This is my entry for 's contest, "What do you want to see in Season 4?"

I want to see an actual, genuine, not done-under-the-control-of-some-creepy-person's-mind kiss between Sheppard and Weir, and I think Weir's leaving Atlantis would be the perfect excuse for just such an occasion. (it's also a great excuse to draw my first SGA fanart ever )
Here's the accompanying mini-fic to go along with the pic, sorry it's kinda long:

Elizabeth Weir stood at the edge of the gateroom balcony and gazed down at the floor below, lit only by the soft lighting in the walls and the shafts of moonlight colored by the stained-glass windows. The Stargate stood as a silent sentinel, its empty arch a reminder of the countless traumas and triumphs she had seen these last three years. How many times had she passed through that shining blue surface to worlds and galaxies unknown? How many people had she seen walk into this very room, each with their own story to tell? Yes, it was here in the halls of Atlantis—joined intimately to the Pegasus galaxy by the Stargate she contemplated now—that she had encountered and cajoled enemies and allies alike, all bound together by the threat of the Wraith. The city of Atlantis was no longer just a base, but a home that she had never imagined she’d want to leave.
And now she was.
Two duffel bags, each containing her most precious belongings and some of the things she’d acquired during her stay here, sat in front of the Stargate, their bulk casting a shadow across the floor. She’d planned to leave first thing in the morning, but right now waiting seemed pointless; it would be easier, she thought, to steal away now than to face the people she’d come to love and respect and wish them farewell for good. The SGC wouldn’t be expecting her this soon, of course, but she was sure they wouldn’t mind. They, after all, had been the ones so eager to seize her control of Atlantis from her in the first place. Resisting a bitter laugh, she turned and crossed the floor to the control panel, keying in her IDC before she had a chance to change her mind.
The Stargate hummed to life with the usual series of clanks and whirrs that had become so familiar to her. As soon as the wormhole had stabilized, she returned to the balcony for one last look, taking in the ripples of blue whose brightness played across the floor. She’d always been mesmerized by that pattern, the unearthly beauty of it; but she’d never realized how much she would miss it until she stared at it now, trying to imprint the image on her mind.
She had almost reached the bottom of the lighted stairs down to the gateroom floor when the pound of footsteps reached her ears. She tensed, hand immediately reaching for a P-90 that wasn’t there, but it was only Sheppard. He slowed to a halt and looked as surprised to see her there as she was to see him, his brow furrowing in a way that would have been comical if it was directed at anyone else.
“Doctor Weir. You’re leaving?” He crossed his arms and approached her, frowning a little.
Elizabeth attempted to inject some humor into her voice and shrugged lightly. “I thought I’d avoid the morning rush and just ship out now, rather than bother everyone with it tomorrow. Why aren’t you sleeping?”
He ignored her question and waved at the empty room, looking unsatisfied with her excuse. “Hell of a way to go. You think we won’t notice you’re missing?”
“Colonel Carter will be here in the morning.”
“Yeah, well, she’s no Elizabeth Weir. I still can’t believe you’re doing this.”
“Neither can I,” she replied softly, glancing away to stare into the Stargate. How many times had she looked through its depths before, willing him to emerge safe and sound?
“Elizabeth, for what it’s worth…” She looked back to see him rubbing his neck a little bashfully. “I—we, we’ll miss you. A lot.” His next words tumbled out in a rush, fast but heartfelt, his gaze as serious as she’d ever seen it. “You’ve been the best leader this expedition could have, through all the times we thought we were gonna die, when we thought you were going to die…all the choices you made were what kept this city in one piece, and no matter what the SGC says, I trust you.”
“John…” she whispered, tears starting to well despite her best efforts to quell them. Damnit, this was why she’d wanted to leave now instead of later. “My choices are what got us into this mess. I was trusted with making Atlantis a success, and what’s happened? We trusted Wraith and let them into the city we swore to protect, we’ve ruined our chances with so many potential allies…” She trailed off, the number of her failures mounting in her mind.
“Since when has that bothered you before?” He took a step toward her, hands spread incredulously. “Who cares about the Genii? They were against us the moment I told them we had C4, remember? Blowing up stumps, ha! You can’t blame yourself for that. For any of it. We were on our own and we had to do what seemed right—we couldn’t see the future. We’ve survived, and that’s what’s important. And I, for one, can’t see how Colonel Carter could do anywhere close to as good a job as you have.”
She had to laugh at the defiant look he gave her. “Come now, she can’t be that bad. She is military, after all. She’ll probably bring some level of expertise to the command that I never would have thought of.”
“But she’s not you.”
“I have to go, John. I’ve had three years here. Three years of wonder and excitement and danger; but it’s time for a fresh perspective, don’t you think? That’s how leadership works!”
“You don’t actually believe that, do you?”
She sighed and dropped her hands. “No, you’re right. I don’t. But I don’t have a choice. If I did, I’d stay in a heartbeat. How could I give all this up? The city, the Ancient technology…helping people fight the Wraith… getting to know you. All of you.” Shoulders slumping, she dropped her gaze and bit her lip against the tears threatening to form again. She hated that she felt so weak now, on the verge of stepping through the Gate; of all the memories they’d shared over the last three years, she definitely didn’t want him to remember her crying the last time he’d ever see her.
“Elizabeth.” Frustration and regret mingled in his voice; before she realized what was happening, he’d crossed the two paces between them and enclosed her in his arms, settling her head against his shoulder. One hand lightly rubbed her back between her shoulderblades, smoothing away the tension that had knotted there for weeks. “It’s not going to be the same without you,” he whispered sadly.
She stayed silent for a moment, soaking in the unexpected show of emotion from the usually stoic Sheppard. She had only been this close to him a handful of times, and now might be the last. “What are you here for?” she asked finally, drawing back to meet his gaze.
“I guess…” He paused to tuck a loose curl back behind her ear, “I just wanted one last chance… to say good-bye.” He leaned down and their lips met softly, soon turning into a kiss that couldn’t begin to express three years’ worth of unspoken questions and lost opportunities. But it came close.
And it was just the way Elizabeth had expected it.

=======

I couldn't have done this without some awesome resources from DA, whose authors I thank immensely:

Model reference from ~PuppetMuse-Stock
Stargate from ~Fune-Stock
Event horizon tutorial from ~m4ri7