Coming Home

Spoilers: Not intentionally, but references to both seasons may slip in on occasion.

Rating: T for some mild language and potentially disturbing images in some chapters.

Disclaimer: I do not own Stargate Atlantis or any of the characters associated with it, unless you count Jesi.


Chapter Nine

Jesi sank into the vacant chair, trying to read her brother's inscrutable face as he lay with his arms crossed, eyes staring at the ceiling. After several silent minutes, she sighed and leaned forward, resting her hand over his.

"When are you going to let me in?"

Sheppard's eyes skimmed over her face before bouncing away. "I don't know what you're talking about."

"Yes you do. Cut it out, John. You and Rodney are hiding something from me. We used to share everything, but you've put a barrier between us. I don't like it." She squeezed his hand and smiled when he turned and met her gaze. "Whatever your hiding has something to do with me doesn't it?"

Sheppard expelled a deep breath. She was right; Rodney was right. He was being too overprotective, but he didn't know how to be anything else. He'd been protecting Jesi since the moment their mother had placed her in his arms. She'd been so small and pink and wrinkled; her little eyes had tracked to his and held. She'd reached out, wrapping her tiny hand around his pinky finger, squeezing tightly, and he'd lost his heart. It was hard to reconcile those images with the beautiful woman sitting beside him, still squeezing his hand, her eyes still tracking his face.

"Yes, it does." He turned his hand over and captured hers, squeezing back lightly. "I'm sorry I keep trying to protect you. It's a long-standing habit, one I'll probably never break." He pulled her hand up to his mouth and kissed her knuckles tenderly. "But I promise to work on it..."

"You can start by telling me what's going on around here. Why all the secrecy?"

Sheppard explained to her about the mysterious message to the SGC. When he finished, he sat watching her face for signs of fear, but read only determination.

"Let me get this straight... the message was signed with your encrypted signature, but you didn't send it?" She asked.

"Exactly. Rodney's trying to figure out how that happened, but he doesn't think we'll ever know who actually sent it."

"I don't care who sent it. I'm glad they did because I love it here. For the first time since Tony died, I feel like I have a home again, a life, people who need me. I'm happy, John." She glanced down at their joined hands, then back up at his face. "May I ask a strange question…"

"Sure, you can ask me anything, kiddo... Sorry!" Sheppard smiled.

"Is Atlantis alive?"

Sheppard's smile turned to a grimace. "What has Rodney been telling you? If he's filled your head with ghost stories, I'll..."

"No, no! I'm asking because... well, sometimes I hear things... feel things... It's hard to explain." Jesi turned red under his serious scrutiny. "Am I crazy?"

"No, you're not. I feel the same things. I'm sorry. I should have explained when you first arrived." He dropped her hand and settled back against the pillows. "The ATA gene we carry allows us to interface with the city's technology. If you ask Rodney, he'll tell you the things you've experienced are related to that technology."

Jesi leaned back in the chair. "But you think differently?"

"No, I feel differently. McKay has the synthesized version of the gene. He can interact with some, but not all of the Ancient technology, and not on the level that you and I can. Because we carry the gene naturally and in a much higher quantity, we experience the city differently than the others."

Jesi's eyes lit up with excitement. She'd been waiting to talk to John about her feelings, but he'd been so concerned with her safety she hadn't wanted to scare him.

"General Landry explained to me that our family has the strongest natural level of ATA gene found on Earth to date. He said we're the last direct descendants of the Ancients. Part of the reason I agreed to join the expedition was an overwhelming feeling that we're meant to be here, John, to be a part of Atlantis again. I think she feels the same way."

"By 'she'… you mean Atlantis?" Sheppard's concern shot up a notch. "And by 'feel' you mean alive?"

"Yes, I mean Atlantis." Jesi could tell she was freaking him out, but she pressed on. "You feel it to, don't you, the constant thrum of energy coursing through your subconscious? It seems to originate from the walls and floor. Does Atlantis whisper to you?"

Sheppard opened his mouth to deny it, but something in her eyes stopped him. He'd promised to tell her the truth, no more secrets. Still, his answer surprised them both.

"Yes... I mean, yes I hear something that sounds like whispering. Sometimes I hear a warning voice inside my head when things are hinky on a mission. I always chalked that up to military instinct, but maybe there's more to it..."

Jesi nodded thoughtfully. "I think she watches us. I felt a presence with me right after we disengaged from the device the last time. As Carson was treating me, I felt comforted by the darkness. I felt the same way the first time, in Rodney's lab."

Sheppard's eyes narrowed as memories flooded into his mind… whispered words of encouragement and comfort. "I did hear something," he gasped. "I didn't remember until now, but I heard it." He looked at Jesi in amazement. "You may be on to something."

A jolt of awareness accompanied by a sense of well-being flowed through them. Sheppard closed his eyes and took a deep breath, the tension of the last few hours seeping away. Whispered sounds echoed in his mind, not words exactly, but understood on some deeper level. Atlantis is home. He belonged here; he belonged to her.

Beside him, Jesi did the same, her head lolling back against the chair, her sense of belonging solidifying with the gentle hum running through her body, reminding her of the soft caresses her mother had bestowed upon Jesi when she was a child.

The sensations lasted only seconds, and the siblings opened their eyes as the power ebbed.

"See, that's what I'm talking about! You did feel that, right?" Jesi asked excitedly.

"Yeah... I did." Sheppard replied looking at the walls with wonder. "I've never felt the power that strongly before."

"The voice in my dream did say we'd be stronger working together." Jesi grinned. "Maybe Atlantis is helping us use the artifact. So, when do we get to fly again?"

Sheppard laughed. "That's my girl! As soon as Carson says it's okay, we'll try again."

The man in question chose that moment to bustle into the room, followed closely by a nurse carrying the promised breakfast.

"Sorry we took so long. There was an altercation in the cafeteria. One of the marines made a rude comment about Ronon's doughnut and… well, let's just say you'll be having company shortly. The poor marine needs treatment for a split lip and a cut above his eye. Ronon moves fast, considering his injury. I'd hate to face him when he's in top form!"

Sheppard scowled. "Where's Ronon now?"

Beckett helped the nurse settle the food in front of his two patients. "Teyla hustled him out of there before security showed up. I'm not quite sure where she took him, but she'll keep an eye on him for me. Now, eat up! I've seen you naked, Colonel, and you'd better eat every bite. Only then will I release you."

"I'm so gonna kill McKay!" Sheppard groaned.

Jesi eyed her brother's lithe frame with concern. She'd have to ask Rodney to explain the significance of that little comment.

Beckett grinned, and then bustled off when said marine entered the infirmary on a gurney, moaning and holding a bloody strip of cloth to his eye.


Beckett released his patients with instructions to rest for two more days followed by one week of light duty; they were to check in with him each morning.

As he exited the infirmary, Sheppard tapped his radio, his voice deliberately calm.

"Ronon, where are you, buddy?" He waited a few beats, his calm façade cracked, slipping into a scowl. "Damn it, Dex, come in!"

"Colonel Sheppard," Teyla's hushed voice tickled his eardrum. "Ronon is with me. I am instructing him on Athosian meditation techniques. I believe meditation might help curb his anger."

Sheppard relaxed. "Ah, yeah, I see how that could help." He couldn't hold back a chuckle at the image of the big warrior meditating.

"Shhh, Colonel, you are going to break his concentration." The subdued words carried steel.

"Too late. What, Sheppard?" Ronon asked abruptly.

"Ah, sorry to interrupt your... meditating, or whatever. I heard about the incident with the marine, and I wanted to see how you're doing. You know, with the whole tailbone thing."

"I'm fine," was the terse reply.

"Okay... well, indulge me. What happened this morning?" Sheppard asked.

"Corporal Evans insulted my manhood. I proved myself."

"Thank you for that lovely, in depth report! I want details, Dex!" Sheppard ground out, exasperated. Pulling information from Ronon was futile if the Satedan wasn't in the mood to cooperate. Sheppard heard a softly expelled breath.

"Evans said my doughnut seat was the perfect color; yellow for a yellow belly chicken. I don't know the meaning of many of your... words... but I could tell by his tone that he was insulting me. I punched him... twice." Ronon snorted once before continuing. "I expected him to have a better defense, but he went down easily."

"Listen, Ronon... I understand he insulted you, but you really can't go around punching the marines. You might need them to save your sore ass! You need to clear the air with him..."

"Already did. I stopped by the infirmary while you were in the shower. We talked, and I agreed to show him some moves when we're both healthy."

"Good... that was good thinking. So, besides meditating, what do you and Teyla have planned for the day?" Sheppard asked.

Teyla's mild voice cut in. "We are planning to relax and follow Dr. Beckett's instructions, as should you, Colonel. Are you not supposed to be resting?"

"Traitor! I'm standing outside my quarters, if you must know. I'll rest if Ronon agrees to stay out of trouble for a few hours!"

"Not a problem, Sheppard. I'll just go sit on my doughnut and meditate!"

"I will keep Ronon from any harm." Teyla's patient voice interrupted. "Rest, John,"

"Just call me Rip!" Sheppard quipped.

"Who?" Teyla and Ronon asked in unison.

"Sleepy old dude? Well, he was younger when he fell asleep, but... never mind. Sheppard out!"


Sheppard entered his quarters, his eyes taking in the messy space. He hadn't spent much time in here since Jesi arrived, and it showed. He spent the next hour putting his home to rights. When he was satisfied with his efforts, he stretched, feeling sore and more than a little sleepy. Much as he hated to admit it, Beckett was right; he needed the rest.

He stretched out on his neatly made bed, reaching for his I-Pod. He tucked in the ear buds and selected some soothing instrumental music, anything to help him sleep. He folded his arms under his head and closed his eyes. His thoughts wandered, reliving his conversation with Jesi about Atlantis. And what was up with that little power surge he'd felt earlier? That was... different.

He slouched down, dropping his arms to his sides and allowing his body to sink into the mattress. A small vibration shook the bed slightly. He thought about opening his eyes to check it out, but felt strangely sluggish. The familiar cooling sensation crept into his mind, soothing and calming him. Phantom whispers wrapped around his tension, the words clear.

Don't fight, John. It is imperative that you understand. Please... come to me.

His breathing slowed and John Sheppard surrendered, letting the voice have him.

Hello, John, you're a sight for weary eyes.

Sheppard opened his eyes, not surprised to find himself standing in the park where he loved to run. Muted blue-hued light cast a monochrome glow over the panorama. He scanned the area, searching, pleased to discover the object of his curiosity sitting on one of the park benches wrapped in a flowing white robe with gilded seams, satin slippers on her feet.

He walked over and stood, studying her. She looked old, her back hunched with the ravages of 10,000 inactive years. Long, gray hair hung down to her knees; her deeply wrinkled face, strangely appealing. Gnarled hands covered in onion paper-thin skin clasped the head of a walking stick. She tapped the stick on the stone path three times and smiled a toothless grin with her pale lips.

"Come sit with me, child." Her aged voice skittered deep within his body, his skin alive with her energy. She may be ancient, but she was far from decrepit.

"Atlantis, I presume?" Sheppard quipped.

"So quick with the witty words; your ancestors would be proud to see you, standing there so full of life and promise." She tipped her head back, looking up at his cynical face with wise gray eyes. "Sit."

Not one to argue with his elders, Sheppard sat on the bench gingerly, careful not to harm Atlantis.

"Do not worry about me, child. You cannot harm me." Her all-knowing eyes sparkled with mirth. "However, it is kind of you to show such concern."

"I, ah, expected you to look... different." Sheppard ducked his head with a rueful grin at her sharp bark of laughter.

"You mean younger?" Atlantis reached over and patted his hand with withered fingers. "When your kind first arrived, I looked older than what you see before you. Each system your people repair, each technology you master helps to restore my youth."

"By repairing the city, we repair your image. Is that what bringing me here..." Sheppard waved his arms indicating the surrounding area. "is all about? You want us to restore your former glory."

Atlantis adjusted her body slowly until she sat facing Sheppard. "We have much to discuss, child, but let's not rush. Indulge an old woman, and walk with me." She braced her weight on the walking stick and used her other hand to press up on the bench railing, struggling to stand.

Sheppard sprang to his feet, quickly grasping her arm and helping her to rise. She looked so frail; he hesitated for a moment.

"Are you sure you want to walk? I don't mind sitting on the bench."

"I thought you might like a tour while we talk." She tucked her arm through his and started moving, the tap of her walking stick in time with their progress reminding him of a pedometer.

Sheppard studied her face surreptitiously as they strolled down the sidewalk. He listened intently while Atlantis pointed out buildings along the way, explaining what they used to hold, or what functions they'd served all those years ago. He felt humbled. Hers was a rich history, and she held information on every Ancient who'd dwelled within her walls. She was a living family tree just waiting for him to pluck from her the fruit of knowledge. Circling around the park, they eventually returned to the park bench from which they'd begun. Atlantis stopped, looking up at the abandoned buildings.

"You and your sister are the key to rebuilding all you see before you. I have been lonely all these years, empty and sad. I should be filled with the sounds of children's laughter, music, joy, love,... life." She sank down onto the bench, pulling Sheppard with her. "In order to awaken all the mysteries and wonders at your disposal, you need to first make the Pegasus galaxy safe from the Wraith. That is why I asked you to come see me. You have the answer, yet you choose not to recognize it."

"You're talking about the artifact. I assume you were the voice telling Jesi and I to work together. We tried, but it didn't work the way I thought it should." Sheppard looked out over the abandoned park, worry weighing heavily on his shoulders. "We couldn't control everything."

"Child, life is not always about being in control. Sometimes one must choose to let go, to trust in something intangible. One must learn to follow ones instinct. You have it, but you lock it away behind layers deep inside where no one can reach the genuine you." Atlantis reached a hand over and grasped his chin, turning him to face her. "It is time to take that leap, John." She stood, this time with no need of assistance from him.

"It is time for you to return. Do not give up on the device, as it holds the answer to peace in the galaxy. Your Doctor McKay is superior, but only you can unlock the true power contained within the device. Do not be fooled by its appearance. Like you, it holds many hidden layers. You must look below the surface, beyond what is seen with the natural eye, to reveal the truth." With that, Atlantis turned and headed down the path.

"Wait... Don't leave yet. There's so much I want to ask you!" Sheppard rose and watched her shuffle away. She turned once and allowed a quick wave before the scene before him evaporated into oblivion. Her cracked voice drifted back through the thickening darkness.

"We shall speak again, John. You must rest first, only then will you be prepared to meet your fate."


TBC