Big Changes — Chapter 7

Tony was trying to be patient. This week’s senior staff meeting was longer than usual which was to be expected since a launch date had been set. They were 16 days out from Atlantis taking to the sky to head back to the Pegasus Galaxy. Almost everyone agreed that the best way to keep the Wraith from finding Earth was to send her back to gather intel and destroy as many as possible. Tony was antsy because he was going to drop a bomb after the meeting was finished. He had waited until today because General O’Neill was on the City. This meant Tony could brief him without alerting anyone there was something big happening and Tony was convinced whatever was happening was big.

“I believe that is all the reports we have for today. Remember, we will have another meeting in four days to cover any urgent matters,” Mr. Woolsey stated, “Dr. DiNozzo has asked Colonel Sheppard and Dr. McKay to remain behind.”

“Do you want me to leave, DiNozzo?” Jack asked.

“No, sir,” Tony said, “This will affect more than the City and I believe you’d rather know now than later.”

“Well, damn,” Jack muttered, “That doesn’t sound good.”

Mr. Woolsey coughed as Tony moved closer to the head of the table, “I understand you have a report, Dr. DiNozzo.”

“Yes, sir, but first does everyone know about the city hierarchy program that Dr. Ozolinsh found?”

Everyone but Jack nodded. He waved a hand and said, “Assume I know nothing.”

“Okay,” Tony took a deep breath, “Dr. Ozolinsh joined Atlantis a little more than a month after she landed on Earth. He is a historian with a Master’s in Computer Science which I would’ve had thought would be an odd mix but turns out to be extremely valuable on Atlantis. During the course of his first assignment, he found a city hierarchy program. It is basically a list of job titles and who is assigned to them. As a joke, he filled in then Lt Colonel Sheppard as the Magister Militum.”

“Master of the Military,” Jack injected and Tony nodded, “Dr. McKay as the Magister Scientificus.”

“Master of the Scientists, and Woolsey as?”

Dominus Civitatem,” Tony answered, “Governor of the City but he isn’t a gene holder like Sheppard and McKay, and that makes all the difference. You see, being gene holders Atlantis acknowledges and recognizes them as fulfilling those roles which is why she started sending them the reports the protocols generate. Now, according to the program, the second in command for the Dominus Civitatem is the Praefectus Vigilum.”

Jack leaned back in his chair, “The Prefect of the Police. Not a bad description of your job.”

“Exactly,” Tony agreed, “which is why someone entered my name in the program. As a gene holder, I was high enough in the hierarchy to start receiving reports that would normally go to the Dominus Civitatem.”

Tony took a drink of water and looked to Woolsey before continuing, “If you like, Mr. Woolsey, I can forward to reports to you but I’ll warn you they are difficult to interpret.”

“Thank you, Dr. DiNozzo, I’ve seen some of the reports that Dr. McKay and Colonel Sheppard receive and, while do I appreciate the offer, I am content for you to update me as necessary. “

“Of course, sir. Now Dr. McKay in his role of CSO can prohibit types of research on the City.”

John’s hands tightened into fists as Rodney put his coffee cup down heavily with shaking hands and Mr. Woolsey looked horrified. Jack looked around then turned to Tony, “I’m not going to like this, am I?”

“No,” Tony stated flatly, “No one in this room will.”

Jack sighed, “Keep going, DiNozzo.”

“Since Dr. McKay is recognized as the Magister Scientificus, the City treats his orders as CSO as orders for that role as well. There is a protocol for the Dominus Civitatem to be alerted if inconcessus, or prohibited, research is done on the City.”

Tony paused and looked at Sheppard who was clearly struggling. His eyes were a solid black and his skin seemed to darken as they watched.

“Looking a little blue there, Sheppard,” Jack said eyeing the clearly angry Colonel critically, “Do you need a break?”

Sheppard took a deep breath as Rodney laid a hand over one of his fists, “No, sir, I’ll maintain.”

“See that you do,” Jack ordered, “McKay, what research have you banned on the City?”

“Cloning and the Wraith retrovirus,” was the abrupt answer from a visibly upset Rodney. He took a deep breath, “Cloning research is restricted to the Asgard and only at Area 51. The Wraith retrovirus was deemed untenable.”

“Who?” Sheppard asked in a harsh voice.

“I’m not entirely sure,” Tony hesitated, “The files I received were deleted. Drs. Chaudhri and Simoneit were very helpful but the dates of the files can’t be confirmed nor can we track where they went to or where they came from. What I do know is that at some point, Dr. Jennifer Keller,” Tony stopped as Rodney started to violently and colorfully curse in several different languages.

“Enough, McKay!” shouted Jack, “Save it for later. Continue, DiNozzo.”

“Dr. Keller conducted a series of experiments in attempt to clone the Colonel,” he paused until Rodney quieted down again, “As far as I can tell, she was unsuccessful and eventually moved on to attempting to isolate the genetic changes made by the Iratus bug and the retrovirus. If I’m interpreting the data correctly, she was acting under orders from someone outside of Atlantis, possibly even outside of the SGC. Most of this was done before Dr. McKay formally banned the research, at least in his role as Magister Scientificus.”

Tony took another sip of water and continued, “Regardless, at some point she started working with Dr. Brent Mills who was then stationed at Area 51. The information I received shows they worked together on a project but I’m unclear what the goal of that project was. This continued until about 6 months after Atlantis landed. I understand Keller wanted to remain on Earth, and she and Mills traded jobs around that time.”

“Yes,” Mr. Woolsey answered woodenly, “It seemed like a suitable trade at the time.”

“At that point, Dr. Mills took over the research here on the City and he appears to have cut her out of the loop. I’m unclear if that’s because whoever ordered the research wanted her removed or because Dr. Mills wanted to protect his interests,” Tony paused and focused on the General, ”I’d like to question her, General O’Neill. The files I have are conclusive proof of her involvement but not of its illegality. We can’t charge her based on what I’ve found but she may be able to offer some valuable intel about Dr. Mills’ involvement. Due to the nature of the employment contracts, I exercised my right to review Dr. Mills’ current research and we do have enough to question him as a person of interest.”

“Where is Mills, now?” asked Jack.

“On assignment off base,” Rodney answered, “He had a commitment to a conference that couldn’t be re-scheduled. He is due back in 5 days.”

“That’s your time limit,” Jack said pointing at DiNozzo, “Get what you need so we can arrest his ass when it lands back on the City.”

“Yes, sir,” Tony replied, “I understand you’ll be having dinner here before leaving for Nellis and visiting Area 51 in the morning.”

“You betcha, you want to catch a ride?” Jack asked and, at Tony’s nod, stood, “Right Woolsey, you promised to show me something or other. Let’s do that while McKay calms Sheppard down. You can’t go out looking like that, Sheppard, someone might think you’re a demon and try to gank you. DiNozzo, you’re with me and Woolsey.”

Tony scrambled to follow General O’Neill and Mr. Woolsey as John laughed humorlessly. The windows darkened but not before Tony saw Rodney crawl into John’s lap.


Tony rang the chime on Dr. Addams’ door and it silently slid open. The sound of Nest, Benton and Rodney singing as Rodney and Nest played her harp spilled out into the hallway. Jack, Ray, and John were sitting on the couch raptly listening.

I Walk the Line on a harp?” Tony laughed when they stopped.

“They love me,” a smiling John said.

As Nest walked towards the kitchen, she called out, “At least Rodney does. Benton and I just like to sing.” Everyone laughed and she came out with a bottle and seven glasses, “Let’s have a drink.”

Jack picked up the bottle, “Laphroaig An Cuan Mor Single Malt Scotch Whiskey. You have bad news, don’t you?”

Nest’s lips twitched, “Yes, Jack, I do.”

“Is it at least related to DiNozzo’s?”

Nest and Tony exchanged a look, “Tony’s is a small part of the bigger picture I’m seeing.”

“I want a double,” Jack whined.

Nest poured him three fingers of scotch saying “Better make it a triple.”

She poured the rest of the glasses and handed them around. Once everyone had one, she held her glass up and said “Slàinte.”

Everyone echoed her and took a small sip. She then turned to face Ray and Benton seriously, “What I am about to discuss is to be considered top-secret. I would prefer that you not speak of it but if you must, do so only in areas you have personally cleared for listening devices.”

Both men nodded. Satisfied, she turned to Jack, “Do you know how long I’ve being doing threat assessments?”

Jack swallowed a sip of drink, “About 25 years. Since you started with the CIA.”

“Yes,” Nest agreed, “You are also aware due to my language skills that once I started working for Interpol I basically worked with all the major governments.”

“And a good number of the minor ones,” Jack agreed.

“Do you know what my accuracy rate on threat assessments is?”

“I’m really not liking where this is headed,” Jack swallowed the rest of his scotch, “About 95%.”

“Holy Accuracy Batman!” Tony exclaimed.

“Yeah, Boy Wonder,” Jack replied, “it’s impressive. Where you going with this, Nest?”

Nest took a deep breath, “I completed my threat assessment for the Stargate Program.”

Rodney downed the rest of his drink, got up to pour himself another and refilled Jack’s glass. “First, Tony. Now, Nest. This is turning into a terrible day,” he said to Jack.

Jack clinked his glass against Rodney’s and looked at Nest, “I take it you have some concerns.”

Tony snorted, “You could say that.”

Nest shared a small smile with Tony before continuing, “Yes. I’m seeing a pattern developing and it paints a bleak future for the SGC.” She reached into a pocket and handed a flash drive to Jack, “This contains all the research as well as my official report. Tony was kind enough to review it and I revised it to include his feedback.”

Jack gingerly took the flash drive, “Give me the highlights.”

“I’ve determined there is 79.98% probability that the Trust is working to criminalize the SGC.”

“Criminalize?” asked Ray, “I don’t understand and what’s the Trust?”

“The Trust is an interplanetary terrorist group based on Earth. They are Earth Human Supremacists and Isolationists. I believe their endgame is a totalitarian government that controls all of Earth. The remnants of the Ori fleet are still out there and I expect them to use this threat to unify Earth.”

“Ba’al is dead,” Jack said wearily.

“Yes,” Nest agreed, “but the organization he left isn’t. They plan to blame the SGC for the Ori invasion. Claiming that the SGC committed genocide and in doing so destroyed their religious leaders. They’ll point to us as the problem and the solution will be arrests and executions. I predict they’ll try to negotiate a non-aggression treaty. I don’t have enough information to predict if the Ori will be interested in or honor such a thing but I expect the Trust to offer up all of the SGC as war criminals as proof they aren’t interested in making interplanetary war.”

John gave a short brittle laugh, “What about the Wraith?”

“The Trust don’t view them as an issue believing they are safe in this galaxy,” Nest explained, “One of the reasons they want Atlantis off Earth is the concern that the Wraith will follow her here. Even they agree keeping the Wraith out of this galaxy will be easier than fighting them here. Most concerning is their reaction to Teyla’s gifts” she leaned back in her chair when John leapt off the loveseat he was sharing with Rodney.

Tony watched his friend’s eyes edge black for the second time in a day, “You know, the eye thing would be cool,” he said absently, “if it wasn’t a side effect of having turned into a bug.”

The men in the room turned to look at him in horror as Nest giggled. Eventually, John chuckled and rolled his eyes, “Only you, Tony, only you.”

“He’s right, you know,” Jack pointed out.

Rodney snapped his fingers at the two men and said, “Enough! Nest, what do you mean by their reaction to Teyla’s gifts?”

“The flash drive I gave Jack has intel from every source I could access,” she explained, “knowledge of Teyla’s gifts was restricted to Atlantis personnel and a select few at Cheyenne Mountain but I’ve found mention of it in reports from both Russia and China. Neither one of those countries should have access to that information.”

“I’ve started looking into a possible leak coming from Atlantis,” Tony injected, “It’s one of the things I want to discuss with Keller.”

“Christ,” Jack said scrubbing his face, “This is why you pushed for all the supplies. You’re setting up Atlantis as the fallback position.”

“Yes,” Nest answered, “At the rate the Ori fleet is moving, they could be in Earth’s solar system as soon as three years but no later than five. The Trust have started maneuvering to weaken Earth’s defenses.

“They’ve cut the 304 program funding so no new ships will be built,” Rodney said, “and cut the budget of the 302 program by a third since we’ve been on Earth.”

“The information you gathered is on here?” Jack patted the pocket where he put the flash drive from Nest.

She nodded and added, “I’ve also included the contacts I could share with you. They are the ones I trust to give you good intel without me. I’d like you to add them to the Tagged list. There also is an expanded report for your eyes only.”

“Understood and if they help us, I’ll be glad to add them,” Jack looked at John, “We need to beef up your military supplies. Work with Lorne on an updated list and get it to Walter ASAP, I’ll see what I can do about filling it.”

John nodded, “Woolsey and Nest came up with a plan to ramp up our personnel once we’re in Pegasus, I’ll forward it to you as well.”

“There is some stuff at Area 51 that could be transported to Atlantis,” Rodney started, “We’ll be more secure as we can lock it behind doors and restrict access based on gene status.”

Jack nodded, “I’ll talk to Carter and Danny. I’m sure they’d have a list of stuff that can be moved here. How much of the City did you clear?”

“Cleared for use? Or explored?”

“Either. Both.”

“We’ve explored and mapped 100% as of yesterday. Cleared for use is less than 30% but that’s enough housing for 20,000 based on two people per bedroom.”

“We can increase that fairly easily,” John injected, “In a lot of rooms, it’s just a matter of cleaning the trash out.”

“And some minor repairs,” Rodney agreed, “We were focused on mapping and exploring for the last two years.”

“I don’t even want to know how you talked the IOA into outfitting Atlantis with supplies for an unoccupied housing unit,” Jack giving Nest a narrowed eyed glare.

Rodney snorted when Nest said, “I’m sneaky.”

“Sneaky?,” Rodney retorted, “So sneaky I didn’t even realize until last week that it wasn’t one housing unit but one housing unit per country in the IOA.”

Jack whipped his head around to stare at Rodney who laughed, “That’s right, Jack, she managed to outfit us for over 15,0000 refugees.”

Nest laughed when everyone else, except Tony, looked at her in shock.

“15,000?” asked Ray.

Benton answered him, “There are 24 member countries in the IOA and each housing unit can accommodate 650 people if there are 2 people per bedroom.”

“Yes,” Nest said smugly, “and I acquired enough household goods and long-term storage food for 1 per country.”

Jack gaped at her, “How did you even decide what to buy?”

“One of my long-term undercover assignments was working with refugees,” Nest smirked, “I got a doctorate in Home Economics out of it.”

“No,” Rodney pointed at her, “We do not discuss that ridiculous degree of yours.” Rodney muttered in Welsh under his breath as the rest of the room laughed.

“Home Ec?” joked Ray, “I didn’t think they taught that anymore.”

“Not in the US,” Nest allowed, “I earned mine from the University of British Columbia.”

Jack turned to Rodney, “You gotta admit that’s almost as funny as her Ph.D. in International Relations and Diplomacy.”

Rodney glared at him as he continued, “Face it, McKay, the idea that an assassin has a degree in Diplomacy is downright funny.”

“Now, Jack,” John slyly said, “She only facilitated a change in government with a strategic beheading one time.” At this Rodney turned his glare on John who just smiled beatifically as Nest laughed.

There was a buzzer from the kitchen. Nest stood, “Dinner will be ready to eat in about ten minutes.”

Benton stood, “May I be of assistance?”

“Yes, thank you.”

The pair left the room and Ray stood up, “I’ll just go help them.”

Tony stood and walked across the room to the bottle of scotch. He poured himself another drink and said, “There really isn’t anything we can do tonight. Why don’t we have a nice dinner and talk about anything but work?”

“Sounds like a plan, Tony,” Jack said as he held out his glass for a refill, “Been fishing lately?”

John and Rodney burst into laughter at the look of horror on Tony’s face.