I'm sorry for the delay in posting - a combination of lots of family, busy, and getting side-tracked. This chapter moves kind of slow. I'm filling in gaps and setting the stage for later events, so please be patient.

The Mind of Atlantis - Chapter 13

"Rodney?" Rodney McKay turned around to see Sheppard standing in the doorway to his lab. McKay noticed a weariness to the pilot's face that spoke volumes about the toll the events of the past few weeks had taken on the man.

"Are you released or escaped?" asked McKay, wondering if he should call Beckett.

"I"m released...as of twenty minutes ago. I wondered...could I borrow you for a few minutes?" Sheppard asked hesitantly.

"Major, I'm actually working right now. Some of us have more to do than lie around the infirmary recuperating from our latest disaster, you know. Maybe later. Besides, I'm betting Carson told you to rest in your quarters, which you are most decidedly not doing." McKay tossed off the snide remarks in his usual fashion and Sheppard's expression remained neutral through it all.

"No problem, McKay. I'll take care of it by myself. Sorry to have bothered you." Sheppard's reply was delivered calmly, without any sign of anger or sarcasm, sending warning bells screaming in Rodney's head. He had no idea what Sheppard was about to do, but it was obvious that McKay needed to be there for him.

"Wait...I'm actually kind of ready for a break." McKay stood up and closed his laptop. "I'm in. What did you have in mind?"

Sheppard smiled and the relief on his face reassured McKay that he had made the right decision. "Something cool, McKay. Come on and I'll show you."

Twenty minutes later at the far end of Atlantis, Sheppard led the way down several flights of stairs with McKay struggling to keep up.

"You sure are moving...fast for...someone...who spends...half his...time...in the infirmary," McKay panted.

"We've really got to get you on some type of exercise program, McKay," responded Sheppard.

They reached the bottom of the steps and walked down the corridor. As they turned the corner, Sheppard stopped dead in his tracks, causing McKay to collide with his back.

"Hey!...Give a person some warning, Major. Maybe we should get you a set of brake lights." McKay stepped up to stand beside Sheppard, who was staring at a spot on the floor. "What are you..."

McKay caught Sheppard's arm as he started to sway and only then did he notice that all the color had drained from the Major's face.

"What's wrong? What do you..." And then it hit McKay like the proverbial ton of bricks. "This is where Marchaeus was killed, isn't it?"

Sheppard just nodded sadly. "I can still see..." Sheppard bit his lower lip, no longer able to find his voice. In his mind, he saw himself/Marchaeus having the life drained out of him by the wraith. His chest was beginning to tighten and the room was beginning to spin when McKay took him firmly by the arm and propelled him down the hall and around the next corner.

Sheppard leaned against the wall , breathing heavily. A shiver went through him as he tried to push the sights and sounds and the pain of death from his mind. "Thanks," he whispered softly.

McKay now understood why Sheppard had wanted him to come. He was facing his own death and he didn't want to face it alone. McKay was glad that he had pulled his head out of his rear long enough to realize that Sheppard had really needed him. It suddenly occurred to him that he couldn't remember the last time someone had needed him. Just him. Not his genius or his ability to fix things, but just him. Sheppard had needed a friend, not a scientist. He found this realization both exhilarating and frightening.

"McKay...you okay? You look almost as shaky as I feel."

McKay took a deep breath. "I'm okay. What about you? Should we keep going?"

Sheppard nodded, the color returning to his face. "Yeah, I'm okay now. Let's go. I've got something really cool to show you." He led the way down the hall. A few minutes later he stopped and looked at the wall in front of him.

"Why are we stopping? There's nothing..." McKay stopped mid-sentence as Sheppard waved his hand in front of the wall and a door slid open. "Wow...how did you...never mind." He followed Sheppard into a small room with what looked like large, old-time computers lining the walls.

Sheppard went immediately to a console that looked almost like a desk. He sat down in the chair in front of it and quietly stared at the structure, lost in thought.

"Do you know what to do?" asked McKay, mistaking his hesitation for uncertainty.

"I know what to do," he replied softly. He reached out and gently caressed the tiles on the console with his index finger. He almost seemed oblivious to the fact that McKay was there. "He was the last person to touch these. His last act before dying was to shut Atlantis down. He sat right here, McKay...right where I'm sitting."

McKay didn't know what to say. He just stood looking at Sheppard for several minutes. He finally reached out and touched Sheppard's arm. "You aren't Marchaeus. You're still alive...and you're living in the here and now. At some point...you're just going to have to let go."

Sheppard bowed his head and sighed deeply. "I know, McKay. I've watched a lot of friends and family die over the years and none of them hit me like this. This is stupid. I'm falling apart over the death of man I've never actually seen or talked to."

"No! It's not stupid. You have a tie to Marchaeus unlike anything any of us have ever seen. You lived part of his life through his eyes. You went through death with him. How much more of a tie to someone can there be? You may not have ever met the man, but you probably know him better than you know most of us. Heck, you may know him better than you know yourself. And because you have watched so many people die...maybe that makes this seem a lot worse. You know, like cumulative effects or something. Look, I just want you to remember that you are John Sheppard, not Marchaeus. What happened to him was...sad...but it's not what happened to you. You are still here and you still have a life and Atlantis still needs you...WE need you."

Sheppard sat staring at the console for a moment and then turned his face up to McKay. "So...are you studying under Heightmeyer or something? Sounds like you might be after her job?"

"Hey, a guy's got to have a second choice of professions in case the first one doesn't work out...although the thought of you people trying to make things run without my genius is frightening and pathetic at best."

Sheppard smiled. "Thanks. I seem to be saying that to you a lot lately."

"It's okay," grinned McKay. "I think I still owe you a few. Okay, now what's so cool about this place? I hope you didn't drag me all the way down here just to play closet psychiatrist."

Sheppard's expression brightened. He quickly touched several of the tiles in sequence and looked back up at McKay. "How would you like to meet Atlantis?" He touched one final tile and the panel lit up. Atlantis appeared beside them.

"Atlantis, meet Dr. Rodney McKay. Rodney, this is Atlantis." Sheppard would have given just about anything for a camera to prove that McKay was actually struck speechless.

Atlantis reached out and touched McKay on the arm. She frowned and cocked her head to one side. "You have Ancient in you...but it is different...and it is not as strong."

McKay pulled his arm away from her. "Yes...well...mine is different...It's something we call gene therapy. I wasn't born with the Ancient gene, so our doctor...added it to me," he attempted to explain.

"That is interesting. You must tell me more later." She turned to Sheppard, making McKay feel sort of like an inferior who had been dismissed. He was somewhat disturbed by the feeling, aware that he was usually the one dismissing people that he felt were inferior to his intellect.

"John...I'm glad to see that you are all right. I do not understand how this happened."

Sheppard looked confused. "But I saw in my ...dream or vision or whatever the heck that was, that Marchaeus left...his memories for me. I thought I was supposed to access it...that it was supposed to happen."

"It is true that Marchaeus left much of his life for you to see. I was surprised when you accessed it without coming to this room. You should have had to access it through this control console. Apparently your tie to Marchaeus allowed you to interact with the program without coming here. The link was further strengthened when you visited his quarters. What I really cannot explain is..."

"Atlantis, what is it?"

Atlantis took Sheppard's hands in her own. "You should not have seen any more of Marchaeus's life after he shut me down in this room. You should not have seen, much less experienced, his death. I cannot explain that."

Sheppard looked flustered. "Then how..." he said softly.

McKay looked at Atlantis. "Did you see Marchaeus die?"

Atlantis looked sad as she turned to McKay. "Yes...I saw him die...and I could do nothing."

"That's it. The Major has a very strong connection to you and to Marchaeus. I'm guessing you also had a very strong connection to Marchaeus. The tie didn't really end when he shut you down...at least not the connection between you. You recorded things that happened in his life through your connection to him. That connection didn't really end until he died."

Atlantis looked horrified. "That would mean...that I did that to you. I hurt you..."

"No...you didn't hurt me. I'm okay. And...it was something I needed to see. I needed to know the whole story."

Atlantis glanced over at McKay. "You are very wise for someone who is not...Ancient...by nature."

McKay just grinned smugly. "They don't call me the answer man for nothing!"

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Sheppard and McKay entered Weir's office. Beckett had arrived just ahead of them.

"Is everythin' all right?" asked Beckett, ever worrying about his charges.

"We're good," replied Sheppard. "I have someone I want you to meet."

Beckett and Weir looked at each other, shrugged their shoulders, and turned back to Sheppard and McKay. "Okay," said Weir. "I'll bite. Who do you want us to meet?"

"Atlantis," said Sheppard.

Weir raised one eyebrow at them. "How is that possible? I thought you were the only one who could talk to Atlantis."

"I was. When I accessed Marchaeus's memories, it showed me how to...activate Atlantis so that she can appear and interact with pretty much anyone in the city. She'll be able to help us a lot more now. It also allows her to move around the city a lot more freely and opens up a lot of her functions."

Weir sighed loudly. "Are you sure this is a good idea?"

Sheppard looked crestfallen. "What do you mean is it a good idea? What are you implying? Atlantis is trying to help us revive the city. We need her."

"I'm just saying we don't know an awful lot about this whole situation and it sounds like you've just given her more control. I wish you had contacted me before doing this."

Everyone but Sheppard jumped when Atlantis suddenly appeared beside Sheppard. Her hand went immediately to his arm. "Do not be angry with her, John. She is just watching out for the members of the expedition. It is her job to be suspicious. Perhaps she is right. Perhaps you should have discussed this with her before reactivating me."

Sheppard was trying to breathe deeply and slowly and control the anger he felt brewing inside. "Actually, I think this means she doesn't trust me to make decisions."

"No. That is not it. I do trust you. I just prefer to be cautious. I don't know Atlantis, so I don't know whether to trust her or not."

Sheppard sighed and then looked straight at Weir. "Elizabeth...do you trust me?"

She met his eye contact and held it. "I trust you, John."

"Then you trust Atlantis. I know you don't understand, Elizabeth, but we are linked. She is in me and I am in her. I would know if we couldn't trust her. She's here to help us. Show me that you trust me."

Elizabeth continued to look at Sheppard, her mind racing. She finally relaxed her tense shoulders and let out a deep breath. "I trust you, John. If you say we can trust Atlantis, then I trust her too."

The tension in Sheppard's face eased. "Thank you Elizabeth. You won't regret it. She can help us."

Elizabeth smiled at Atlantis. "I think maybe we got off on the wrong foot. Let's start over. My name is Elizabeth Weir and I'm very glad to meet you."

Atlantis smiled and bowed her head slightly towards Elizabeth. "I believe that we can help one another."

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It was several days later when Sheppard finally convinced Beckett and Weir to let him continue the training process. The next step was to carry out the simulations on one of the consoles in the training room. The only way Weir had allowed the activity was for McKay to check everything out first and for Beckett to be sitting in the room with a medical team. Sheppard whined that all the fuss was not necessary, but Weir and Beckett overrode him. He was not happy when Atlantis agreed with Beckett and Weir and made several obnoxious comments about having three mothers.

When everything was declared clear, Sheppard went to work on one of the consoles. McKay and Beckett watched in fascination for a while as he worked through several simulations, alternately bringing up screens, moving tiles around, exchanging crystals in a side panel, or punching buttons on a section that looked like a keyboard written in Ancient. Eventually, they got bored and embarked on a run of card games with a deck Beckett carried in his medical bag. McKay would periodically check various laptops he had set up around the room and then return to their game. Beckett was noticing that Sheppard had been at it for several hours and was about to suggest he take a break when the Major stretched and yawned. He started to get up from his position sitting in front of the console when Beckett appeared beside him and pushed him back into the chair.

"Are you finished, Major?"

"I'm done."

"How do you feel?" asked Beckett as he took his pulse.

"Good. A little stiff from sitting so long, but otherwise okay." Sheppard waited patiently while Beckett continued his check, taking his blood pressure and temperature and listening with his stethoscope.

Beckett crossed his arms and looked down at Sheppard. "Major...as near as I can tell, you're fine."

"I think that's what I said." Sheppard grinned at Beckett mischievously. "Hey, I feel pretty good. Maybe we could do a session in the chair this afternoon."

"No!" said Beckett and McKay in unison. They looked at each other briefly and then back to Sheppard.

"Okay...it was just a thought. When then?"

Beckett looked uncomfortable. He still didn't like the idea of Sheppard getting back in the chair. He was still remembering what had happened the last time. Sheppard sensed his unease.

"It's okay, Doc. We have the chair thing worked out. It won't be like last time."

"I'm not so sure, but, I guess if Elizabeth okays it, you can go day after tomorrow."

"Doc...what about tomorrow? I feel good."

"Major...I said the day after tomorrow...and not a minute sooner." He jumped as Atlantis appeared beside John and just a couple of feet away from him. "Bloody...do you have to be doin' that?"

Atlantis smiled at him. "I am sorry doctor. I did not mean to startle you." She touched his arm reassuringly as she spoke and smiled even more. "You have the...gene. You are strong in the gene...not as strong as John...but still strong."

Beckett looked embarrassed. "Well...yes I do have the gene. I'm not very good at activatin' things like the Major though. Sometimes...I'm a little dangerous."

"I could help you control your abilities more, if you like. You cannot be a key, as John is, but there are many things you would be capable of. We may speak of this later."

Beckett nodded. "Later would be good. I need to get the Major through these trainin' sessions in one piece first. Are you sure the chair will be safe for him this time?"

"I am sure." She said it with such confidence that Beckett found himself relaxing and worrying a lot less about the situation.

Atlantis turned to John. "You have done very well. I was not expecting you to finish the first set so quickly. You have assimilated the information rapidly. The training will not take you long."

"Good. I guess we go again day after tomorrow then." Sheppard looked over at McKay. "You hungry, McKay, cause I'm starving."

"Starving, naturally. Carson, want to join us in a trip to the mess hall?"

Carson considered the offer. "Well, I am a wee bit hungry myself. I guess I will join you lads for a bite."

Sheppard looked at Atlantis. "I know you don't eat, but you're welcome to join us."

"Thank you for the offer, but I believe I have other things to do," Atlantis replied. And then she was gone.

Sheppard, McKay, and Beckett left the training room and headed for the mess hall. Although none of them said anything, they were each relieved that the session had gone so well and that they were walking leisurely to the mess hall instead of rushing desperately for the infirmary.

TBC