Chapter 2

A/N character list:

Lt. Aidan Ford- 3rd member of John's team.

Major Evan Lorne- 2IC of John's team.

Lt. Elizabeth Weir- Briefing officer.

General O'Neill- Commander of Sheppard's base.

Laura Cadman- Flight leader.

Colonel Marshall Sumner- Sheppard's former CO based in Afghanistan.

General Scott Mitchell- Former Ghost leader current commander of all JSF forces known for an appreciation of Spec-ops and a sense of humor. (End War Universe character)

General George Hammond- Head of the Agency.

Agent Ronon Dex- Legendary among agents and soldiers alike he works alone and is well known for his skill in any kind of fight.

Doctor Jennifer Keller- Agency Doctor

Doctor Rodney McKay- Scientist at research outpost 1- 2nd in command on Project Thor and Project lead on Project Zeus and numerous other projects.

Doctor Cortana Halsey- Scientist at research outpost 1- Project lead on Project Thor and numerous other projects.

John and Teyla were omitted because there history is a major part of the story.

Chapter 2

2 weeks ago

Research outpost #1

She sat in her plush office reviewing personnel records for her next mission. She was leaving for another mission in a few hours but her future mission had just hit its first snag. Her partner Ronon Dex had been called away on another mission. She didn't look forward to working with a partner but she was being forced to for this mission. She'd graduated a few years behind Agent Dex but he was legendary among them and whatever he was being called away for was obviously important. She dismissed another soldier he lacked the ability to keep a secret something that would be important for this mission. As she opened the next folder she stopped at the name. She recognized it and she was immediately taken back to a time eight years ago.

8 Years Ago

He smiled down at her while his hands lazily explored her body. She returned the smile and snuggled closer to her lover. She laid there quietly thinking about their relationship and how it had grown. He'd caught her eye on the first day when he claimed he could fly anything and the instructor promptly challenged him to fly an experimental helicopter. John hadn't been daunted by the prospect of flying a new untested helicopter and promptly flew around the grounds a few times before landing. During the years of hard training that followed they quickly formed a friendship he was by far the oldest one there at 24 the youngest being a mere 15 years old. She was part of the older crowd at 20 but the oldest ever to graduate was 26 meaning that John was often subject to extra scrutiny as he would be 30 at graduation.

Many believed that he was a spy planted to attempt to sabotage them. The thought had crossed her mind but she had dismissed it initially but now she realized they'd broken a lot of rules and if anyone saw them they'd both be thrown out of the program. They'd been dating for a long time but if anyone questioned they could always claim they were just friends and even the small quick kisses they'd shared in public could be excused as those of friends. But once they'd become intimate it had became impossible to claim they were just friends and the idea that he was a spy returned. He was by far the oldest to the point that he could have graduated if he had been one of the youngest initially only to turn around and spy on the next group.

It was hard to believe that someone would undergo six years of training just to do it all again but the agency was paranoid. As she laid there up against him listening to his rhythmic breathing she found herself unable to fall asleep. Her mind was in overdrive considering every possibility from marriage to John being a spy. As she considered it more and more she realized that while she had initially been the aggressor in the relationship, she had been the one to ask him out on a date and she had initiated their first real kiss, but now he had been the one to take things to the next level she hadn't resisted and had in fact welcomed his advances but she couldn't shake the idea that this was all an act. She realized that the best way to protect herself from being thrown out was to head to the instructors and tell them that they had had sex. The more she thought about it the more she was able to convince herself that John was a spy. By the time she drifted off to sleep hours later she was certain he was a spy and hoped that being honest with the instructors would be enough to prove that she was still committed to the program after four years. She wasn't concerned with what could happen to John because she believed he was spy and of course he wouldn't be punished for doing his job.

10 hours later

She felt like crawling inside a hole and dying. She'd convinced herself that John was a spy and had stopped allowing for the possibility that he was going to be the oldest agent and that he was attracted to her. She had woken early and gone to her instructors confident that she would survive this. The meeting had been short and when they'd thanked her and asked if she had any questions she'd decided to risk it and ask if he was a spy when they laughed and told her no she felt her entire world shatter he'd been her friend since the first day there and now he was gone. She just sat there stunned she had been so totally sure that he was a spy to the point where the idea that he wasn't had stopped registering with her. After a few minutes she realized that she had just single handedly ended his dream he was going to be kicked out of the program immediately and would forever be branded as one of the failures. The program was long, six years total training time, and hard, only the absolute best were even considered, but once you got in very few ever dropped out she'd once been on base with a dropout and it wasn't pretty he'd been taunted, teased, laughed at, and became a source of amusement for his fellow officers none had treated him like another person. When she saw his eyes she knew it wasn't an isolated incident it happened to them wherever they went which probably explained why most went into civilian life and did everything they could to hide their past but she knew that wouldn't be an option for John. After telling them everything she'd managed to find a bar they'd often gone to and she curled up in one of the booths and attempted to drown out here sorrow with alcohol. It hadn't worked and when she left she still had to deal with everyone.

There were only twenty or so of them on base so word spread quickly and accurately. She heard the story from her friend Anise that John Sheppard had been taken from her quarters in handcuffs. After some more wrangling she'd gotten the name of one of the men who'd taken him away. With a name and armed with years of training she tracked him down within the hour and managed to get some answers. Unfortunately the answers weren't something she wanted to hear when the guards had raided her room he'd been there still sleeping and when they got him up he'd begged to talk to her or leave her a note but they had strict orders that he was to have no contact with anyone still in the program. He'd even attempted to subdue them but they were trained for just such a situation and were able to overcome him. He'd then been dragged unceremoniously from her room and brought out for processing where he was informed of what he'd done and how they had found out. He told her that John had stopped struggling and stopped asking to contact her at that point and had simply signed everything they asked him to.

After that incident she'd thrown herself back into her training with fierce determination hoping that no one would be able to see how empty her life had become without him. Everyone had missed John he was the person everyone turned to with problems partly because he was the oldest and partly the suspicion that he was a spy made him seem like an official way to get a problem dealt with. She also knew that now she was no longer trusted by anyone. It had been obvious that they had been close to everyone but when they'd learned just how close they were and what she'd done no one was able to trust her again. The lack of trust didn't bother her Agents worked alone except in special circumstances and the idea that her and John ever had a shot at being a real couple was foolish at best but that was no comfort to her heart.

8 Years later

As soon as she read the name she knew he was the only one she could do the mission with in addition to the training he'd already received he had racked up several dozen victories against the enemy and had managed to slip behind enemy lines and rescue a fellow pilot. She hoped that perhaps this mission would make up for what he'd lost but she knew it never would even if they survived.

With her partner selected she turned her attention to the only thing that gave them a shot at completing the mission. The file was slim only a few pages but she didn't need much more than an update on it. The update was on the first page but unlike previous updates she noticed that this one contained some censoring, "Looks like security is getting a little paranoid."

The following report has been edited for security reasons.

To: Agent Teyla Emmagan

From: Project Thor lead, Cortana

Latest Update on Project Thor.

We have made excellent progress the system is almost (Deleted). However we need to know the specifications of your partner as you know each (Deleted) is specifically designed for each user so that it may operate at (Deleted). The (Deleted) and (Deleted) in the (Deleted) should allow you to complete your mission however we are also attempting to (Deleted) a new (Deleted) into the (Deleted). If we get it working in time it should make the mission a breeze and I know you'll absolutely love it, we're calling them (Deleted). I bet you're excited now come on (Deleted)? Hell with those things I'd go into (Deleted). Anyway I'll probably see you down in the lab today or tomorrow and if you wait till tomorrow (Deleted) has to head out to some field base in (Deleted) so it'll just be us girls down here. Hey maybe we could (Deleted)? It'd be fun and you know it :). We wouldn't need to hide from (Deleted) so we'd have all day to (Deleted).

Sincerely, Cortana

PS dam those guys from security are making me hand this over and allow them to screen it well hopefully some of this gets to you and if you want a better update just come on down to the lab.

She understood most of it having been down in the lab a few days prior for a personal update from the team. She sighed and grabbed her papers it looked like she'd have to make the trip all the way down to the lab not that she really minded she and Cortana were good friends but Doctor McKay was always down there and he was annoying to say the least. The lab was buried deep in the dark recesses of Atlantis and unlike many of the clean labs she loathed to visit, Cortana's lab was well known for its relatively unclean feel. She also hated being forced to change into a clean suit but Rodney and Cortana had worked hard to make sure that the lab allowed everyone to wear normal clothing a right she always took. While waiting for the elevator she decided to give it a day and head down there tomorrow when Rodney would be gone. She took the elevator back to her room and for the first time in many months dreamed not of the war or a mission but of John and how she had hurt him.

She woke slowly to sunlight streaming in through her window. Agents were not forced to wake up at a certain time and were given the freedom to do whatever they wanted unless they had a meeting or a mission. She grabbed her handgun from her dresser and got dressed in her usual uniform. She didn't bother to make sure it was up to her usual standards as she knew she would be shedding it once she was down in the lab alone with Cortana.

End Chapter 2

A/N Reviews are always appreciated.

Well It didn't accept some of what I did (blackouts) so I had to go back in and do it again so unfortunatly a few of you have got some major spoilers. Hopefully you'll forget what you read though.