Title: Hope Will Triumph

WARNING: Spoilers for S4, this will be an AU of S4,

Disclaimer: None of the Stargate Atlantis characters are mine, as much as I may wish.

Summary: Starts right after This Mortal Coil. Knowing that Elizabeth Weir is gone after the events of This Mortal Coil, John Sheppard and the rest of Atlantis team try and move on. But they still can't shake the feeling that somewhere out in Pegasus there's something, or someone worth looking for. Horrible summary yes I know.

A/N: This is my first Stargate Atlantis fic, so please bare with me while I get this show on the road. Enjoy.

Atlantis

John Sheppard sat heavily on his bed, running his hands over his face, still in his dress blues. It felt like he had aged ten years today. Looking through his hands his eyes wandered over the room, despite the changes in Atlantis over the last few months and the neglect it had faced; somehow it had stayed as though nothing had happened.

'Ironic isn't it? We have a year out of hell and this city goes on just like nothing happened'. The bitter thought passed through John's mind before he could stop it. His eyes fell on part of the reason for the pain he and other Atlantis personnel were feeling at the moment. On the bed next to him sat the pot he gave Elizabeth Weir for her birthday during their first year of Atlantis. Next to that was her father's pocket watch; he had told Rodney that he was sending all her things back to Earth, but after further review he couldn't send these two items, one signified their first year in Atlantis, the other the nights he found her toying with the watch.

Tears gathered in the corners of John's eyes as he picked up the watch. How many times did he see her playing with the thing after a difficult decision, or after his team had just got back from a disastrous offworld mission? Atlantis wasn't going to be the same without Elizabeth Weir, her way of command, giving people like him chances, the late night balcony talks, these were some of the things that made Atlantis, Atlantis. Nothing could ever fill the void left there, not another leader, though Sam Carter had done her best, there was only one leader for Atlantis and she was gone.

John got up and looked out at the city he had come to call home. Rain poured down in sheets, as if the planet itself was mourning along with them. The ceremony earlier was simple and short, there was no body to view or send back to Earth. A quiet gathering, Rodney had given the eulogy, and was surprisingly elegant. Teyla stood next to Ronan, tears silently coming down her face while Ronan had stood silent, fighting to contain his emotions. Later at the reception, Teyla had come up to John and told him that her baby's middle name would be Elizabeth in honor of the fallen leader. Just after he saw Sam Carter and Jack O'Neill talking quietly in the corner, he knew Elizabeth had been in charge of the SGC briefly, but hadn't expected the general to come to the Pegasus Galaxy to say good-bye. He was touched, touched truly, and he was sure if Elizabeth could see she would have been too.

As John watched the rain fall he saw the lights of Atlantis shut down slowly, and some cries of shock as the lights went out on people that were still up.

"What's going on?" John asked into his earpiece, unconsciously gripping the watch tighter.

"Yes Rodney, what's going on?" Sam's voice came over the earpiece.

"I don't know, hang on a second!" The astrophysicist yelled.

"Rodney…" John was getting aggravated.

"It seems…" Rodney's voice broke. "That Atlantis is mourning."

"What?" Sam was confused.

"Look at a laptop that's connected to the city's mainframe. They're battery powered so they still should work." Rodney said quiet.

John raced over to his laptop and powered it on. As soon as the screen loaded completely Atlantis' message was shown in clear script across the screen. "LONG LIVE ELIZABETH WEIR, THE FIRST LEADER OF ATLANTIS!!!! MAY SHE FINALLY FIND PEACE."

"Truer words have never been spoken," John murmured, looking at the pocket watch. He looked out at the city. "Even Atlantis misses you Elizabeth. Rest easy." The words came easy and hard now that she was gone. "I love you."

Elsewhere in Pegasus:

Deep green eyes gazed out at the sea of stars as the ship silently traveled through space. The eyes narrowed in hate as they saw a Replicator vessel attacking a Wraith ship, her second in command was awaiting her order. Turning she spoke harshly, "Destroy them."

"Yes ma'm."

The woman went back to looking at the stars from a different window, not wishing to see the battle. Sadness filled her as she looked at the planet that Atlantis once called home. 'John'. She hoped he was staying out of this war.