Jack could get used to this; he was back in the field, fighting the Goa'uld, working with Daniel, Teal' c but most of all working with Carter. Sure it was a little odd, who was giving the orders, who was following them. He was a General, she was the commander of the base but mostly he loved every second of it.

Sam and Rodney had spent the hours following Stephanie's arrest trying to wipe her program from the system. With no success. Every time they booted up the computers they declared nothing worked and the Wraith were coming. The only hope of the city being saved rested with Jack working the chair. His gene was stronger than John's and therefore he had more control.

Normally Jack liked long odds for success but he usually preferred to fight with a P90 or a ZAT, not a chair. He did not do sitting patiently very well.

Sam shut down the computers for the last time and decided they would have to go with Jack especially since he had spotted another mother ship approaching on the long range censors.

The first ship would be within weapons range in a few minutes. Sam realised she had to put the cities fate in Jack's hands. She was a little freaked at that. Of course she trusted him with her own life but now she had to entrust hundreds of lives under her command to him. She knew deep down he could do this or would die trying. However the last time he had done anything like this with Ancient technology his mind was Ancient and then he had to be frozen. So she had issues over the whole thing, irrational issues that were not even worth voicing but issues nonetheless.

Jack and John went down to the chair room. Teal'c joined them, the time had come.

"Sir" Sam spoke through the earpiece "we might only get one shot at this, make it worthwhile"

"Don't worry Carter it's in the bag" Jack said trying to calm her

Jack sat back in the chair, concentrated, located the ship and fired. Ba'al's attack ship disappeared from the radar.

"Direct hit Colonel" John reported to Sam

"Congratulations General" She replied back heaving a sigh of relief

Jack sat up after studying the radar maps "The other ship has turned and has gone back, I think we did it" he said

Everyone was delighted, Jack could hear the cheering from where he was. However in the chair room there was an oppressive atmosphere developing.

Jack sat back in the chair and discreetly nodded his head at Teal'c indicating for him to leave John and him alone.

Teal'c raised his eyebrow to enquire if this was a wise course of action.

Jack simply nodded in return.

Jack looked at the younger man trying desperately to find a way to avoid the coming conversation. However he had decided on the plane to Colorado that if he saw John he would talk to him. Otherwise, if Sam stayed, his imagination would go nuts the whole time she was on Atlantis.

"General, permission to speak freely" John said looking at his superior and instinctively knowing what they were about to talk about.

"Go ahead" Jack said relieved that John was going to start.

"Well Sir I would like to apologise for aahh kissing Colonel Carter the last time you were here. It showed disrespect to Colonel Carter, the uniform and you Sir. You have my word that it had never happened before and it will never happen again"

Sheppard finished, looking at his superior officer for his reaction. There didn't appear to be any.

"Aaahh Sir, if I may ask do you plan to write a report about this, like it deserves"

"No Sheppard, you are right it does deserve it but I already made that decision. The visit wasn't official, it was unexpected, Jack came on holiday with his friends to see Sam. General O'Neill stayed on Midway. I' m here to talk to you as Jack not your boss" He really thought he should get a couple of name badges so that everyone knew who was talking.

"OH" was the only reply Sheppard could formulate.

Jack continued "Sam and I thought you have a right to know what happened. You are about to become one of the few people in the Program that know this, we would appreciate it if it went no further" They had discussed this on the flight. Sam wasn't too happy at his plan to talk to Sheppard but had finally agreed to this.

"Yes Sir"

"Sam and I have been together for a few years. We were never together when we were at the SGC. We got together when we were far enough out of the chain of command. The President knows, and he appointed her to be head here before he asked my opinion so there was no favouritism."

"I never thought there was Sir"

"Anyway" Jack continued "a couple of months ago it seems Ba'al started to mess with people's heads. He effectively split up 8 couples including Sam and I using fake letters and e-mails. When Sam kissed you…" oh he felt really uncomfortable saying that. "she believed I was with someone new, getting married and going to be a father" he stopped

"So that's why she was so sad" John surmised

"Yeah, look Sam is a very private person and we don't want any of this to become city wide gossip" Jack said sternly, irrationally angry that John knew how Sam had been feeling when he had no idea.

"I understand Sir" John said and then continued

"Sir, if I may ask, is she planning to stay?"

Jack looked at the younger man and for the first time since coming to Atlantis for this visit realised that he really did have nothing to fear.
"I think so, Sam has never run away from a challenge in the 11 years I have known her. Mind you I would prefer her to stay on Earth but I would never hold her back"

John looked slightly shocked at that admission.

"Sir if I may continue to speak freely, why don't you visit more? It must have been well over five months since you have seen each other. Everyone else who has a partner back home gets time off every month or the partner comes here if they are at the SGC it is part of their agreements. Although there have been less recently, oh that was Ba'al's plan" John said finally putting the pieces together, he continued "Why have you not come?"

As soon as he finished John wondered if he had said to much and was about to apologise when he saw the pained look on Jack's face

"Sam didn't want me to come, she was worried what people would think, if it would undermine her authority. Very few people know about us, she didn't want that number to increase" he really needed to stop this conversation, why was he still talking again?

"Sir now that I am aware, you have my word that if you come a reason can be found, heck the fact you work the chair better than anyone is bound to be good for a couple of visits."

Jack smirked at that "The thought had crossed my mind."

"Sir you said earlier that Jack is here not the General, why not let Jack visit and leave the General. No-one here is likely to comment on your relationship. No-one else in your position is apart as much."

Jack was beginning to get back in control of his emotions and for once his mouth that had said way more than he had planned.

"I'll take that under advisement thanks Sheppard, lets get back or Sam will think I've killed you."

The deadpan serious way he said it showing he really could have done that without a second thought gave John the shivers.

In the control room Sam and Rodney had finally managed to get the computers to listen to them and were wiping Stephanie's program from it. Jack and John made their way into the room

"Well Carter, I believe that our work here is done" Jack said with a twinkle in his eye

"Well done Sir" she replied

"You know it is really a shame that we finished this without getting to shoot ole Bocce" he said quite irreverently.

"Can you picture his face now though, his whole plan thwarted by us meddling kids" Daniel piped up

"Indeed" Teal'c answered causing the others to stare at him, unsure he actually knew the television reference

"I was introduced to Scooby Doo by a very excitable Cassandra Frasier many years ago. I find it strange yet enjoyable" Teal'c explained

"Well boys we have saved the day" Jack said to Daniel and Teal'c and then looked at Sam

He could see the concern wash over her face as she moved toward him.

"Are you leaving now?" she asked uncertainly

"Well that depends, can we talk in your office?"

She nodded and they both moved towards the office and sat down, one on either side of the desk.

"So, I talked to John" Jack started "are you planning on staying here?" To Sam the question seemed a little out of left field but Jack really wanted to know what she wanted for her life.

Sam looked down and didn't meet his eyes

"I want to finish my tour Jack, I have a job to do. You know that"

He nodded

"I was sent here for a year with the option to keep going" she paused and took a breath. "I don't think I want to stay after that. She finally looked up at him and held his gaze

He was smiling

"So that would mean you would be back in 3 months then?" He asked wanting to ensure they were on the same page

"Yup"

"Cool, so about me staying for a bit. You know I worked incredibly hard to organise the trip for me and the boys. It would be a shame to go home without celebrating our birthdays"

"With everything that has been going on I forgot it was my birthday" she said with a wistful laugh

"Well Carter, we will just have to remedy that" he stood up from the desk and was about to leave her in peace then turned back to look at her;

"John had some interesting thoughts about me visiting you, how maybe Jack could visit while the General stays home. Maybe it's time to come out of the closet a little bit" he asked warily focusing on her eyes to check her reaction.

After a moment to think she finally responded "Yeah I think this might be the right time" she smiled a little at him

"Ok, well its official I'm on holiday, I think it's time for a spot of fishing, how about it Carter"

They sat on a pier at the outskirts of the city much like they did in Minnesota both lost in their own thoughts.

"Jack, when I get back how about we do something about our undefined relationship"
"What did you have in mind" hoping he knew what she was hinting at having mentioned it before her job here.

"Well if the offer still stands I would really like to get married"

He smiled, "Whatever you want Sam, whatever you want".

Authors Note: Well here we are at the end of my first major story. Thanks to all who read and especially those who reviewed. It meant a lot. I have others to share with you but they will take a bit to get organised. Hope you enjoyed the ride and that it finished to your satisfaction.