Disclaimer: I do NOT own Stargate or any of its Characters.

This is a continuation of my first story, Stargate and A Different Direction. This is a work in progress and I am honestly not 100% sure where I am going with this story. I would appreciate any reviews/suggestions you might have. But please no flames. If you do not like it you are welcome to stop reading it.

Chapter 1

Jack smiled down at the woman in bed with him, his beloved wife, Samantha O'Neill. He couldn't help but simply watching her, remembering everything that had happened since they had been rescued from that island. The four months alone with her on the island had literally been paradise, but the six weeks since had been heaven. Being married to her was better than he could have ever imagined. Simply being able to touch her, hold her, hug her, kiss her in public was more than a dream come true, but being able to hold her like this, being about the make love to her, with her was…well there wasn't a word for it. It simply was the best experience of his life.

Placing a hand on her slightly rounding stomach, his smile grew even larger. He couldn't understand what he had ever done to deserve this happiness. To be allowed to love this amazingly beautiful woman, and to be given love in return. She would never truly know what horrors just knowing her saved him from; what an amazing gift she had given him by giving him a second chance at being a husband and a father. To again know the joys of holding both wife and child, was something he never felt he would be worthy. He had failed his last wife and son. Completely and utterly failed them. He had let his job come between them. The knowledge, or lack thereof, of what he did while away on missions created an insurmountable barrier between him and his family. One that he was never able to fix. Then in a span of 3 months he had lost them both. That loss left him a shell of his former self and only meeting Sam truly brought him out of it again.

It had taken a while for him to admit, even to himself that he loved her, and it had taken even longer to admit just how much. It had confused him at first, but he had eventually come to accept that his love for her, and now their unborn children, went deeper than that for his previous family. It had upset him at first, but he had finally come to realize what a gift it truly was. He would do anything in his power to protect them, to make them happy. To be there for them and to make sure, without a shadow of a doubt, that they knew just how much their lover meant to him. Reaching up he gently cupped Sam's face, tenderly stroking her cheeks and lips with his thumb. Leaning in he placed his lips gently against hers.

The brush of his lips against hers, causing her to wake. He couldn't hold back his tears as he whispered, "I will spend the rest of my life trying to earn the love you have so freely given. I will protect you and our children until my dying breath. I will do whatever it takes to prove that I am worthy to be loved by you", before kissing her gently.

Sam could feel the desperation and fear as he kissed. She could taste his tears as he held her close. Pressing her body to his, she tried to meld them together. When he finally broke the kiss he buried his face into her hair, crying gently as she held him close, whispering to him, "shh…darling you never have to prove yourself to me. You never have to earn my love…It's yours, it's always been yours. I love you Jack. I love you more than I ever thought it possible to love anyone."

Pulling back he choked back more tears, "Why? Why, would you settle for me when you could have so much more? I've got too many scares, too much baggage."

Trying to control her slight annoyance, she reached up to wipe his tears away, "You listen to me Jonathan O'Neill. I never want you to think like that again. I never settled for you. Being with anyone else would have been settling. I love you. YOU, Jack O'Neill, scares, baggage and all. You are a good man. You have a good heart and I am proud that you choose me to love. You are a generous lover, a loving husband a giving partner and you will be an amazing father. Never, never, doubt my love, my devotion, or desire for you." She pulled his face to hers for another kiss, trying to make him understand, without words how much she loved him. She wasn't sure what had gotten into him, but she knew enough to know it much be big. Even with his new found openness he never showed tears.

Finally breaking the kiss Jack pulled back to look at her she smiled softly up at his as he gently stroked her check, "I'm sorry baby…" He started, but was silenced with a finger on his lips.

"You have nothing to apologize for, Jack." She said softly, running her finger through his hair, "Do you want to tell me what that was all about?'

Jack sat up and looked down, trying to fight his own emotions. He looked up again when Sam placed a hand on his chest, "I can't help you, love, if you shut me out."

Jack signed, but kept his eyes locked with hers, "Today is the day that Charlie shot himself." Taking another deep breath he continued, "I failed him as a father and I failed Sara as a husband. I'm afraid Sam…I'm afraid that I'll fail you, fail our children. If something happened…If I lost you…" He shook his head, "I love you so much more that I have ever loved anyone. I couldn't…" Damn he sucked at this.

Sam had tears in her eyes as she moved to straddle his lap. Cupping his face she leaned in and kissed him softly. "You didn't fail them, my darling, what happened was a terrible thing, but it wasn't your fault." She kissed him again, "You could never fail me, and you will never lose me. We all have fears. I fear that I won't be a good mother that I won't make you happy as a wife, but I have never, never, feared you failing as a father or husband."

"Now we are both being stupid." He smiled softly, "You are a wonderful wife, and you will be an even better mother. Maybe I don't tell you enough what an amazing person you are. You are intelligent, selfless, caring, compassionate, devoted, loyal, strong, independent, passionate, and beautiful, and I love you with all my heard, body, and soul."

She was cry softly as she kissed him passionately. They held each other close, trying to regain some control, trying to take comfort from each other. There was nothing sexual about their gestures, about their caresses. It was all about comfort and love. "Thank you." Sam eventually spoke. "I love you, Jack. You and these children really are my life."

"I love you too, Sam. You have given me so much to be thankful for." He kissed her again, gently first, then deepening it. He was just sliding his tongue along hers when the earpiece next to the bed buzzed to life."

Colonel Sheppard to General O'Neill, Colonel O'Neill.

Sighing Jack pulled away and picked up his earpiece putting it in he activated it, as Sam put hers in, Go ahead Sheppard

Sorry to disturb you, Sir, Sam, but we will be arriving at the planet in two hours.

Understood, Jack Smiled at Sam's excited look. Sam and I will be there shortly. O'Neill out. Putting the earpiece down he sighed, "Well, shall we get a shower. It seems we've reached the end of the yellow brick road."

Sam sighed, "I would rather spend the next hour and a half making love to you. He said two hours."

Jack smiled scooping her up, "let's compromise. I'll make love to you in the shower."

Her only response was to start sucking on his neck, causing him to moan as he carried her into their private showers. She had missed this. They had been taking showers together the past month, but hadn't wasted the water, but she decided she didn't care as Jack pressed her against the wall, under the hot water and captured her mouth in a demanded kiss, "Jack…"

An hour and a half later they joined the group on the bridge. Jack looked happier but his eyes still had a haunted look. As soon as he entered he was surrounded by Janet, Cassie, Daniel, and Teal'c. Janet and Cassie pulled him into a tight hug, while Daniel and Teal'c stood by offering support, "I love you Jack." Cassie said quietly.

Jack pulled the girl close, "I love you too, Cass, but I'm fine guys." Looking around he said, "Really, Sam's helped me I'm fine. How did you know anyway?" He asked they all turned to look at Daniel.

"I'm sorry Jack. I just…" Daniel started but stopped when Jack cut him off.

"Don't worry about it Danny. I appreciate your concern" Looking around he caught the rest of his command teams confused looks he sighed, and felt Sam tighten the grip on his hand. "Eight years ago on this day my son, Charlie, managed to get a hold of my personal side arm. He accidently shot and killed himself. Three months later my wife, Sara, took her own life out of grief." He stopped and closed his eyes, wanting to tell them the rest, tell them the part that only Sam knew.

Sensing his dilemma, Sam spoke, her voice was soft as she tried to comfort her husband, "Jack was a POW at the time and didn't know anything had happened until he woke up in the base infirmary." She looked around at the horror stricken faces of their family, then up at her husband. She rested her head on his shoulder allowing him to hold her close. Before anyone other than the command team showed up she said, "Please don't tell anyone else. Jack's POW status is highly classified and the rest is too personal, but you are family and deserve to know the truth." Everyone was silent, nodding agreement, unsure of what else to say.

Eventually Jack gathered his control again. He kissed Sam gently on the lips, before turning to others. Slipping back into General mode, he asked, "What's out status, Sheppard?"

Taking Jack's lead John said, "We should be arriving any moment. We will be dripping out of Hyperspace a safe distance from the planet to run scans before approaching."

"Excellent" Jack smiled, "And out survey party?" He asked Teal'c

"Waiting for your orders, O'Neill." Teal'c said with a bow.

"Good Thanks, T. Will you go collect 5 more sets of weapons for the two of us, Jacob, Danny, and Sam?" With a bow of his head he left. Jack smiled, "Sheppard, Can you give me ship wide?"

John nodded and activated the intercom, "Good morning campers." Came Jack's voice. Same smiled at her husband's excitement. "In a few minutes time we will be dropping out of hyperspace at Atlantis." They could all hear a cheer go up around the ship and have some more room, but I must ask you all to wait a little while longer. A small survey team will scout the city and make sure everything is safe before we begin to disembark. When we drop out of hyperspace I must ask you to please stay either in your quarters, the mess hall, or the gym. The rest of the ship is off limits to anyone who is not on duty. I will try my hardest to get everyone off this ship before the night is out. As always, Thank you for your corporation. O'Neill Out." He looked over at Sam who smiled at him from her place by the scanner control. Teal'c entered, passing out the Zat's and 9 mils with extra clips, just as they dropped out of the Hyperspace. Everyone was excited as their new home planet came into view. Turning to Sam he asked, "What do your scans say, Sam?"

Without looking up she answered, "The atmosphere is identical to Earth's, though the temperature on the planet is pretty consistent. Right now it's ranging from between 65 degrees to 80 degrees. The surface is ¾ ocean with one large land mass, with trees and mountains."

Jack watched as she went over some more data talking softly to Rodney. After a few minutes he asked, "What about life signs, power readings, the city?"

Rodney was the one to finally answer, "There are no human life signs, only wild life. There is nothing else." He was still looking at the screen.

"What do you mean, nothing else Rodney?" Elizabeth asked.

"Just that. There are no signs of a city or a power source." Rodney answered.

Everyone was silent, lost in thought and confusion. What could that mean? Why was there no sign of the city?

After several long minutes Jack spoke, "Sam, can you adjust the scanner to scan underwater?"

All eyes turned to look at him for an explanation, "We all know that legends have some bases in facts. They have to come from somewhere."

Daniel nodded, "He's right. Something had to cause people to start saying that Atlantis sank." He thought for a moment then spoke again." We know that the Ancients were the first evolution of Humans on Earth, but left millions of years ago. The data we found in Antarctica said that the Ancients returned to Earth but we are unsure as to why. Some ascended while others returned through the gate and lived out their lives on Earth."

"So?" John Asked

"What if they left because they lost the city or maybe they sank the city to preserve it?" Jack said, "The information we found gave the gate coordinates, gave locations or important labs, information on ZPM's, so they obviously wanted someone to find it again."

"If they wanted someone to find the city why would they not tell them if they sank the city?" Selmack reasoned

Jack shrugged, "Maybe they did and the data was lost or maybe it was a strategic move. Only someone who had the ancient gene can operate the ancient tech, so maybe they figured if you were smart enough to get here you were smart enough to put two and two together, so they planted the myth."

"There is only one way to know for sure." Daniel advised

"Right" Jack agreed, "Sam, can you modify the scanners?"

"Yes, sir." She ignored Jack's frown. She knew he hated her calling him sir, but it was a hard habit to break.

"She's an AF officer, Jack" Jacob said quietly, "It's been drilled in her. You are still her commanding officer and her training demands she answer you with, Sir."

Jack sighed, "I know. It just reminds me of the last 6 years, not being able to have her in my life." He ran his hand through his hair. "She's also my wife and I would never place my wife below me like that. I don't want a docile house wife. I want an equal."

Jacob smiled, "Sam knows that, Jack. She just has to get around 12 years of military protocol. At least she is no longer calling you General." He smiled as Jack laughed and placed a hand on his shoulder. "You are a good man Jack, and you make Sam happy. You, both deserve to be happy."

Nothing else was said because Sam spoke, "Found something, Jack." She said making sure to emphasize his name.

Jack smiled, God he loved this woman, "what did you find, Sam?"

"There's a large structure on the bottom of the ocean. Large enough to be a sunken City." She said with a smile, causing them all to cheer. "No live signs, but there is a very powerful energy source keeping a force field active, holding back the watery."

"Samantha O'Neill." Teal'c said, "Can we beam through the force field."

"We can but we will only be able to send two people at a time." She smiled at him. There was another cheer that went up.

"Give me ship wide." Jack said with a large smile, "We have located a city beneath the water's surface". He could hear the cheers all over the ship. "There are no life signs, so it looks abandoned. Survey team gear up and report to the transport room. We head out in 10 minutes. O'Neill Out."

Turning to his team he said, "Sheppard, you are in charge. Rodney we need to gather as much data as we can from here, about the land and the geography. Find a good place to sit down and unload the animals. Elizabeth, Janet, Jennifer we need to prepare the people and equipment to unload. We will be in control every 30 minutes, but I want a constant lock on out transmitters. If anything goes wrong I want us beamed out immediately."

"Yes, Sir" Cam the collective reply, causing him to groan.

"General" Cassie spoke with a smile. She loved bugging him. "I would like to accompany you to the city."

Jack studied the young cadet before him, his adopted niece. He was proud of her and how far she had come over the years, but he was extremely proud of the AF officer she was turning out to be. She was extremely intelligent, and picked up on things fast. She was at the top of her group in both the academic and physical portions of the training. Out of the 46 adults old enough to join the internships 27 had choose to join the military training program. Within two weeks they had unanimously elected Cassie as their representative on the command team. The trainers had unanimously chosen her to be the team leader of the group. She was slated to graduate with and officer's commission of captain, if she kept this up. They were all damn proud of her. She had even been working with both Sam and Daniel on the side to get extra training. Making a decision he smiled.

"Alright Cadet, pick 4 of your best people and you five will join us. Consider it an impromptu to field test. You have 5 minutes to get geared up and join us." He watched her face light up.

"Yes, Sir!" She saluted as she left they could hear her on the radio, "Cadets James, Cook, Price, and Johns gear up and report to the transport room in 3 minutes for survey duty."

The others laughed at the excited, "Yes, Ma'am" that came over the radio.

Shaking his head Jack smiled, "let's go we have work to do." He, Sam, Daniel, Jacob, and Teal'c left to join the group. As they walked Jack took Sam's arm and held her back. Allowing the others to pull ahead he looked her in the eyes, "Sam, I know you can take care of yourself, but please be careful. We don't know what's down there and I don't want anything to happen to you and the twins." He searched her face and only found understanding and love.

"I'm not going to stop you from doing your job, and I know you would never put yourself in danger. Just promise me you will be careful. I love you and can't lose your now."

Sam smiled at him. She loved this man. God! How she loved him. He wasn't afraid to tell her his fear. He would do anything he could to protect her, but he wasn't going to stop her from doing her job. "I promise I'll stay close to you, dad, or Teal'c. Jack I appreciate that you aren't trying to hold me back. I love you so much for that." She kissed him gently then pulled away. "Come on, my love, let's join the others." Jack simply nodded and led the way.

When they walked into the transport room everyone was waiting on them. There would be a total of twenty people on the survey team, half scientist and half military. "How many of you have the Ancient gene?"

"Natural of Therapy?" Radeck questioned

"Either" Jack watched as 16 of them raised their hand, including Sam, Daniel, and Cassie. They had learned that the SGC had been working on a gene therapy that would activate someone's dormant gene, but Janet had found the answer in Sam's blood. Since Jack was a strong natural carrier, so were the twins. Something in the interchange between mother and fetus caused Sam's gene to activate. Janet was able to localize the cause and use it to create the gene therapy. It was effective in 75% of the people. She had tested the command team first. John didn't need it, he was a natural carrier almost as strong as Jack, but the rest did. It worked in Daniel, Cassie, Janet, Jennifer, and Elizabeth, but Rodney, Jacob, and Teal'c were un affected. It was quickly distributed amongst the group to those who weren't natural carriers.

"Alright" jack continued "We are beaming down in groups of two. Once there split into groups of 5, one cadet per group. Stay close until you are told to spread out. T, you're up first with me." Looking at the transport operator he said, "Locate the Stargate and beam us in next to it. 30 seconds between groups."

"Yes, Sir!" the young Lieutenant said and quickly transported Jack Teal'c out.

The two arrived in front of the Stargate in total darkness. Flipping on their flashlights they quickly pulled their Zats and began looking around, while the rest of the team was transported in. The room was large; scanning the light around showed the Stargate to the back and stairs on three sides, two sets going down, one set up. Flashing the light up he found some other room.

"That's it; we're all here, General." Major Black Said.

"Good" O'Neill said then hit his earpiece, Deadelus, this is O'Neil we are all here. We will make contact in 30 minutes.

Understood General, Good luck came John's reply.

"Sam, Daniel, T, and Cassie you're with me." Jack said, "The rest of your pair up and spread out. Don't leave this room yet. I want to check up there, just keep an eye out."

"Yes, Sir!" Came their collective reply. Even the civilians respected him enough to obey him. Jack motioned his group forward towards the stairs leading up. Teal'c covering their six with Daniel and Cassie on either side. They all immediately put Sam in the middle. No one on the team would think twice about protecting their pregnant 2IC, especially the command team. They didn't get far however, because as soon as Jack touched the first step the light came on and a voice sounded behind them "greetings" it said causing them all to spin around.