They both sat in silence before the President gave Jack a look and asked, "How can you be sure that it's you son?"
"The report mentions a mental link between Doctor Weir and Colonel Sheppard," Jack said, "There is also a link between Colonel Carter and myself, that's how I'm sure sir." He paused for a moment before saying, "We've both agreed that we don't want to go back to the way things are now, we've waited long enough and it I have to retire then so be it."
The President was silent for a moment, studying Jack intently. Jack didn't move under his intense gaze, he just sat and waited to see what would happen next. The President then began to laugh. Jack was shocked, as was Sam when he explained what was happening, so it took him a moment to ask, "Um sir, what's so funny?"
"What's funny Jack," the President said, "Is that you look like you're about to stand in front of a shooting squad." The President shook his head before saying, "I have read most of the mission reports from when you were on SG1, and I've seen the two of you together, it's obvious how you feel." He saw Jack stiffen at his words. "Nothing was ever said because both General Hammond and myself agreed, as did the Joint Chiefs, that neither of you would ever willingly, or knowingly, break regulations but should the need arise for a loop hole we would figure something out," he paused and then continued with a smile, "It's the least we can do for two people who have saved the planet so many times."
Jack's mouth dropped open and he could feel Sam's shock through the link, although she wasn't saying anything.
The President continued, "There are a few options at your disposal. One, or both of you, can retire, but we need the two of you too much for that to happen. You could go against regs and face court martial, or," he paused to study Jack's face for a moment, which Jack was keeping as blank as possible, "Or, you could take this." He stood and walked back to his desk, opening one of the draws and pulling out an envelope. He walked back to Jack and handed it to him.
Jack slowly opened the envelope and pulled out the piece of paper. He set the empty envelope on the table and unfolded the paper that was inside.
By order of the President of the United States of America Lieutenant Colonel Samantha Carter is here by removed from the chain of command of Lieutenant General Jonathan O'Neill.
Where matter of discipline or promotion apply Colonel Carter's direct superior shall refer to the Joint Chiefs or the President should his verdict be challenged or unsuitable.
The letter was then signed by the President.
Jack looked up at the President and then back at the letter and smiled. "Thank you sir."
The President nodded, "General Landry has agreed to this, the only person we need to check with is Colonel Carter."
Jack nodded and listened as Sam said, Tell him I accept Jack, and thank him for me please.
Jack nodded again and said, "Carter says thank you sir, she accepts."
The President smiled, "I rather thought she might. She just needs to sign it, as do you, and everything will be fine."
He went to the sideboard and pulled out a bottle of scotch and two glasses. "I won't tell anyone if you don't," he said as he poured some of the amber liquid into each glass before he handed on to Jack, who had stood and moved to stand beside him. "To happy endings," the President toasted.
"And fairy tales come true," Jack said, raising his glass.
They both drank and put their glasses back down. "So," the President said as they walked back to the sofa, "I take it that you're going to Atlantis as soon as you can?"
Jack nodded. "Yes sir. Carter's been asleep too long already."
Hey, Sam's voice sounded in his head, You're making it sound like this is my fault.
Jack chuckled and the President raised an eyebrow. Jack tapped the side of his head and the other man nodded his understanding. Jack stood and said, "Now if you'll excuse me sir, I have a plane to catch."
The President nodded again and they walked to the door. Jack opened it and made it half way across the next room before the President called after him, "Congratulations General."
Jack turned around and smiled, "Thank you sir."
So there you go, the President knows and it looks like he's all for Sam and Jack :D