Chapter 28: A change of leadership.

John awoke the next morning just as the sun was beginning to stream through his bedroom windows. He had an incredibly busy day ahead of him starting with a meeting in Woolsey's office with Woolsey, Rodney and Ronon after breakfast.

Snuggling into bed he realised that Teyla was no longer in bed with him. He couldn't hear any children screaming, so he assumed that they were still asleep. He lay in bed and scanned to room, not really wanting to get to out of bed yet. Finally he saw her standing on their balcony watching the sunrise. He was tempted to go to her, but a few more minutes of sleep would be nice. In the end he decided to get out of bed and join her on their balcony.

He slipped on some sweatpants and a t-shirt and went outside and put his arms around her.

"Good morning Sweetie, how are you this morning," he asked kissing her neck.

"I just wanted to enjoy some peace and tranquillity this morning, before the day starts. This time tomorrow you will be the leader of Atlantis and a few days from now Woolsey will be leaving, which means things will never be the same again."

He sighed, knowing that she was one hundred percent right, but things certainly were different to what they were five years ago, or even a year ago. "I know what you mean Sweetie, but things are always changing and things today will be different to what things will be five years from now. This time seven years ago, I didn't even know you existed, but now I am married to you, we have three beautiful children and I couldn't be happier."

She turned and looked up at him, "John I know that life changes and believe me when I say that my life changed for the better when I met you, but for now, I feel like being melancholy."

"That's fine by me sweetie, but for now let's just enjoy the peace and quiet, while the children are still asleep."

Unfortunalty the quiet didn't last long, because Torren chose that moment to come into their room and ask, "Dad, what's for breakfast?"

It didn't take long for things to get back to normal, he thought turning to his son.

"Why don't we have some cereal and toast this morning?"

"Fruit loops?" Torren asked using his ubiquitous puppy dog eyes.

"Yes I think we have some in the cupboard, but how about you go and play for a while and I'll come and help you get some in a minute."

"Sure Daddy," he replied and John was relieved when he left the room.

He turned back to his wife, put his arms around her again and started to kiss her neck, hoping to get her back into bed for a bit longer.

"John please stop doing that, otherwise you know what will happen." Teyla begged with a smirk on her face.

John raised his eyebrow at her, as certain parts of him became excited, "and what would be wrong with that?"

"Well nothing, but how would you explain it to Richard if you were late?" She asked with a teasing looking in her eyes and it was one that John knew well. She usually put on that look when she was daring him to do something.

"Well I could tell him the truth." He smirked, before kissing her neck again.

They didn't have a chance to continue the conversation further, because Charin decided that it was time to wake up and start screaming and it wasn't long before her twin brother joined her.

"Great," he muttered, before leaving his bedroom to go and collect one of the twins and he hoped that Teyla was following to collect the other one. Once he had arrived in the twin's room, he picked Charin up out of her cot and Teyla picked up Tobias. He then headed out to the kitchen to warm up their milk.

Torren was in the lounge room playing when they walked in, "Can I help Daddy?"

"Sure T.J., can you look in the cupboard and find some baby food and then when I've given Charin her bottle, maybe you can feed her while I get breakfast?"

"I know what to do, Sally let me feed baby Peter." Torren replied eagerly.

John smiled, he was best friends with Sally Smith and he seemed to spend far too much time with her these days, "Great, then I won't have to tell you what to do," he smirked.

It wasn't long before Charin had finished her bottle; she totally loved to eat, just like her uncle Rodney. John put her in her highchair and gave Torren a few pointers on how to feed his sister.

Just as John started to organise breakfast the door chime activated. Looking at his watch he realised that it was only 0700 hours. Who the hell is at my door this early in the morning, it's probably Rodney here to be annoying again. Walking across the room, he hit the door panel and to his chagrin Rodney was standing outside his door.

"What do you want McKay?" He asked trying to keep his patience.

"I want to know why you've been avoiding me since our last mission, it's very annoying!?" Rodney asked forcefully.

He screwed up his face and rolled his eyes, "McKay now is not the time for that conversation; we have a meeting with Mr Woolsey at 0900 hours I will talk to you then!"

He closed the door before Rodney had a chance to say anything else. When he turned back to look at Teyla, he noticed that she was staring at him.

"What?"

"Do you not think that you were a little rude to Rodney?" She asked with a blank look on her face.

He hated it when she looked at him like that, because he had no idea whether she was angry with him or not. Not that it mattered, since he was getting sick of Rodney turning up unannounced and trying to get him spill the beans on what was going on.

"I just wish he'd keep his nose out of what is going on. He will find out soon enough and then he'll really have something to complain about." John said as he went back the kitchen to finish getting breakfast.

Once the twins had been fed and they were playing in the playpen that had come on the last Daedalus run, John, Teyla and Torren sat at the table to eat their breakfast. He sensed that Teyla was a bit annoyed with him for the way he had treated Rodney, so they sat and ate in silence. Torren didn't seem to understand, so he babbled away talking about what he had to do that day. They listened to him and added a comment now and then, but other than that there was dead silence.

At the end of the meal he stood up and started to load the dishwasher, without saying a word. He wasn't really sure what to say to Teyla right now, as she was clearly in a bad mood with him.

They spent the next two hours in silence, with the only conversation coming from Torren.

"What time is Torren due in day-care?" John asked right before he was ready to leave for Woolsey's office.

"Dave will be picking him up in about five minutes." She replied shortly.

He went up behind her and put his arms around her. "Well I have to leave now," he said kissing her on her neck.

She pulled away from him and walked towards their bedroom. "I will see you later at the ceremony John."

"Where's Momma going Dad?" Torren asked looking up from the toys he was playing with.

"I don't know buddy, but can you keep an eye on your brother and sister, while I find out?"

"Sure Daddy."

John left the room and followed his wife; he really wanted to know what her problem was. Surely there was more to it than the way he spoke to Rodney earlier.

He walked into their room and found her lying on her bed. Lying down beside her, he put his arm around her and held her close. "What is wrong sweetie, have I upset you in anyway?"

She turned to face him and he could see that her eyes were red from crying, "I do not know. I guess for the first time in my life I am worried about the future."

He cuddled closer to her, "Why do you think that is?"

"As I said before, I really do not know, but do not worry about me, I am sure that I will get over it. You must go to your meeting now and hopefully I will feel better this afternoon."

He leant in and kissed her on the forehead, "I will see you at the ceremony."

"Are you ready to come out and keep an eye on the children now?" He asked hugging her tighter.

"I will be out in a minute, can you wait until then?"

He nodded and left the room and headed out to the lounge to find that Dave was already there, "hi Dave do you mind hanging around for a little while and keeping an eye on the twins. Teyla should be out in a minute and then you can take Torren too childcare."

"I don't have to be in the office until 09:30, so I guess I can hang around for a while."

"Thanks Dave and I will see you at lunch."

Leaving his apartment he thought about what the rest of the day would hold. At least there were some things to look forward too and seeing Major Lorne and Major Teldy get their promotions certainly was one of them. Having to talk to Rodney and Ronon and tell them what was going on, was not.

OOOOOOOOOOOOOO

Rodney sat in Woolsey's office, along with Ronon and Woolsey. He was anxious to know what was going on and he hoped that Sheppard and Woolsey could finally tell him what Sheppard had been so secretive and rude about since their last mission.

He looked at his watch and realised that Sheppard was two minutes late. How dare he be late? Sheppard had told him off for being late on more than on occasion, so he was just one big hypocrite.

"Mr Woolsey how long do I have to sit here and wait for Sheppard," he asked feeling frustrated and annoyed.

Woolsey sighed, "I am sure that there is a perfectly good explanation, as to why he is running late. He does have other responsibilities."

This made Rodney furious, what the hell was going on and why was Woolsey siding with Sheppard.

"Do you have somewhere you have to be?" Ronon asked with a smirk on his face.

"Yes as a matter of fact I do. I have some very important experiments that need my attention, so I don't have time to wait for messy haired fly-boys!" He answered brusquely.

At that moment John walked through the door, "I'm sorry I'm late, but I had to wait for Dave to get to my place to look after the twins."

"Great excuse," Rodney mumbled under his breath.

That comment got him an intense glare from John, "Would you rather I brought them with me McKay?" Sheppard asked with a hint of sarcasm in his voice.

"Now that everyone is here how about we get started?" Woolsey suggested. When everyone had calmed down and sat down, he started the meeting. "The reason I have called you here Dr McKay is to inform you that I will be heading back to earth in two days' time. My replacement has already been informed and I will be handing over command to him at the promotion ceremony this afternoon."

Rodney was left speechless; Woolsey was leaving Atlantis and they were getting another leader, who the hell would that be? Probably Coolidge, was his first thought.

He heard Ronon speaking, but it took him a while to realise what he was actually saying, "So are you taking over Sheppard?"

It was Woolsey who replied for him, "Yes he is and he has the endorsement of the IOA and Stargate command."

Rodney was finding it hard to process the conversation going on in the room, "so if Sheppard is taking over here, what will you be doing at the IOA and who will be Sheppard's 2IC?"

"I will be taking over as the head of the IOA committee, Dave Sheppard will be Colonel Sheppard's 2IC and Major Lorne will be head of military operations, with Major Teldy as his 2IC." Woolsey explained succinctly.

"What happens to our team," Ronon asked with a look of hurt on his face.

"Well Chewie, I thought that it was time that you led your own team. I have some ideas for team members, but ultimately it will be up to you." He turned to look at McKay before continuing, "Rodney you can choose to stay on a team with Ronon, or you can spend more time in your lab, it is your choice."

Now Rodney really didn't know what to say, the team was splitting up, so that Sheppard could go and lead Atlantis. What the hell was he supposed to say to that? Looking around the office, he saw that Ronon and Sheppard were smiling at each other and Woolsey was just looking at him.

"Congratulations Sheppard. When you get a chance hand me that list and I will look over it, I have a few suggestions of my own of course and I would still like Dr McKay on my team if he is willing?" Ronon told John and slapped him on the back.

Rodney looked up at Ronon and wondered whether he really wanted to be on a gate team that didn't include Sheppard. Teyla had left the team a long time ago and he had come to accept that, but now with Sheppard leaving he didn't know what to do.

"I will let you know Ronon."

Woolsey stood up in front of him and Ronon, "the only people on Atlantis who know that I am leaving and Colonel Sheppard is taking over are in this room, as well as Major Lorne, Teyla, Dr Keller, Dr Beckett, Dave Sheppard and Jane Raven. I suggest that you don't tell anyone else before the ceremony this afternoon."

Rodney nodded and Ronon made a grunting sound, before Woolsey looked at them again. "You're both dismissed."

Rodney was in total shock as he left the room and he wasn't sure what to think. One thing he knew for sure was that things were changing and he didn't like it.

OOOOOOOOOOOOOOO

John watched as Rodney and Ronon left Woolsey's office, when it suddenly dawned on him that in two days' time this would be his office and that freaked him out a little. The leaders that preceded him were incredible people and he wasn't sure that he could ever hope to do as well as them.

His thoughts were interrupted when Woolsey spoke to him, "how are you feeling John?"

"I'm definitely feeling apprehensive, I don't know if I could ever do the job as well as you, Sam or Elizabeth."

"Don't be too hard on yourself John; I think that you will find that you are every bit as capable as the three of us have been and don't forget you have the support of the IOA and Stargate command." Woolsey encouraged him.

"Thank you Richard, I should go and get ready for the ceremony now, since I want to meet General O'Neill and General Carter when they arrive at the gate."

Woolsey stood up and shook his hand, "I will see you at the gate."

John left the room and looked at his watch, he had exactly one hour before he had to be back in the gate room to meet the Generals. As he left Woolsey's office he stood out and looked over the balcony into the gate room to see how preparations were going for the ceremony. It looked as if they were almost finished, which was probably a good thing, as the ceremony was due to start in less than two hours.

OOOOOOOOOOOOOOO

By the time Rodney reached his apartment, he decided that he was angry, with Sheppard and even angrier with his wife. How had Jennifer known about this and not told him. He walked through the door to find that she was sleeping, how dare she sleep at a time like this.

"Jennifer, wake up!" He shouted at her as soon as he got close.

He watched as she jerked awake and looked around the room, with panic in her eyes.

"Rodney what's going on, Is there a medical emergency?"

"No, I just want to know why you didn't tell me about Woolsey leaving and Sheppard taking over. Woolsey told me that you knew about it." He whined with a pained look on his face.

"The reason I didn't tell you Rodney is I only found out about five minutes before you did, Woolsey spoke to me this morning after I had finished my shift. So if you would kindly leave me alone I would like to get some sleep before the ceremony this afternoon."

"Oh, I'm sorry to wake you up then." He said feeling a little sheepish, "I will head back to my lab for a while, before I have to get changed then."

"You do that Rodney and make sure you're not late!" She suggested and he could tell how annoyed she was.

He quietly left the room, not wanting to disturb her any longer.

OOOOOOOOOOOOOOO

John stood by the stargate, with Woolsey alongside of him, ready to welcome Generals' O'Neill and Carter to Atlantis. They were coming via the midway station, which seemed to have become the normal route between the SGC and Atlantis in recent times.

He had been forced to wear his dress blues, which annoyed him greatly, but if he was going to be part of the ceremony and help with the promotions of his staff, he was told that he should be wearing it. He figured that he didn't have to wear it that often these days, so he probably shouldn't complain. In fact the last time's he'd worn it was at his wedding and that was a year ago.

He'd had no idea why O'Neill had insisted on coming rather than Landry, so he'd asked Woolsey about it and Woolsey had told him that the General had wanted to preside over these promotions himself. At the time he'd accepted it, but now he wondered why General Carter couldn't have just performed the ceremony.

A few minutes later the Chevrons lit up and the wormhole sprang to life, "It's General O'Neill's IDC." Chuck announced.

"Lower the shield." Woolsey told him.

He watched as General O'Neill exited the wormhole followed by General Carter.

"Richard, it's good to see you again," General O'Neill greeted him and shook his hand.

"It's good to see you Jack." Woolsey replied accepting the handshake.

The General then turned and nodded at him. "Colonel Sheppard," he said emphasising his rank.

Before he knew what was happening Sam's arms were wrapped around him, "John it is good to see you again!" She exclaimed with exuberance.

Once she had finished the hug he cleared his throat, before he was able to speak, "General Carter, congratulations of your promotion."

"John what have I told you about calling me by my rank. It's Sam remember."

He looked at her and took a deep breath, "I know and that was fine when we were the same rank, but you're a General now."

Jack snorted, "since when have you ever followed the rules Sheppard and will you stop calling me General, it's Jack. I've told you that a million times before as well."

"Yes sir," he replied, still feeling a little up tight.

"At ease Colonel, before you sprain something and don't call me sir, call me Jack." Jack reiterated for him, before turning to face Woolsey again, "now that the pleasantries are over let's head to your office Richard, as I have a few things to discuss with you."

John stood by stargate and watched Sam and Jack leave with Woolsey, it was only half an hour until the promotion ceremony now and the gate room was beginning to fill up. It had been decided that the gate would be taken off line for the duration of the ceremony, so that they didn't end up with any nasty surprises.

Twenty minutes later, he stood on the balcony overlooking the gate room. He almost laughed when he had stood on that exact spot and thrown McKay over the balcony. He'd only been in Atlantis for less than a week at the time, but at that point he knew that he and Rodney were going to become good friends.

When Jack, Sam and Richard came out of Woolsey's office, he walked down the stairs to the gateroom where a podium had been set up at the bottom of them. It didn't take long for the crowd in the gate room to quieten down, once they saw them.

He smiled when he saw his team sitting in the front row, along with David and Jane. Teyla and Jane were doing the best they could to manage the children between them. Sitting behind them were rows of military personnel, scientists and auxiliary staff, all sitting side by side. It was a testament to what his predecessors had built on Atlantis and his hope was that he would be able to build on the foundations that, Elizabeth Weir, Samantha Carter and Richard Woolsey had built.

He heard Jack clear his voice and begin, "ladies and gentlemen, our purpose here today is twofold, we are here to promote some fine young men and women, for outstanding service to Atlantis and the second reason is that Richard Woolsey has decided to take a job on earth, so we will be instating a new leader. I will hand over to Richard now and he will be able to explain everything to you."

The gateroom erupted into a cacophony of noise, chairs were scraped along the floor, some people started to murmur and then there were others that spoke loudly. As John looked around the gateroom he also saw a lot of shocked faces and that was exactly how he felt when Woolsey had told him.

Woolsey stepped forward, cleared his throat and to John's relief everyone quietened down almost instantly. "I know that this may come as a surprise or even a shock to many of you, but believe me when I say this is one of the hardest decisions I've ever had to make. It has been my absolute honour to serve as leader for this expedition and it has been my privilege to work with many fine men and women, but I just can't sit by and watch good men and women die and that is the reason I am leaving. I am not a trained soldier, so it is something I don't think I will ever get used too. I will be leaving in two days' time after the weddings of David Sheppard and Jane Raven, and Ronon Dex and Amelia banks. But I will not be leading the expedition after today, so now I will introduce to you my successor Colonel John Sheppard."

The gateroom erupted into applause when his name was announced and John felt slightly uncomfortable and nervous with all of the attention. "Thank you Richard. I want you to know that I am honoured to be taking over as the leader of this expedition; I know that I have huge shoes to fill.

When I first came to Atlantis, I wasn't even the military commander and Dr Elizabeth Weir was the leader of the expedition. On our first mission we lost our military commander and Elizabeth put her faith in me to take over that position. Initially I made mistakes and it took me a while to find my feet in the role, but with Elizabeth's help I found my way and she stepped in and fought for my promotion to Lt Colonel. And when Colonel Carter took over she continued to believe in me." He took a breath and looked at Woolsey before continuing," when Richard took over, I didn't know what to think of him, but very quickly I found that he was just as good at leading the expedition as Colonel Carter and Dr Weir. It has been a privilege working with him and if I can do the job half as well as him, I will be pleased. I will hand you back to Mr Woolsey now to announce the other changes."

John stepped back and Woolsey stepped forward again, "With Colonel Sheppard taking over as the leader of the expedition, it has been decided that a civilian will be put in place as Colonel Sheppard's 2IC and that person is Dave Sheppard. A new military leader has been decided as well and that person is Major Evan Lorne. If you have a problem with anything that has been said here today, please see General O'Neill and voice your complaints. Now we will take a few moments and then I will hand over to Generals' O'Neill and Carter to begin the promotion ceremonies."

Richard stepped back and the gateroom broke into applause again. John was relieved that the announcement had been made. Now he had to spend as much time with Woolsey over the next few days, so that he could do the job by himself in two days' time.

TBC…