old. Her joints ached and her hair had faded to a sprawl of deep grey. Time had come for new vigor in the city, new dreams to cast over the broken ones.
Outside, in the Gate room, a full display of the world's finest gathered in rank and stature to watch the changing of the guard, to watch the great Elizabeth Weir pass the crown of command to the young and the bright and the beaming. Had she been like that once? she wondered.
A part of her had hoped to stay in the city, but knowing that a ship honored only one captain, Elizabeth gracefully accepted a presidential offer of intergalactic ambassadorial status with a wink and a promise that she'd "let things get settled first". Within the hour, she'd be on Earth, finding land legs on a world that hadn't been her home since she saw a Lantean sunrise.
Only the door wouldn't open.
Elizabeth didn't waste her energy on forcing open the panel or calling for a tech. She merely stretched out her hand and gently stroked the door frame. The metal was cool beneath her touch, but the smile in her voice was warm and open.
"You can't keep me here forever, John. You have to let me go sometime."
Still the doors held tightly closed. The band started up outside and some proud men in dark suits started across the walk to escort her.
"I'll be back again, someday."
Still no movement.
"I'll miss this, dearly," she continued. "I'll miss our life, together." She smiled sweetly at the men approaching, though they neither heard nor saw her speech. "And if you were here with me, I'd be home forever, in any galaxy."
She folded her arms in her hands. They were almost at the door.
"But now I have to go and help make this city into a new beacon that will shine across galaxies and all throughout time, for the good of all we have accomplished here."
The men stood within a stride of her, political smiles and picture perfect hair, ready to sweep out the old and cheer in the new. With a hiss and a clash of cymbals, the door slipped open and the music rose to a triumphant stride, all but drowning out a little voice whispered by lips long stilled by death.
"God save the queen."