Disclaimer: I do not own Stargate Atlantis or any of its characters. This is just for fun.

Note: This is a sequel to "Mind of a Child" and begins about two weeks after that story ends. They are both set about midway through the first season.

Mind of Atlantis - Chapter 1

"I still can't get this one to work," said Rodney in exasperation. Sheppard walked over to the console and stood looking at it, one hand cradling his chin as his elbow rested on the other arm now folded in front of his chest. He moved his hand across the panel, but nothing happened.

"Oh...got it." He shifted several tiles around and then sat in the floor beside the platform. He laid back in such a way that he could lean his head under the console and began poking around.

"Do you really know what you're doing?" asked McKay, bending over and trying to see what Sheppard was up to.

"Yes, McKay...for the forty-third time today, I know what I'm doing. You're giving me a headache." Sheppard really did have a headache, but it wasn't just now kicking in. He'd been fighting it since he climbed out of bed that morning. He could feel the exhaustion creeping in and weighing him down. Beckett was going to have his hide. Beckett had released him from the infirmary one week ago with instructions to rest and take it easy. He'd gotten bored after a couple of days and started bothering McKay in his lab. Three days ago, the daring duo had decided to check out the ancient lab that had reduced Sheppard to a six-year old (at least in mind, if not body) not so long ago. They just poked around checking things out for a couple of hours the first day, but had been hard at work trying to get things up and running the past two days. Sheppard was beginning to think there might have been a valid reason for Beckett telling him to take it easy.

"John Sheppard?" A faint whisper.

Sheppard sat up suddenly, banging his head on the edge of the console as he failed to completely clear it. "Ow! Dang it! What?" He pulled his head out from under the console, rubbing the top as he glared at McKay. "What do you want?"

McKay looked confused. "I don't want anything...except maybe for you to hurry."

"Then why did you call me?"

"Look, Major, I didn't call you. I didn't say anything. Are you done yet?"

Sheppard shook his head. "Oh...I thought I heard my name...uh, yeah, I'm done. Let's try it again." He stood up and moved his hand across the face of the console, lighting it up like a Christmas tree. "There, told you I knew..."

McKay glanced up in time to see Sheppard starting to lean unsteadily to one side. Grabbing Sheppard's arm, he steered him to a chair and pushed him into it. Sheppard leaned forward and put his head in his hands.

McKay looked at his watch. "Oh, holy crap. It's almost 10 o'clock. If Beckett knew I'd had you hear this long...We've got to get back and get you into bed. Are you okay? Do I need to call Beckett? Of course if I do, we're both doomed to an eternity of..."

"McKay!" Sheppard sat up and looked at him. " I'm okay. Just got a little dizzy, okay?"

McKay realized for the first time how tired Sheppard looked. "Why didn't you tell me you needed to quit? You know how I get caught up in what I'm doing. Just tell me you're tired and we'll take a break."

Sheppard gave a small smile. "Hey, McKay. I'm tired. How about let's take a break?"

"Funny. Very funny." McKay had been around Sheppard enough to read the lines in his face. "You're hurting, too. Headache?"

Sheppard was surprised that McKay had picked up on that. "Yeah...a little one."

"Liar," he snorted. "Can you make it back to your quarters?"

Sheppard looked annoyed. "I'm tired...not an invalid. Of course I can make it back."

McKay nodded. "Good. Let's get out of here then...before Beckett finds us."

"Sounds like a plan, McKay." Sheppard got up and walked over to the large console in the center of the room. He sat down in front of it and placed his hands in the indentions provided for just that. The now familiar blue light came up from the floor and covered him, seeming to hover for a minute as he sat concentrating. Everything else in the room went dark. The blue light returned to the floor. McKay watched for a few seconds before walking over to stand by Sheppard and put his hand on his shoulder.

"You okay?"

Sheppard startled slightly at his touch and opened his eyes. McKay wondered briefly if the man had drifted off to sleep.

"I'm good...just really tired. Let's get back." The control console went dark as he walked away and the room darkened as the two men headed out the door and back to the main part of the city. Sheppard could have sworn he heard faint whispers as they walked quietly down the corridor, but said nothing to McKay. He was pretty sure his exhaustion was causing him to hear things and he didn't want to give McKay any more cause to call Beckett. He had no intention of returning to the infirmary any time soon. But then, you know what they say about the best laid plans...


Sheppard looked around and realized he was on a balcony. It appeared to be the balcony over the southwest pier, his favorite because of both the view and its secluded location. The question of the hour was how did he get here? The last thing he remembered was climbing into bed, so tired he could barely think and his head throbbing like someone inside had a sledgehammer.

"John Sheppard?"

Sheppard turned toward the sound of the soft voice to see a woman with long, blonde hair dressed in a flowing white gown. Her features were soft and her eyes were a bright, crystal blue. "You are John Sheppard. We have been waiting for you."

John's expression illustrated his confusion. "Well, it seems you know my name. Who are you and how did you get here?"

The woman smiled. "I am Atlantis and I have always been here."

"You...are Atlantis? I...I don't understand. The city is Atlantis."

She continued to smile as if explaining something simple to a child. "I...I represent Atlantis...I guess you could say I'm the mind of Atlantis. Everything in the city is coordinated through me. And yet the city is also divided into segments that can be operated independently. But I am the one who makes it whole. I unify the parts so that collectively we form Atlantis."

"You said you have been waiting on me. Me specifically?"

"No, not particulary on John Sheppard. We have been waiting on the builders to return. We always knew they would come back, and now you have. We have sensed your presence in the city and have wondered why you did not seek us out. Have you not heard me calling to you?"

Sheppard thought for a minute about all the times he seemed to feel something in the city...a living presence...a presence he had ignored, assuming he was imagining things. Sometimes it seemed as though someone was whispering in his ear. He knew he had heard whispering as he and McKay left the lab. It had been Atlantis calling him. "I guess I heard...but I did not understand. You have to understand that I'm not really an ancient. I have a gene that they had...well, maybe more than one if you listen to McKay, but I'm not an ancient. I don't know anything about this stuff."

"That would explain why you had your recent trouble that affected your mind. We were glad to see that you were able to be repaired. You seem to be the only one capable of unlocking the quantae so that Atlantis can be fully awakened. Since you have not been prepared, I will guide you as to what must be done and how to use your...gene. You may not think you are an ancient, but to Atlantis you are. You just need to be trained."

Sheppard was getting excited now. "So...you'll help me know what to do? That would be great! There's so much here that is over our head. We're really hoping to get enough up and running that we can protect the city against the wraith."

Atlantis frowned. "The wraith. They are the scourge of the galaxy. I look forward to the day we are rid of them."

"You and me both," said Sheppard. "So...what can you tell me?"

Atlantis smiled and once again, Sheppard found himself feeling like a child in the presence of a much older and wiser adult. "First you must slow down. You are draining your energy too quickly. The consoles that you have been activating, the ones with the quantae, draw energy from the person using them. You must actually form an interface...a bond with the technology. This was not a problem in the grand days of Atlantis. There were many people who were trained to operate each one and they took turns so that no one person became too weak. You have been trying to operate several by yourself with no time to recover in between. Is there no one else with this...ancient gene?"

Sheppard sighed. "We do have others with the gene, but mine seems to be...stronger, for lack of a better word. We could bring some people down and try, I suppose."

Atlantis paused and frowned again, cocking her head as if she was listening to something. "You may if you wish, but you are right that yours is the strongest. It is you that we have been sensing, so I do not think any other will have the ability to unlock the quantae. They may be useful in the future, however. Once you are trained and have the technology set and initiated, you may instruct it to run with the assistance of others with the gene. It must still be you that starts and stops the process, as well as makes any adjustments in its function. We will discuss this later. You have done too much these past two days. You must rest and then we will proceed. But you must allow me to guide you. If you do not use the technology properly, it can be dangerous."

"Yeah," Sheppard sighed. "Tell me about it," he said, remembering his recent time with the mental capacity of a child. "Is that why I had that headache all day...because we worked too long?"

"Yes. And if you continue without a proper recovery period, it can have serious consequences. I must go and let you rest. I will visit you again when you are ready and tell you what you should do next. But I will always be here and I am always listening."

"Was that you today...in the lab?" Sheppard asked, suddenly remembering hearing his name.

"Yes, that was me. I was trying to find a way to communicate with you."

"Well...I'll be listening from now on. I just didn't understand before."

She put her hand on his arm. "I know you feel at home here. More at home than you have ever felt before. The reason is because you belong here. Atlantis is your home. It is where you were meant to be. Together, we will make the city alive again."

Sheppard smiled at her, knowing in his heart that she was right. He was home.


Bang! Bang! Bang! Sheppard, lying on his stomach, jerked his head up at the sudden, loud rapping caused by someone beating on his door.

"Major! Are you in there? Open the door." He put his face back down into the pillow. Rodney McKay. What did he want and what time was it anyway?

"Just a minute!" he yelled toward the door. He twisted around and swung his legs over the side of the bed. He started to get up, wishing the door would open on its own. The door swooshed open to reveal McKay with his hand in the air as if to knock, Carson Beckett, and Elizabeth Weir. They stood there looking surprised for a few seconds, until McKay finally voiced what they were all thinking.

"How...how did you do that?"

Sheppard was as surprised as any of them. "I...I just thought that I wished the door would open by itself...and it did. Cool. Now I can get into that." Sheppard went to stand, but swayed unsteadily. Beckett was beside him almost instantly, taking him by the arm and guiding him back down to the bed.

"Take it easy, lad. Have a seat and let me have a look at ya'."

"Wait a minute," Sheppard said irritably, pulling his arm away from the doctor as he stood back up. "Nature is calling...and very loudly I might add." He shouldered his way past the doctor and into the bathroom. He returned a few minutes later and, at Beckett's direction, sat back down on the edge of the bed.

"Why are all of you here? Did I miss a meeting or something? And what time is it?"

Elizabeth sat on the edge of the bed beside him. "We were worried about you. No one's seen you all day and we couldn't raise you on the radio. John...it's five o'clock."

"Five? As in 1700 hours? You're kidding!" John began frantically looking around for his watch. How could he have slept almost 18 hours? And the kicker was that he still felt drained and he still had that killer sledgehammer headache. He realized that he was really hot, too.

"Calm down, Major. Yes, it's really five p.m. That's why we were worried about you. Have you slept all this time? And you might as well know, lad...Rodney told me everything." Beckett eyed him suspiciously, a warning to tell the truth.

Sheppard scowled at McKay. The traitor. "Yes...well, no...er, uh, actually yes." He was getting confused. He remembered being on a balcony talking to someone, but he couldn't remember to whom or when it had happened. He thought it was recent, but he couldn't actually remember going to the balcony or leaving the balcony. His headache was escalating and, as he put his hand to his forehead, he felt the sweat slicking his brow. He felt slow and sluggish and he was starting to feel dizzy again. He was vaguely aware of Beckett saying something about a fever and hands helping him lay back on the bed and then the darkness swirled in and washed him away.


Beckett sat down at his desk and looked across it to Elizabeth Weir and Rodney McKay.

"Carson, what happened... is he okay?" asked Elizabeth, worry lines etched into her face.

"He'll be fine. As near as I can tell, he's overdone it - now there's a surprise. He's exhausted, slightly dehydrated, and running a bit of a fever. He'll be my guest for a few days 'til his temperature is back down and he's properly rested." Carson glared at McKay. "Rodney! Are ya daft, man? What were ya thinkin' , workin' him in that lab all those hours when ya knew he was supposed to be takin' it easy? We almost lost the Major Sheppard we know in that lab and ya drag him back down there and near work him to death."

"First of all," McKay said angrily, "I didn't drag anyone. He was bugging me to do something because he was bored. You know how he is. He can't just sit still, he's got to be doing something all the time. He's like a child..." McKay cringed at the unintended reference. "Well, you know what I mean."

Beckett sighed heavily. "I know Rodney...but next time...can't you just tell him no or at least quit a little earlier or call me and I'll come after him. If he's not going to look after himself, then we'll have to help him."

"I'm sorry. You're right, of course. We didn't intend to stay long and...we just got caught up in what we were doing. I didn't realize it was so late or that we'd been there that long. I didn't...I didn't mean for him to get sick." McKay's first thought had been to defend himself, but that had quickly given way to guilt over Sheppard's condition.

"I know lad. I didn't mean to be so harsh with you. It's only been a week since I got him out of here and I'm a wee bit worried about the Major. I've seen entirely too much of him lately. Why don't we go check on him?" With that, Beckett stood and headed for the door. Weir and McKay followed right behind him.

Sheppard seemed restless as they approached the bed, moving around under the covers and mumbling softly in his sleep. Beckett stepped up and checked his IV line. After he took the Major's pulse, he turned back to McKay and Weir. They were both leaned forward and concentrating, trying to hear what Sheppard was saying. Beckett listened for a minute, but couldn't make any sense of it.

"Do you hear that?" McKay asked Weir, disbelief on his face.

"I hear it," she said, "but I'm not sure I believe it. How is that possible?"

Beckett stared at the two in confusion. "What are you two talkin' about?"

McKay looked over at him. "Can't you hear him, Carson? He's speaking Ancient."