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Author's Chapter Notes: Final chapter is up! Hope you all like the ending, I tried to make it a happy one!


“Checkmate.” John informed his companion, Elizabeth turned to him, her eyes blurred.

“Wh-what?” Her gaze rested on the chess board, made up of far more black pieces than one would expect for a reasonably matched game. “Oh.” She said blankly.

John rolled his eyes, beginning to clear them away, “that’s three games in a row,” he said sternly, “now either I’m a lot better than I realised, or something’s up.”

“Maybe I just want to play a different game,” she suggested, stretching up from her position, lying flat down on the floor.”

“Sure, I don’t have an objection to that. Shall we go and raid the SGC’s store cupboard and make the impossible choice between ludo and snakes and ladders?”

Elizabeth couldn’t help a laugh escaping her lips and John shook his head; the lack of board games was one of the many thing on a very, very long list they missed about Atlantis.

But as usual she hadn’t actually answered his question. “Elizabeth?” John also got to his feet, his lean frame unsupported by crutches for the first time in weeks. “What’s really up?”

She shrugged, turning away to make her already perfectly neat bed. “I’m fine.”

“Sure you are.”

He took a step closer to her, frowning as he saw the faint tightening around her eyes and the thin line are lips formed. “John...you’re leaving tomorrow.”

He felt as if a lump of lead had just dropped to his stomach. It wasn’t that he didn’t want to go back to Atlantis –just the opposite – but he just couldn’t take the thought of leaving Elizabeth again; so soon after they were both finally safe once more. All that time he’d been so focused on bring Elizabeth ‘back’, on rescuing her he hadn’t really thought much about what would happen afterwards. Somewhere in his mind he realised that there always been a certainty that ‘return’ meant back on Atlantis. Picturing Elizabeth back on Earth – anywhere on Earth; the SGC, Washington, the Pentagon – was just wrong...

She was still watching him, John hadn’t actually answered yet. He wiped his hand over his face. “Oh.” He replied inconsequentially. “That.”

Elizabeth just shook her head so he tried again; “well General Landry said the IOA are finally finished with you, you’ve been given clearance to leave the base; you can go back and get a job, I heard the Pentagon are interested.”

“Of course.” Her voice was blank and disinterested.

“Hey,” he ran his hands through his hair, “you know...you could always apply for your old position...on Atlantis.” There he’d said it. His stomach tightened as her head snapped up.

“John. We’ve been through this.” Her voice was weary, “there’s no way they’d consider me; I was a replicator for two years. Can’t you understand that?” John gritted his teeth. “Besides; they already have a perfectly able commander.” She added as an afterthought.

‘But –”

“John, just drop it please.” She said, with an air of finality, “It’s not going to happen.”

“Well what do you want me to say?” John snapped, “How am I meant to answer when you’re sitting around here...here – moping! What am I expected to do to make you feel better? Elizabeth you want to go back and I’m willing to bet most of Atlantis wants you back too. I don’t get why you’re refusing to do anything about this!”

“It’s not that simple –”

“I know! But I still...”

“Um, Doctor Weir? Colonel Sheppard?” They both swung round abruptly as a nervous marine stuck his head round the door.

Elizabeth took a deep breath, sending John a murderous stare. “Yes. Sorry. What is it?”

“Um, General Landry wants to see you ma’am, he – he says it’s important.”

She smiled warmly at his, (it still beat John how she could disguise her moods like that.) “I’ll be right there, thank you.” The door swung shut and Elizabeth’s expression change instantly.

“No.” She cut him off before he’d even opened his mouth. “I refuse to discuss this again John, it’s simply not worth going over. Is that understood?”

He shrugged, “fine.” He’d learnt a long time ago not to get into these battles with Elizabeth.

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“Ah, good you’re here.” General Landry looked up, from the papers he’d been shuffling. “Sit down.”

John dropped into the chair opposite and Elizabeth sat down next to him, the General leaned forward a little, “relax you two please,” he said, “you’re steaming up my office.”

John winced; apparently he couldn’t fool everyone, “yes Sir.”

“Now, I’ve just received the most...interesting letter.” He laid a sheet of paper flat on the desk, “informing me of Mr Woolsey’s resignation from the position of commander of Atlantis.”

“What!” John sat up abruptly, echoing Elizabeth’s yelp of shock.

“Please,” he gave a chuckle and waved his hand, “control yourselves and let me explain. What I received was not an official form but a personal, confidential letter informing me of his immediate resignation on certain conditions.”

“And they would be?” Elizabeth prompted when the General didn’t seem to be planning to finish the sentence.

“Your immediate reinstatement as the commander of Atlantis.” Instead of leaping up this time Elizabeth sagged down, collapsing in her chair, all colour draining from her face. John could hear her give a faint gasp under her breath. Despite all of this though she remained completely controlled, her voice steady as she answered him. “General as...generous as Mr Woolsey’s offer is I have a feeling the IOA would not be very supportive of that idea; or Stargate Command and the Pentagon for that matter.”



“That’s because you haven’t been around for a while,” General Landry said, “a lot has been changing around here, thing’s you should probably know about before you make your decision.” Elizabeth nodded; John could see the colour gradually returning to her cheeks. “As I’m sure both of you will be delighted to hear,” Landry said, “the IOA are losing support and power in all factions; they now have very little sway over the decisions made both in Stargate Command, and on Atlantis. The military on the other hand are stronger than ever and have been pushing for more control on Atlantis,” a frown settled on Elizabeth face at thus, “though to no avail.” He added, Elizabeth’s features relaxed at this and she laced her fingers together, General Landry appeared not to notice.”

“Meanwhile,” he went on, “Homeworld Security and the Pentagon are leaning more and more towards the possibility of releasing information on the Stargate program to the general public. Now – calm down,” he added sternly as both John and Elizabeth opened their mouths to protest, “I believe that possibility is still far into the future but – as they wanted when you first became commander of the SGC Elizabeth – they would like some good civilian faces to present to the public if that does ever happen. The last thing they’d want, even less so than some grumpy, hard faced General,” here he gave a wry grin, “is any more strong supporters of the IOA in positions of power. When – if – they receive word of Mr Woolsey’s resignation, it is highly unlikely they would allow any of his colleagues to replace him. The IOA knows this and no matter how much it pains them to admit it, they would prefer to see you as commander of the expedition rather than any Colonel they are terrified the military are going to push into power; they still have enough sway to prevent that from happening and find a compromise.”

“I.e. me.” Elizabeth interrupted quietly.

John snorted and General Landry’s eyes twinkled, “well done.” He said proudly, “From the ways its heading, they’ll put and keep you in Atlantis if it’s the last thing they do. The only thing they can do.”

“Anything but the lot holding the guns.” Elizabeth muttered and he chuckled.

“Exactly. The military for their part would far prefer you to any other civilian who is loyal to other ‘teams’. You’ve worked with them before and despite your two year imprisonment they still trust you more than any of the other blood-thirsty wolves prowling around.”

“So basically, what you’re saying,” John said, his head swimming from all this information, “she makes everyone happy; military, Homeworld Security, Pentagon and the IOA?”

General Landry’s eyebrows quirked, “yes Colonel; that is precisely what I’m saying.”

John glanced over at Elizabeth who had a faraway look in her eyes, staring thoughtfully into the distance. “C’mon Elizabeth,” he begged inwardly, “you can’t ask for better than that.”

“Doctor Weir?” General Landry asked. “It is of course your choice. Tell me when you reach a decision.”

Elizabeth eyes snapped back into focus, “oh don’t worry General,” she said without hesitation, “I already have.” She glanced at John, who was aware of a sudden tightening in his chest. “I’m returning to Atlantis.” It released and he let out a silent sign of relief.

General Landry face broke into a broad smile, “I’m glad to here it.”

“There is just one thing; I don’t quite understand though,” Elizabeth said, “why did Mr Woolsey offer to resign in the first place? Moreover why was it on the condition that I should take his place?”

“Ah, yes, I thought you’d ask that,” Landry said, “and I’m afraid I don’t have the answer so I suggest you ask the man himself.” John exchanged a perplexed glance with Elizabeth as the General heaved himself out from behind the desk, “the scheduled dial in should be just about;” he paused, “now.”

“Atlantis’s IDC Sir!” Walter called from the Control room.

Landry laughed at the surprised look John knew would be written all over his face. “Well come on then.”

Sure enough as they came into the control room, the gate was active; illuminating the normally dark space and Richard Woolsey’s face was clear on the screen. After receiving the weekly update General Landry gestured to Elizabeth. “Mr Woolsey,” he said, cutting him off the warbling he was beginning to launch into, (thankfully for John who had suffered enough of endless twittering back on Atlantis with the combined might of CO AND McKay.) “I think somebody wants a word with you.”

With unusual sensitivity Landry drifted away, leaving only John nearby to overhear the conversation. “Mr Woolsey,” Elizabeth said warmly, tilting her head up at the screen, “how are you?”

“I’m well,” he replied, pausing awkwardly, “I – ahem, assume you received news of my letter.”

Elizabeth nodded, “I did,” she also hesitated, “actually that’s what I wanted to talk to you about,” John saw her take a deep breath, “Mr Woolsey, why exactly did you...resign?” She down on her lip, a subtle sign of emotion, “and why on the condition I would be reinstated?”

The question hung in the air and Woolsey stared off, silent. He stayed silent for so long that John began to think he wasn’t going to answer. “Doctor Weir,” he said at last, “as I have told you before; I do not believe in inconsequential facts getting in the way of the truth. I have also told you before; I have observed Atlantis, observed its people, how they treat each other...how they treat you.” He sighed, “And what I have discovered one again is the truth is you belong here.” John couldn’t stop his jaw from dropping, “no matter how successful I am in this position, no matter how much the people of this city come to respect me I am aware the city is not the same place it once was unless you are leading it. I have seen the way they look at you Doctor, the way they report to you.” Here he gave a dry chuckle, shaking his head ruefully, “The fact,” He said, “that you were held prisoner by our enemy for two years is – I believe – the inconsequential information that must not be allowed to overshadow what I am sure is right: Your return to the city. You and Sheppard coming back.”

Elizabeth nodded her head, and John could see her eyes shining, he himself was in shock, unable to comprehend that the normally clueless Woolsey could have decided this. “Talking of Sheppard,” Woolsey was going on, “is he there?”

“Um, yes Sir,” John said quickly stepping forward, his mind going into first gear, “actually Sir there was something I wanted to ask you –”

“I can very well guess what you wanted to ask Colonel,” Woolsey cut him off, “and I am now ordering you to remain on Stargate Command for the duration of what I’m sure will be a rather sticky uncomfortable process of Doctor Weir’s reinstatement.”

Just when he didn’t think he could be more surprised – John was, “thank you Sir,” he said when he could speak again.
“You’re welcome Colonel, though I can’t say I envy either of you. Now; Woolsey out.” With that the gate shut down.

John turned to Elizabeth, licking his lips, “what just happened?” He ran his fingers through his hair, “Is that really the same guy I wanted to knock in the head?”

“I don’t know,” she said, once again staring off into the distance, at some invisible skyline John was unable to see, “but it looks like I have a lot of work to do.”

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Victory didn’t come fast and it certainly didn’t come easily. Elizabeth couldn’t count the number of meetings and debriefings she had to attend, how many times she would stumble into her room exhausted, a pounding headache throbbing between her temples. John joked that she had gained more wrinkles and grey hairs in those weeks than her whole three years running Atlantis, to this she merely gave him ‘the look’ and he fell silent or offered to book her a massage.

However exactly three weeks and five days after Woolsey handed in his resignation Doctor Elizabeth Weir was reinstated as Commander of the expedition of Atlantis – lost city of the Ancients. Her return was one memory that would remain held in Elizabeth’s mind, a glittering jewel – delicate but unbreakable, held above the rest.

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Elizabeth closed her eyes briefly as the gate activated, listening to the familiar sound of the whoosh and splash, a sound she realised, she had come to associate with coming home – going home – having another team, another part of her family return to the cocooning safety of Atlantis, letting the city wrap its warm arms around them.

She opened her eyes quickly again as John nudged her gently with his shoulder, “Time to go.”

She smiled up at him, hoping her eyes conveyed at least a fraction of the depth of the gratitude she felt right now, he smirked softly back at her, “hey Elizabeth?”

She turned to him, aware that her lips were curving into an uncontrolled smile at the thought of where they would be in mere seconds. “Yes?”

“Just...” he grimaces in embarrassment “I’m glad you’re coming back.”

Elizabeth’s smile deepens, genuinely touched at the emotion in his voice, “thank you,” she replies simply, “I’m glad I’m coming to...thanks to what you did.”

He shrugs, “it was nothing,” he twists his head away, “any one would have done it.”

Hesitantly, still unsure of what his reaction would be she lays a hand on his arm, “but only you did.”

He gives another shrug and she knows him well enough to see the barriers he always erected when people tried to thank him going up – John hates being shown gratitude, he never seemed to believe he really deserved it. “Well you rescued me,” he points out, “I guess we’re even. Shall we go then?”

She nods in acceptance. “I don’t think anything could stop me now.”

Barely turning back to give a parting wave to the General, technicians and IOA representatives watching up in the gate room the two of them walked up the ramp and without hesitation disappear through the event horizon.

They emerge blinking in confusion – something was wrong, inky blackness surrounded them, barely able to see hands three centimetres in front of their face it was....dark? “Uh, hello?” John calls, “anyone home?”

There’s a brief flicker and the space is illuminated in light, Elizabeth let out a barely stifled gasp as she was met by over a hundred pairs of eyes all fixed on the two of them, everyone perfectly assembled, motionless in the deafening silence. She glanced at John who shook his head in aimless confusion, the two of them switching their gaze from one person to another. Chuck gave them a grin from the technicians in the control room, Jennifer smiled on behalf of all of the medical staff assembled on the opposite balcony, and Zelenka even gave a wave, standing at the head of all of the scientists gathered at the top of the stairs. Both Amelia and Lorne saluted leading the military at either side of the room and Halling gave a bow followed by Jinto and Kanaan –a cooing Torren in his arms – standing with half of the Athosians on the sweeping stairs.

And there; in the centre of the room stood their team; Rodney, Teyla and Ronon, their faces expressionless but somehow holding barely suppressed excitement and all encompassing joy; in front of them Woolsey stepped up. “Doctor Weir, Colonel Sheppard,” he gave a smile inclining his head, “welcome home, if you could just move forward please.” Mystified Elizabeth and John did as he commanded, taking a cautious step forward. With a heart jerking flash the two of them were caught up in a beam of glowing golden light, cut off from the rest of the gate room, eyes screwed up, almost blinded. A small console rose smoothly from the ground in front of them, dazzling white.

Woolsey’s voice floated towards them, disfigured, mutated but to their intense shock, calm and efficient, even a little bossy – at least this was going according to some sort of plan. “Both of you place one of your hands on the console.” He ordered, they exchanged confused glances, but obeyed, John’s large hand settling quietly next to Elizabeth delicate one. They let them lie there for a couple of seconds before – with an airy chime of acceptance – the light vanished and the console sank peacefully back into the floor. Woolsey gave a satisfied smile.

“Thank you;” he nodded calmly, “what you have just completed is known as the ‘Initiation Process’ something Doctor McKay has been working on for weeks now,” Rodney opened his mouth at this; no doubt to launch into an extremely long, drawn out explanation of what he’d done, how much sleep he’d missed and exactly how immensely complicated it had been. However to their surprise he closed his mouth (without anyone telling him to) and let Woolsey continue. “From what we’ve read in the data base the city will only accept the genuine leaders of Atlantis; not stewards or caretakers, something even most of the Ancient commanders here were, nothing else but the true born leaders.” The two of them exchanged another glance, only this time one of awe, amazement and possibly a little pride. He gave them a smile, not the usual thin-lipped affair but broad and honest. “Congratulations, the city is now under your responsibility. “ He added the last couple of words in a lower tone “welcome home.”

He stepped back and the other three placed their hands together, softly beginning to clap, clear and strong. Within moments the entire room was roaring with the sound, smiles breaking out in every corner of the room, everything glowing with light and love. Fighting the lump in his throat and the tears building up behind her eyes, Elizabeth and John reached out and linked their hands together, calloused to smooth, rough to soft, the touch gentle at first before tightening into an unbreakable grip, holding each other to the sound of Atlantis’s welcoming song.

Welcome home indeed.


Chapter End Notes: I apologise that John and Elizabeth didn't get together in the end, as I originally planned however there will be a sequel. :)

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