Stargate: Colonel Samantha Carter goes Rogue

Sunday Nov 10, 2019

This story has been updated; there were paragraphs that were incomplete and misspelled words, I trusted spell check to fix certain words it did not get all of them. Sorry about that my typing got ahead of my brain. If you find something wrong please let me know.

Comments and suggestions are needed to make this a better story.

This will contain the stories of all three series SG-1, Stargate Atlantis, Stargate Universe.

S. Carter, J. O'Neill, D. Jackson, Vala Mal Doran, C. Mitchell, H. Landry aw' heck let's just say all of them will eventually show up in this story

WARNING: Not intended for young ones if you are offended easily do not read this. It is intended for mature readers over the age of 18, some foul language and sexual innuendos are in this.

***Disclaimer*** I am not affiliated in any way with Stargate or MGM.

This is my first story it has been rattling around in my head so much I am unable to get a good night's sleep.

I am NOT a writer! Please bear with me as I go thru this story, it will stick as close as possible to the Stargate canon. Some of the characters in this are not my own. I would like to thank barjamr for his story, without it the creation of this one would not be possible, having used a couple of paragraphs of the Ancient military base description in this story. IMHO, it is necessary for the flow of this story.

Prologue

Five years after the City-ship Atlantis returned to earth the IOA was still squabbling about whether to let it return to the Pegasus Galaxy, two years ago the crew of Destiny contacted them to say they were in the next galaxy. Their ship is old needing a complete overhaul in a shipyard.

A former naval office had major find in the Pegasus Galaxy it set the IOA off like a rocket, finally deciding to strip Atlantis to the bare wall just leaving the cloak up so as not to startle the people in the USA. They were afraid it would cause mass panic if the world ever found out about aliens.

Chapter 1

Getting Chewed out

Colonel Samantha Carter USAF is really mad, having just come from a meeting with the IOA after getting chewed out by them for letting Former Navy Lieutenant Commander Mark Taggert takes a fully operational Ancient military base located in the Pegasus Galaxy. Taggert had taken over the base only to find two Zpm's sitting at ninety-four percent after ten thousand years no less! AND on top of that the IOA could not steal the base from Taggert; he managed to become commander by setting the Ancient system up to respond to his DNA lockout protocol. Just like Helia, Captain of the Ancient warship Tria had done when she returned to Atlantis. This placed Atlantis in her hands and forced all systems to lock out everyone in the city-ship. Oh and Praesidos has a complete copy of every advancements the Ancients/Alterans ever made included in the database are advancements that Atlantis did not have! What that bunch of fat cat politicians would never know was Samantha helped Mark Taggert setup a series of lockouts on this planetoid.

Praesidos also has a few different manufacturing facilities… including one for building and charging Zpm's. A small shipyard capable of building more Scutin class warships, this type of ship is almost twice the size of an Aurora class Science vessel. One was already completed and sitting in the docking area. The place was enormous; just about a third of the size of Atlantis, and that was merely the main facility.

It had once supported five thousand people in its prime, and was not just a facility to house the troops. It also has manufacturing capabilities for just about any Ancient military weapons, replacement parts for many items that the Ancient's had created and on top of that many research labs.

The base is built into an asteroid. It could actually be considered a planetoid, to be more precise. It is in the middle of a vast asteroid belt in an uninhabited system.

There are no inhabited systems adjacent to it. A bonus when it came to security and one aided by the fact that you could not recognize the base as such from the outside. If someone had done the improbable and happened across this particular planetoid, they would not have seen or detected anything that suggested it was not exactly what it appeared to be.

The IOA was threatening to have her brought up on charges of dereliction of duty, for allowing it to happen. A court-martial was in Samantha's future and a dishonorable discharge. Carl Strom head of the IOA is also threatening to blackball her from ever getting a job in any scientific field. The only job he said she would be able to get was cleaning toilets in Antarctica. Carter thought he was going to stroke-out in apoplexy over Taggert's find. By the time the meeting was over she hoped the whole IOA would!

Strom had a condition to his statement, IF Sam agreed to take part in the dismantling of Atlantis the city-ship in Groom Lake national park next to Area 51 with the cloak still up. It was moved there after a fishing trawler had almost hit it in the quarantined sea area 5 miles from the Golden gate bridge near San Francisco.

Luckily the US Coast Guard stopped the trawler before it was close enough to see under the cloak.

Major General Jack O'Neill USAF stopped her after the meeting. Letting her know getting tossed out on her ass was never going to happen. It would be over his dead body and just play along for now to see what the IOA was up to. O'Neil pulled Carter into a private conference room activating a white noise generator to tell her of his suspicions. The IOA is in the pocket of the Lucian Alliance and how hard he is trying to get the evidence to prove it. It is possible some if not all have been exposed to an improved form of Nish'ta, without the weakness of being able to use an electrical shock to disable it. Seth had used the compound on Sg-1. Oh and to make matters worse the Lucian Alliance now has control of what was left of The Trust.

The General intended to remove the IOA permanently from control of the SGC and replace it with Homeworld command. Still this did not calm down the normally cool-headed Colonel.

"Sir I have had enough of this crap, As much as I love my job, I want out of the Air-force before they try and throw me out, I have an idea I want to run by you on the Hammond. Can we beam up there and talk about it now?"

"Sam you know if I just ran off now there would be too many questions, how about we talk about it when I get home tonight."

"Jack you agreed NEVER to mention that we are living together or the fact we were married in secret outside of our home we maybe neighbors but we are still not supposed to be involved! Remember the Air Force's rules about fraternization between officers of different rank. If Strom ever heard about this he would have all the ammo to blackmail both of us into being his puppets!"

"Ok ok Sam; do not bite my head off! Geeezzzzzzzs!"

Jack wanted to hear what the idea is he was tired of the IOA's bullshit too. Nine o'clock that night O'Neill packed it in for the day and headed home. Once he was in the garage with the door closed.

"Hammond come in this is General O'Neill beam me onboard" A bright white light engulfed the General and he found himself standing on the bridge of the USS George Hammond a BC305 class battle cruiser.

"Welcome aboard General"

"Thank you Major Marks, Can you tell me were Colonel Carter is?"

"Sir, the Colonel is in her office."

Jack found Sam busy doing paperwork necessary for running a battle cruiser.

"Sam it never stops does it? The paperwork I mean"

"HUH? Damn Sir you scared the daylight out of me"

"Sorry Samantha I was not trying to, you should have seen the expression on your face OMG it was priceless"

Sam scowled at her boss/husband whispering just loud enough for him to hear "You just wait I will get even"

Jack laughed, "Is that a challenge Carter? I am here about your idea so spill it"

"Sir, Do you remember the asteroid that Anubis tried to hit earth with?"

Jack grimaced

"Oi Vey! Did you have to remind me of that! We nearly died on that miserable rock if it was not for the slimy snakehead Tok'ra, you, me, Daniel and Teal'c woulda' been frozen popsicles after we pull that crazy hyperspace thru the earth stunt. Damn near outa' power just waiting to die was one of the worse things we went thru together."

Sam chuckled "Nope not even close Sir. Please turn-on your party-favor."

Jack activated the noise generator he always carried with him now.

"OK Sam what's up?"

"Well Sir, I would like your permission to find the asteroid and scan it to see really how much naqahdah is really inside that rock, It would take the Hammond about a week to find it and do a scan of it with the improved sensors I created. My plan depends on what the actual ratio of naqahdah to iron is."

Jack grimaced

"Carter that was not very helpful, how am I supposed to convince the IOA that one of our battle cruisers just went out rock hunting?"

Sam was quite mad

"Sir at this point I really don't give a crap what anyone tells that bunch of mealy-mouthed political pansy's, If my plan is going to work I need to know what's in that asteroid. Please tell me you would at least consider it? Holy Hannah Sir, they want to toss me out of the Air Force you know how much I love my job!"

"Carter, I will think of something."

"Thank you Jack, I knew I could count on you. Bridge this is Carter. General O'Neill is ready to return to his house, please beam him down."

Jack suddenly found himself back in his garage grumbling to himself. "Damn I didn't even get to tell her I love her this time."