Chapter 29: Debrief.

John sat staring at his computer. He knew he was supposed to contact Stargate Command, but a feeling of apprehension overcame him, and John couldn't explain it. He knew that O'Neill and Carter would be worried because the last thing Carter knew was an unknown enemy was tearing planets apart. For all Carter knew, there was nothing left of Atlantis. Luckily, Atlantis had survived. But unfortunately, New Lantia hadn't.

Perhaps it was something to do with the fact that although he was physically fit according to military guidelines, he hadn't done the Psych evaluations. But that would have been impossible because their psychologist had died. Even though Carson and Jennifer had deemed him emotionally sound, it still wouldn't be good enough for the SGC or IOA. The thought of being forced back to Earth to face a psychologist scared him, so maybe that's why he was putting off making the call.

He'd just enjoyed a meal with his family, and it was the first time he'd been able to relax for a while, but contacting the SGC was always in the back of his mind. Truthfully, he wasn't as relaxed as he could have been.

He knew it was now or never, so he stood and walked to the control room.

"Chuck, please contact Stargate Command and set up a video link. Then put it through to my office."

"Yes, sir, "Chuck replied, "Right away, sir."

John smiled as he walked back to his office. His staff were so formal when they were on duty. But at least he knew they respected him.

Once seated in his office again, he opened his laptop and waited. He was surprised when Ronon and Rodney walked in a few seconds later.

"Hey guys, what are you doing here?"

Rodney sat in front of John's desk and stared at him, "You didn't think we'd allow you to face the SGC alone, did you? I know you've been putting this off, and considering what has happened to us over the last three months, I don't blame you."

"Aye, lad, I'm with you, too," Carson said, walking through the door.

Ronon nodded and smiled in agreement.

Before the conversation could continue, General O'Neill's face appeared on his computer screen, "It's about time you showed up, Sheppard. Where the hell have you been for the last six months?"

"Well, it's a long story, sir, and may take a while to explain. Do you need us to come back to Earth?"

"No, give me an hour, and I'll come to Atlantis and stay for a few days. Carter can keep an eye on things here."

A sudden thought occurred to him. If Carter was at the SGC and O'Neill was coming to Atlantis, what had happened to Landry? He wasn't fond of Landry but hoped nothing had happened to him.

"Where's Landry, sir?"

"He's decided to retire. But I give him six months before he's begging to return to work. Now, I gotta go, pack my bags. I'll see you in an hour, Sheppard."

"Are you sure you don't want to wait until morning, sir? It's late, and I may need to help Teyla put the children to bed."

"Wait, did you say Teyla?"

"Yes, sir, we found a cure for the poison of the Jazella plant."

"Well, this I'd like to hear about. I'm coming over in an hour. If you don't want to talk tonight, give me some quarters, and we can start tomorrow. O'Neill out."

For a moment, John was speechless as he looked across his desk at Rodney, Ronon and Carson.

"Umm…O'Neills coming over straight away. Well, not exactly straight away, but in an hour."

"Does everyone know what to tell O'Neill?" Ronon asked in a matter-of-fact tone.

"Yes, Chewie. I'm fairly sure we'll just tell him the facts."

"Sure, Sheppard, but does that include our trip back in time?" Rodney asked, "And what about your brain damage and seizures? I know Sheppard's healed, but Carson, what are you going to tell O'Neill?"

"I will tell O'Neill about John's head injury, but I won't mention the words brain damage or seizures," Carson replied.

Carson had told John on more than one occasion he wouldn't mention the seizures, but it was always reassuring to hear the doctor reiterate the fact. Although, O'Neill wasn't dumb and would pick up the fact that something was wrong with John. Carson had deemed him fit according to the military standards, but John knew he'd barely passed the fitness portion of the exam.

"So, do you guys want to start watching a movie while we wait for O'Neill?" Rodney suggested.

"I'm in," Ronon replied, nodding.

"What about you, Carson?" Rodney asked with a hopeful look.

"I'm off to the infirmary to work on some paperwork."

Although John would have loved nothing more than to relax with his friends, he still had letters to write. He'd almost finished the letters to the families of the deceased, and he wanted to finish them as soon as possible.

"I've got letters to write. So I won't be coming."

Rodney nodded and left, "Let me know when O'Neill gets here?"

"Sure, I'll let you all know. But I think O'Neill may like to speak to me before anyone else."

He watched as his friends left the room one at a time. Even though these men were his friends, it didn't change the fact that he was the leader of Atlantis, and his head was on the chopping block if anything went wrong.

Sighing, he looked at what letters to write and decided on writing letters to Corporal James and Lt Peters' families. They had died from an allergic reaction to the white berries found on CXZ-117. The white berry incident had occurred before the destruction of New Lantia. Although James' and Peter's remains were returned to earth several months ago, John hadn't written letters to their families.

For the next forty-five minutes, he worked steadily, and by the end of that time, he was happy to have finished both letters. He was about to start on a third when the chevrons on the gate began to light up.

He rushed to the control room and was surprised to find Chuck still on duty, "Who is it, Chuck?" He asked when the wormhole finally sprang to life.

"It's General O'Neill, Sir."

"Right on time, "John muttered under his breath.

Straightening up, he turned to Chuck, "Drop the shield and let him know it's safe to come through."

John rushed down the stairs to the gate room and arrived just as O'Neill stepped out of the wormhole.

"General, it's good to see you again," He said, giving a crisp salute.

"Call me Jack, Sheppard and stop saluting me?" O'Neill looked around the room before continuing, "Where's your entourage?"

"I'm not sure what you mean, Sir?"

"Beckett, McKay and Ronon Dex. I know they were with you when we spoke over the video link. And stop calling me Sir. It's just Jack. I want the meetings over the next few days to be as informal as possible. Alright?"

"Yes," he was about to say, Sir, but stopped at the last minute, "Jack. And Beckett, McKay and Ronon are watching a movie. They wanted me to tell them when you arrived, but I'm happy not to."

"Okay, then, Sheppard. Let's go to your office because I want to know what happened to you since you look like hell."

He nodded and followed as Jack led the way to his office. John had no idea how the next few days would play out, but if O'Neill seemed relaxed about things, he should do the same.

Once they were sitting in his office - Jack sat behind his desk, and he sat on the opposite side - O'Neill got right down to business.

"Okay, Sheppard. Tell me about the scars on your forehead and the one on your left temple."

He thought the scars had faded to the point where they were hardly recognisable, but clearly, he was mistaken.

"Well, the wound on my left temple was caused by a gunshot wound. And the scars on my forehead are from needles embedded in my skull to power an ancient city. "

There was a look of horror in O'Neill's eyes, even though he tried not to show it, "I'm sure there's quite a story to it, but I think I'll wait until morning for you to fill me in. Let Beckett know I want to see him in the infirmary at 0800 hours, and he can fill me in on medical matters concerning the expedition. I'll talk to you then, and I will then talk to Dr McKay, who can then fill me in on scientific concerns.

"Yes, Jack. Is there anything else before I show you your quarters."

"How are Teyla and the kids? Charin must be about ten months by now."

He didn't really want to tell Jack that Charin had celebrated her birthday a few days ago because he was too tired to go into a long-winded explanation, so he opted for evading the question, "Yes, she's growing up fast, and she looks more like her mother every day."

"That's probably a good thing, Sheppard," Jack said, and John didn't miss the joking tone in the man's voice.

John was beginning to feel weary by this point, so he was grateful when Jack said he was going to bed.

"Would you like me to show you to your quarters, General?"

"No thanks, Sheppard. I'm guessing it's the same room I always use?"

"Yes, Sir. I mean Jack."

Jack grabbed his small bag and nodded at him before leaving his office. Once O'Neill had left, he sat behind his desk and put his head in his hands. So far, things seemed to be going well, but John had no idea what tomorrow would bring. The best he could do was go home and spend the rest of the evening with his wife and children and let tomorrow take care of itself, for it would come soon enough.

oOo

Carson wandered into his office ten minutes before eight o'clock and was surprised to find O'Neill sitting there and talking with Jennifer. He wondered what they were talking about. He hoped it wasn't him.

"Good morning, General, Jennifer."

"Ah, Dr. Beckett, we were just talking about you," Jack said, and Carson couldn't tell whether he was joking.

"Really? What were you saying?" He asked apprehensively.

"Relax, Doctor," Jack began, "Jennifer was telling me what's happening with her and Dr McKay. She also tells me you have a new lady friend."

Suddenly, his cheeks flush red, "Umm…yes."

"Who's the lucky lady, Carson?" Jack asked with a grin.

"Umm…Dr Jasmine White." He had no idea if it would be a problem with the SGC, but he hoped not.

"Relax, Carson. If me and Carter can get married and make it work, the SGC won't have any problems with you two getting married."

"Thank you, Sir."

"Anyway, I must get going now," Jennifer said, standing before leaving the office.

Once Jennifer had left, O'Neill turned to him, and he looked serious, "So, tell me what happened to Sheppard?"

"I can give you his medical files, but if you want to know more, you'll have to ask him, General."

"Okay, I'll read the file, but you need to tell me whether he's fit for command of Atlantis. Because he looks like hell."

Carson sighed because he knew the SGC would ask questions like this and was ready for it.

"I believe John Sheppard is one hundred per cent capable of leading this expedition. He may look tired, but after what we've been through over the last six months, we all are."

He knew it was closer to nine months if he included the time they'd spent in the past, but he wasn't sure how much Sheppard had told him about that adventure.

O'Neill's reply was abrupt and rude. "I didn't ask you if you thought he was capable. I asked if he was fit to command Atlantis!"

"If you look at the medical file, you can see for yourself. John Sheppard underwent military evaluations after he recovered from his injury."

Carson watched as O'Neill slowly read through his report. He hoped O'Neill wouldn't mention that a psychologist hadn't performed the psych evaluation.

General O'Neill looked up from the file he was reading, "Why didn't Dr. Robinson conduct the psych evaluation?"

"Because, unfortunately, she died," Carson said without emotion.

"Oh..," O'Neill replied.

"Rather than explaining how she died, I can give you her medical file. We've lost a lot of people since the destruction of New Lantia. I can also give you their medical files if you'd like."

"I wondered why you were on a different planet." O'Neill began, "Perhaps we should proceed to the conference room, where I can hopefully get the whole story. Can you arrange for Dex and McKay to meet us there?"

Carson nodded, relieved. He was still worried about the possibility of Sheppard having to return to earth, but for the moment, O'Neill seemed satisfied.

"I'm Sorry, Dr. Beckett, but we both know the IOA would want a thorough investigation into what happened to Atlantis. And unfortunately, given Sheppard's head injury, they will insist on knowing he's fit to command Atlantis."

"I know General O'Neill, but if you knew what we've all been through in the last few months, you wouldn't question our ability or fitness to do our jobs."

"You know I'm on your side. Right, Beckett?"

"I believe you are, General. I hope you can convince the IOA that all is well here."

"I'll do my best, but first, I need to be sure all is well."

"All I ask is you speak with General Sheppard, Sir."

"I will. How about I meet you in the conference room in twenty minutes, Doctor? Will that be enough time to contact the others?"

"Yes, it should be."

"I'll see you then," O'Neill said as he stood up and left with a pile of medical reports.

Carson sighed, knowing the meeting in the conference room would be another difficult one. He only hoped that John's recent brain damage and previous seizures wouldn't come to light.

oOo

John sat alone in the conference room, wondering why O'Neill had decided to conduct the meeting there. The last thing O'Neill had said to him was that these meetings were supposed to be informal. Given the meeting was in the conference room, it left John feeling apprehensive.

He was surprised when Carson walked in, followed by Rodney and Ronon. The last thing he knew was O'Neill wanted to meet with him alone.

"Hey, what are you guys doing here?"

"General O'Neill said he wanted us all here," Carson informed him.

Suddenly, he felt uncomfortable, "Am I in trouble?"

"Don't think so, Sheppard," Ronon said, slapping him on the back, "I think O'Neill wants to know all the details of what happened in the other galaxy."

John turned to Carson and asked, "O'Neill didn't ask you any awkward questions, did he?"

"No, he just wanted to look at your medical file. And he asked whether you were fit to command Atlantis."

"And what did you tell him, Carson?"

"I told him you were, and he should look at the medical file for proof."

John could live with that, but the only question was, would the IOA accept Carson's report on his health and fitness?

He didn't have a chance to speculate any further because O'Neill sat down and immediately started to ask questions.

"Sheppard, why don't you tell me what happened after you left the Hammond and returned to Atlantis? We never heard from you after that."

"Well, sir. We tried to contact the Satedans and had no luck. Then we sent Todd to check it out, and he found a dust cloud where New Sateda should have been. New Lantia was destroyed a month later. For the next six months, we were pursued across the galaxy by an unknown enemy. It was about that time Teyla was put in stasis until the doctors could find a cure for the poison in her system. We found refuge in a nebula after we found the debris from the New Athosian home world. It had also been destroyed.

"Did you witness the destruction of New Lantia, Sheppard?"

"Yes, as did several other members of the crew."

"And did you have nightmares, Sheppard?"

"General O'Neill, let me remind you that this isn't a psych evaluation, "Carson warned.

"Sorry, I'm just trying to be thorough. What happened when you entered the nebula."

Rodney took over the conversation, "Well, it was just like any other nebula, made up of helium and hydrogen."

"I don't need a science lesson, McKay."

"Sorry, Jack." Rodney apologised. "Anyway, when we arrived in the nebula, we were sucked into a strange anomaly and found ourselves in another time and galaxy."

"Really?" Jack said, his eyes open wide, "Go on. What happened next?"

We didn't know where or when we were, and we needed answers. I detected a planet nearby, so Sheppard, Carson and I took a jumper to investigate. And what we found was disturbing."

"Why, what did you find?" O'Neill asked, sitting forward in his chair.

"The Hilarians had been using ATA gene carriers to power their city for thousands of years. They had a breeding program in place to make sure there were carriers in each generation. There was a separate area in the city for the gene carriers, and they believed it was a great honour to be able to help their city in this way. The only problem was the power chambers were sending the gene carriers blind before killing them." Rodney took a deep breath before continuing, "Upon entering the city, the Hilarians scanned us and found out about Sheppard's supergene. Naturally, they decided to use him in the chamber, and what was worse was they wanted to use Carson and me in the breeding program."

"I take it that caused the scars on Sheppard's forehead," Jack speculated, "What happened next? How did you get out of there?"

"Well, Ronon and Lorne turned up, "Sheppard began," We also had some help from on the inside. A woman named Sophia and a man named Logo. But do you want to know the worst thing about the situation?"

When Jack nodded, he continued, "The inhabitants of the Hilaring home world were descendants of the ship chasing us through the Pegasus galaxy. Somehow, it arrived in the Galaxy ten thousand years before us."

"How do you know they arrived ten thousand years before you, and which Galaxy were you in?" O'Neill asked with interest.

Ronon took over the conversation, "When Lorne and I landed, we came across a historian named Jonon. Johan was charged with conspiracy against the doctrine and thrown out of the city. Apparently, his ancestor's ship came through the anomaly ten thousand years ago and crash-landed on Hilaring."

"Ronon, that's great. But I don't need a history lesson. Did you ever work out how far you went back in time and where you were?" O'Neill asked, and John could sense his impatience.

Rodney took over the story, "Well, we worked out we went back ten thousand years, and we were in the galaxy known as KK203, which is 60,000 light years away from the Milky Way galaxy. So if we went back ten thousand years, the unknown enemy who became the Hilarian's descendants travelled back twenty thousand years."

"Again, I don't need a history lesson. How about you tell me how you got off Hilaring?" Jack said, and it was clear his patience was wearing thin.

Carson took up the story, "Well, we managed to disconnect General Sheppard from the chamber, but Toth, the council's leader, didn't want us to take John, so Toth shot John in the head. When Toth fired, Voth knocked his hand, so he only managed to graze John's skull. We managed to get John off the planet, but not before civil war broke out. Jennifer and I managed to fix up John before I returned to the planet to deliver medical supplies and power generators."

"Why would they need power generators?" Jack asked, and this time, his impatience was gone.

Caron continued, "There were power failures all over the city because the gene carriers were disconnected from the city, so the Hilarians needed all the help they could get..."

Before Carson could continue, Rodney interrupted, "And the best thing about Carson's visit to Jonan's cabin was the two ZPMs he gave them. Logo found them in the Ancient city on the planet. Voth also gave me a data chip with the computer files from the city."

"It's called Ilaria," John put in.

"O'Neill nodded," Okay, how did you find a way home?"

"Well," Sheppard began, "we found a crashed ancient ship on a planet nearby - well, it took us three weeks to get there. I was attacked by the local wildlife when Rodney, Ronon, Carson and I went down to investigate. Some big bears had taken up residence, and one decided to maul my leg."

Carson continued, "We were transported to a city like Atlantis and ran into one of my ancestors. A red-headed version of Sheppard was there too. They were from Atlantis on a mission of exploration. Anyway, to cut a long story short. They gave us a cure for Teyla and a healing serum, which they had used to fix the General's mauled leg. Jacob and Isaac returned to Atlantis to travel back to Earth after giving us the serum and access to their database."

"So what happened next?" Jack asked with interest.

Rodney took it from here, "We cured Teyla, opened an anomaly and found a way home. We then closed the original rift we went through. It turns out that the original Anomaly was a failed experiment by the ancients from Ilaria."

"Okay, I've heard enough, "Jack stated, "Just make sure your reports are more thorough." He turned to Carson before he continued, "I need to speak with you alone, Doctor Beckett."

John didn't miss the worried look on Carson's face, and he knew what O'Neill would ask the Doctor. John nodded slightly, hoping Carson would get the message he could tell O'Neill about his brain damage.

He knew it had to come up eventually because Carson wasn't very good at lying. He only hoped the topic of epileptic seizures wouldn't come up.

Giving his friend a tiny smile, John walked out of the conference room, knowing his future was in Carson and General O'Neill's hands.

oOo

Once the others had left the room, Carson turned to stare at O'Neill, "What is this about General?"

"What really happened to Sheppard? Don't you think I haven't noticed the slight weakness in his right leg? He also looks way too thin and pale. And you are lousy at lying, Doc."

Carson sighed, knowing the truth would come out eventually, so he may as well tell O'Neill what really happened.

"General Sheppard suffered brain damage in his temporal lobe. We don't know whether it was due to being in the chamber or being shot in the head. He also suffered blindness from being in the power chamber. That righted itself, though."

"What were the side effects of the brain damage?"

"He had a weakness down his right side consistent with a stroke. He had slurred speech and couldn't use his right arm or leg, but he learned to use them again."

"How long were you in the other Galaxy, Dr Beckett?"

"I'll be honest with you, General. I lost count of the weeks, but it was at least nine."

"I'm guessing the serum the ancients gave you cured more than Sheppard's leg?"

Carson nodded, "I injected a small amount into his brain, and the results were miraculous."

"So, did he pass the military evaluations, Doctor?"

"He only scraped through on the endurance test. And Jennifer and I conducted the psych evaluation."

O'Neill sighed, "Look, Doc. I want Sheppard to stay here as much as you do. There's no one more suited to the job of leading Atlantis than him. But I will have to file a report with the IOA. I would also like him to undergo the military examinations again…"

Carson was about to protest when O'Neill held up his hand, "I won't be asking him to leave Atlantis for now. I will have someone sent here to conduct the exams."

"Do you want me to tell him, or will you?"

"I'll need to talk to him before I return to the SGC. So I'll tell him."

"Thank you, General."

"I'll see you later, Carson."

O'Neill got up and left the conference room, leaving him to think. Everything was out in the open now - except for the seizures. He hoped the seizures would never come to light because if they did, it would mean the end of Sheppard's career. At least by disclosing his recent brain damage, Sheppard stood a strong chance of remaining on Atlantis.

oOo

Rodney stood outside the conference room and watched John walk towards his favourite balcony. John had spent a great deal of time there over the last few months, and Rodney knew it was where his friend went to be alone and think.

It was clear now that Carson would tell O'Neill of John's brain damage. Rodney hoped that Carson would never disclose John's epileptic seizures. With the damaged areas of John's brain healed, Jennifer assured him he wouldn't have any more seizures. Rodney only hoped she was right.

He had no idea what to do now; should he follow Sheppard, return to his lab, or go to his quarters?

In the end, he decided he needed to talk to O'Neill and tell him how valuable Sheppard was to Atlantis, and to take him away would be ludicrous.

O'Neill exited twenty minutes later, so he pounced on him, "General, I need to talk to you now."

"What can I do for you, Dr McKay?"

"I need to talk to you in private. It's important."

Jack sighed, and Rodney thought he would tell him to get lost, but in the end, he nodded.

"When Carson leaves the conference room, we can talk there."

Carson walked through the doors at that exact moment, smiled and nodded at them as he walked past.

"Right, Dr. McKay, you have ten minutes of my time, so make it quick," Jack told him when they'd settled in the conference room.

Rodney took a deep breath before starting, "I know Carson told you about Sheppard's previous brain damage. What you don't know is, that he took down a bear and saved my life while he had brain damage. John was able to shoot it with the gun in his left hand. He was also able to fly a jumper. To me, that is a testament to the kind of man John Sheppard is and proves he deserves to stay on Atlantis."

"All I can do is report my recommendations to the IOA, then hopefully, they'll make the right decision."

"Did you know his calculations allowed us to open an anomaly home? The man's a genius and has a Ph.D. Surely, Atlantis needs a man like him."

"I happen to agree with you, Dr. McKay and I will fight to keep him here, but ultimately, the IOA will want to have a say in it."

"I just hope you can convince them, General."

"You and me both, Dr. McKay."

"If you're looking for Sheppard, General, he's on the control room balcony. That's where he always goes when he needs time to think."

"I'll see you later, McKay," Jack said as he left the room.

He watched Jack leave the room before letting out the breath he didn't realise he'd been holding.

oOo

John had no idea how long he'd been standing on the balcony, but it calmed him. It was cold outside, but he didn't care because if the IOA had their way, he would be sent back to earth for good. He was convinced that Carson had disclosed his previous brain damage, and without a miracle, he'd probably have to leave his home. He only hoped that his wife and children would be allowed to join him on earth.

A flock of birds flew by, and an iceberg bumped into the side of Atlantis, bringing him out of his contemplations. The view was better than he'd experienced over the last eight or nine months, and he didn't want to leave. He wanted to have a chance to explore the planet, to fly into space and orbit it. Maybe there was a beach on the mainland where he could surf in the warmer months. If he had to leave Atlantis, he would never know.

Someone clearing their throat behind him caught his attention, so he turned around to find General O'Neill standing there.

"What can I do for you, General?"

"Relax and enjoy the view, Sheppard."

He turned back and rested his arms on the railing, and O'Neill joined him.

"It is beautiful here, Jack said, "and I wish I could stay longer, but I need to get back to Stargate command."

John took a deep breath before speaking, "What will you tell the IOA?"

"I'll tell them the truth. No matter what has happened to you, you're still the best man for the job. Carson and Rodney spoke highly of your abilities, as every other man and woman on Atlantis would. And I'm sure of it."

"Thanks, Jack. Do you know when you'll speak with the IOA?"

"I'm not sure, John. But for now, things will stay as they are. Be assured I will do everything I can to keep you here."

"Thanks."

"Any way Sheppard, I'm going to get my things together. I'll see you in the gate room in an hour because I need to return to Earth."

He nodded and continued to stare at the stormy ocean. Eventually, the General left, leaving him alone with his thoughts.

He knew that Jack would fight for him; hopefully, that would be enough. After everything he'd been through over the last eight or nine months it would be cruel to take him away from his home and family. And when he spoke of family, he didn't just mean Teyla and the kids.

He'd been on Atlantis for ten years and couldn't imagine living elsewhere. There was still work to be done in the Pegasus Galaxy, and he knew he had to be part of whatever happened.

There was a civil war brewing amongst the Wraith, and he needed to be here to fight by Todd's side for peace in future generations. Maybe he could take a team and explore Ilaria two in this time period, and perhaps they could find out what the Ilarians were up to twenty thousand years ago when they crashed on the planet.

He refused to go down without a fight. He needed to see through what he began ten years ago when he stepped foot on Atlantis. Living here had changed him for the better, and he couldn't imagine living anywhere else. Atlantis was his home, and he wasn't going anywhere.

TBC…