The End and Start of a New Day

14 The End and Start of a New Day


Flipping the pages of his copy of Caldwell’s after-action report from one point to another, Balok looked at the officer in front of him. “Colonel, you and your crew spent a little less than two weeks on Atlantis after your rescue. Is that correct?”

Sitting straight in his chair, Caldwell continued to look at a spot an inch above the shoulder of the General and began explaining again, “That is correct, Sir. While we were recovering from our injuries we were only allowed limited access to the City itself. We were housed in a separate residential tower with a number of medical personnel stationed on each floor and the transporters had been reprogrammed to allow only certain predetermined destinations. The few times that I, my command staff or my crew were allowed out of our tower into the main parts of the City, we were escorted by a group of Marines. Daedalus did not have many ATA positive personnel and the few surviving members were among the wounded and thus not up to attempting to override the lockdown protocols.”

Humming under his breath, Balok took his time to write a note on the report in front of him before moving on to the next point on his list. “These lockdown protocols Colonel, are they controlled through the Atlantis mainframe or are they something that was set up via Earth-based technology?”

Taking a deep breath, Caldwell took the time to think through his answer. “As I understood it when the protocols were originally explained to me, the restrictions are controlled by the City and can be released by the strongest gene carrier or their designated seconds. The current access list on Atlantis goes Colonel Sheppard, Dr. McKay, Major Lorne or Dr. Beckett. If those four are off Atlantis a secondary protocol is initialized that allows Dr. Weir and other designated non-ATA compatible personnel to override the gene sequence needed and input a password to shut it off.”

“So there was no chance that even with your gene carriers, you would be able to remove or disable the lockdown and get free access to Atlantis?” and tapping his pen against his paperwork, Balok gazed over the conference table at the three men before him.

Shaking his head Caldwell leaned back in his chair, obviously trying to translate what he knew into a form that his superior officer could easily understand, “Atlantis has been invaded before General, and the personnel assigned to the City are both highly intelligent and highly paranoid. Given those two qualifiers, we had no one aboard with the correct skill level to even begin to be able to get around the security protocols that were in place before Atlantis seceded. And after the secession, I don’t think even Colonel Carter would have been able to break through the new levels of security.”

“I thought that Dr. Novak was part of your crew, Colonel. Wasn’t she trained by Colonel Carter? And hasn’t she been working with the Asgard Hermiod for the last five years? I would have thought her experience with alien technology would transfer over to the computer systems on Atlantis?”

“Sir, Dr. Novak is currently in an intensive care unit at the Academy Hospital. And Hermiod was placed in an Asgard stasis pod shortly after we found him in the rubble of the engine room. Both were too grievously injured to attempt anything.” And breathing deeply, Caldwell’s eyes lost focus as he looked at something Balok couldn’t see. “We weren’t being mistreated sir, just kept out of the way as they took care of business.”

Deciding to push things a bit harder, Balok tried again to find out what Atlantis and her inhabitants had been up to in the days leading to their disappearance, “You reported that after their initial check in with the SGC Weir and her people realized that the Odyssey would be there soon. When they asked you where you and your crew wanted to be ‘Gated to, why did you not attempt to take over then? Also were you in the meeting when the decision was made to fly the City off of Lantea?”

“Sir, I don’t have the ATA genome, and even if I could overwhelm Colonel Sheppard, Specialist Dex, Teyla Emmagen, Dr. McKay and all the Marines stationed in the Gate Room, I wouldn’t be able to operate the equipment,” and shaking his head, Caldwell continued, “We also weren’t included in any planning meetings beyond the one to determine where to Gate my crew to. Finding out that the City had disappeared was as much of a shock to us as it was to you, sir.”

Leaning back in his chair General Balok contemplated the men in front of him. Even though they had returned to Earth minus a third of their crew and without any idea of where Atlantis was headed, they were still holding their heads high. Knowing what he now did of the command staff of their breakaway base, Balok wasn’t all that surprised that they had managed to keep the Daedalus’ crew isolated and uninformed. From all indications, it had likely been done out of both a survival instinct (what the Daedalus crew didn’t know, they couldn’t reveal) and loyalty to their friends.

Plus the crew and their commander in question were well respected by both SGC field and support personnel. This meant that he had to think long and hard about what he was going to do in response to the issues that this debriefing cum inquest was bringing up. From the initial indications, Caldwell and his command crew had followed all the agreed upon regulations to the letter when exiting hyper to do their scans.

When the ship had been fired upon, the mapping mission had immediately been scrubbed in favor of getting their ship out of range of the mystery drone launcher as soon as possible. The second item had been to find someplace safe that they could set down on to either effect repairs or wait for rescue. The third item had been to determine where they were and gather what information they could with what supplies they had on hand. And despite the odds, Caldwell and his crew had managed to fulfill their mission requirements. All of which meant that he couldn’t throw the book at them for their actions before the rescue.

He might be able to find some leeway in the regulations so he could charge them for not attempting an escape during the time that they had spent on Atlantis after the rescue. But given the injuries that the crew as a whole and the command staff, in particular, had suffered, he would need to check with the bases JAG to find out if the idea was even feasible. If there were no legal means available to him to deal with his officers, well there were plenty of scut jobs open even at the SGC. And the old guard wouldn’t have any reason to complain if he did the last. So that was an area that needed to be looked into further.

Nodding to himself, Balok looked over the list he had prepared based on the after action report written by Caldwell and his crew. All the areas of concern had been addressed and there really was no reason to keep them here any longer. Plus having them off base would allow him to meet with the JAG a bit more discreetly. Pushing his chair back, Balok gathered his papers together and stood up, “Alright gentlemen, it looks like we have covered the major points of concern. We will be calling you back individually over the next week, so stay close to the Mountain. Dismissed.”

Time to make some phone calls.


Carson decided to let John leave his tender clutches only after his body chemistry returned to normal and that had taken several days. When he was released he was directed to go to his quarters and not head back to the Chair room nor was he to go to his office. To make sure that John actually followed his orders, Ronon was there to escort him to his room and stand guard on him. Beyond feeling mildly disgusted at the mother-hen routine, John really couldn’t find himself caring too much at that point, he was still too tired.

Stumbling into his room, John found that someone had been there ahead of him and had turned his bed down, and put a bottle of water and the drugs that Carson had prescribed on his nightstand. Whoever it was that had done that, he was going to make sure he thanked them when he woke up. Downing the water and drugs, John crawled into bed without bothering to take off the scrubs he was wearing and was sleeping moments later.

When he finally woke up he did so gradually, feeling peaceful and warm. Neither condition was something that he was used to after living in Pegasus for the last six years. When he managed to get his eyes open, John saw that he was draped over Rodney with his head nestled into his shoulder. Sighing softly, he let his eyes drift closed again and tried to ignore the demands his body was making of him, his bladder wasn’t that painful yet. After what felt like too short of a time, his body won out and he just had to move. Sliding carefully out of the bed to avoid waking his human pillow, John quietly made his way over to the bathroom. Taking care of his personal business, he paused looking at his reflection in the mirror. He looked tired and beyond scruffy with the start of a really good beard and bed head from hell.

Deciding that he needed a better clean up than the sponge baths he had suffered through in the infirmary, John flicked a thought at the shower to get it warmed up. Ducking back out into his room, he saw that Rodney was still sleeping although he had shifted to take over the extra space on the bed. Trying to be quiet, he quickly got a change of clothes and headed back into the now steamy room. Stripping out of his scrubs he got under the hot water and started cleaning all traces of his time in the Chair and the infirmary from his skin, trying to ignore the areas in his mind that felt more than a bit raw. Working on autopilot, John managed to get showered and shaved in record time and then just stood under the hot water and enjoyed the feeling of being clean.

After a while, he finally felt that he was both pruney and clean enough. Shutting the water off with a mental flick he headed out to get ready for the day. Dressed and feeling much more human than he had when he had fallen asleep, John paused at his desk and jotted down a quick note so Rodney wouldn’t freak out if he woke up to find him gone. Propping the note on the nightstand John brushed a kiss over Rodney’s hair and headed out to find food, he was starving.


Walking into the commissary for breakfast Elizabeth couldn’t find it in herself to be surprised that John was sitting at a table nursing a cup of coffee and staring out the gallery of windows. While it hadn’t quite been twenty-four hours since Carson had discharged him from the infirmary, she had never known him to stay where he was supposed to when he was recovering. On the other hand, John did have a tray that looked it had been well picked over, so he had at least eaten something. No matter what Rodney thought, John did eat, he just didn’t eat a lot when he was under stress. So when things got bad, everyone in the know kept an eye on him and let Rodney know when it was time to start nagging. John still hadn’t figured that one out.

Grabbing her own breakfast, Elizabeth walked over to John’s table and made sure that she was loud enough to let him know that someone was coming up behind him. “John? May I join you? And how are you feeling?”

“Oh, hey Elizabeth. Please join me,” and waving one hand at the chair opposite him, John pushed his empty tray to the side to make room. “I feel fine by the way. A bit more sensitive to the ATA, but that happened when I was in the Chair the last time. “

Taking the time to get her breakfast positioned as she liked it, Elizabeth thought over what John had just mentioned. Coming to a decision, she let the comment about the ATA go for now. She would ask Rodney or Lorne first to see if they had noticed any increase in their sensitivity to the City after their shifts in the Chair. Picking up her fork she started poking at the food on her plate and right before she took her first bite looked over at her friend, “I’m glad to hear that you are feeling better, John. And no, you can’t get back in the Chair for a shift.”

Grinning slightly at how well she knew him, John returned to his contemplation of the stars.



It’s been over a year since we left Lantea ahead of the Odyssey. In deciding to secede from the control of Earth we had gone from a multinational expedition force to being an isolated and hunted colony. A colony that no longer wanted to be tied to our home nations, let alone the planet.

Things haven’t been easy. The original plan had us finding a new planet to settle on, one with enough water to allow Atlantis to float on a sea instead of being tied to the soil. But after talking over our options and calling for a City-wide vote, it was decided that we were just going to spend some time out in “The Black”. Can you tell I’ve been watching too much ‘Firefly’? Still, it’s what we’re doing.

Hanging around in deep space has some benefits. One is that we are damn hard to find, what with the SGC and the Wraith both looking for us. Through the long-range sensors and remnants of the Ancients galaxy wide sensor net, we have seen over a dozen separate Tau’ri ships arrive in different areas of the galaxy. Often several ships arrive at a time. They and the Wraith want Atlantis and are looking for us with everything they have. One has to wonder how the war with the remnants of the Ori is going if the SGC is continuing to hunt us, and we all know why the Wraith want us.

The second benefit of us hanging out is we have finally got the City fully explored. We chose an inactive ‘Gate location so we can use the Stargate, and do so to keep in touch with our allies and trade for what we can’t produce, but the unrelenting mission tempo has slowed down. Thanks to the slow down we now have a much more detailed idea of what the City has to offer and she is beautiful. Nothing comes for free though, and we did lose a few people in the course of the explorations, so if we ever get back in touch with Earth we will let their families know, but overall the losses have been few. And what we have found! Rodney almost dislocated his arms in his excited hand-waving a few times.

The third benefit is personal. Rodney and I finally stopped the public tip-toe routine and moved in together. We had found bigger apartments in one of the secondary towers during Year One, but because of our power issues, the decision had been made to not release them for habitation. With the additional two ZPM’s from the Da Vinci we have the power to spare and we can all spread out. So Rodney and I live in one apartment, Teyla and her intended are down the hall, Jon and Daniel are on the floor below us, and Ronon has taken over the apartment across from us. Can you believe he is dating Keller? One has to wonder about those two…

Well with the benefits came the problems. Problem one was something I really hadn’t thought of. Vitamin D deficiencies lead to that lovely thing called rickets, and since we were no longer on a planet orbiting a G-type sun, we weren’t getting an outside source of sunlight so we could make our own. Now we have supplements, but we wanted to save those for any emergencies we might have, and frankly, they don’t work as well as what we can make internally. So it looked like a fix needed to be found before we all started breaking bones or looking like the hunchback of Notre Dame. When we went to look at the life support systems in the thought of changing the settings on the internal light sources, we found that Atlantis had beaten us to the solution. As soon as we had taken off of Lantea, she had switched the lights over to a full spectrum wavelength. Gotta love it when everything works like it should!

Food was the next consideration. We did have some problems at first. While we had the greenhouses spooled up for planting, the Botanists hadn’t had a chance to get everything started. Parrish and his team had done wonders in cleaning out all the crap that had been left behind by the Ancients (and by crap I mean the ten-thousand-year-old dead plants and the soil they were planted in) and flushing the systems, but they had just gotten past the test crop stages. We knew the system could work, and for the original expedition the test crops had been enough to supplement our diet, but now we needed them to go into full production.

So we were eating our stores at first. And those stores were rationed pretty tightly while we waited on the first crops to come in. Getting everything in was an all-hands rotation that took a solid week. We now have actual fields of tava beans, wheat, corn, rice paddies and the start of a respectable orchard. Admittedly the orchard was one of the test crops that started out as a bunch of potted plants in the hallways, but still, we have an orchard on Atlantis. And the trees are starting to produce fruit now. Add in the hydroponic rooms with the hanging gardens and we are set when it comes to veggies. As for protein, well the Pegasus version of tilapia is pretty tasty and it’s growing in the aquaponics bays. So for the most part, food really hasn’t been that big of a problem. Keeping a potable water supply for use by humans and our crops is, which is why the aquaponic bays are such a help.

Oh, we have no red meat to speak of right now, and the last time I had a steak was months ago, but we aren’t likely to go on short rations again or starve. And Parrish has just started growing some of the luxury plants and herbs from Earth and Pegasus. Strawberries and kemi berries are delicious. Did I also mention that we have tea plants growing? I didn’t even know anyone had brought seeds for those through until Parrish mentioned them at the last supply meeting. It seems Peter Grodin had smuggled some in with his gear and turned them over to Parrish for cultivation. What does all this mean? Well besides some nice fruit, we have trade items that are normally hard to come by. So botany and the agronomists are happy and so are our trading teams.

Does this sound like everything is going our way? It really isn’t. For all that Atlantis is a beautiful city and she wants to help us, she’s old. I mean the Ancients left her alone at the bottom of an ocean for ten thousand years. That wore at her and riddled her with problems both large and small. Then we got her bombed within months of her rising, not counting the storm that almost sunk her. So honestly, it was a good thing that the Asurans came along and took over the City when they did.

What, you thought I was upset over that? Well, I was, but they fixed the City. Not just the Stardrive, they fixed the structural damage that we didn’t have the means or the knowledge to do. But everything else? Things like the nanotech labs that had been closed, but not mothballed? The untended gun ranges that were left open with weapons lying about, all unlabeled? Things like an incredibly old Ancient database that had been allowed to operate for untold millennia without even a defragging program run every once in a while? All of this and more was left for us to find. Most of these things have cost us lives or time that could have been saved if the Ancients had taken the time to do things correctly.

What is wrong with the database? The Ancients had been using it non-stop for an unknown number of millennia and there really was no logic to it that we could see or understand. It is really possible that everything that we need is buried within it, but the way the Ancients filed things has to be seen to be believed. The Ancients did label the truly important programs fairly clearly, such as things like life support, propulsion, inertial dampeners, and other housekeeping and weapons programs. Which is a good thing, but everything else? Things like the history of their war with the Wraith, medical information on the plague that drove them out of the Milky Way, how to build ZPM’s, information on the Ori, a list of what experiments were run and what the results are all hidden under file names we may never look under. Access to these things could have helped us a million times over in our war with the Wraith and the Ori, but despite the Da Vinci’s search program, we still have problems figuring out where to look. And so we are left with only the bits and pieces that we stumble over all unknowing and unaware. Rodney has damn near frothed at the mouth when the search program returns with only hints and clues, but no hard data, no matter how he phrases things. Can’t really say as I blame him.

So we will be out here for a while longer, floating around our little brown dwarf star. Once the hunt for us has cooled off a bit more we will say goodbye to the black of space and relearn the light of an actual sun. We’ll go back and check out the Da Vinci and start him up again, and see what other secrets he hides. We’ll settle on a planet again and feel the rocking of an ocean as Atlantis rides the waves. We are still alive. And we will never give up what we have found. Home.



  1. It’s a very sweet end of the book one and i love the epilogue.

  2. Thank you.

    That wasn’t the easiest one to write, but I had a lot of fun doing it and I learned a lot too!


  3. Great story, with good details on what it takes to make a viable colony. And I really like the involvement of Caldwell and Deadalus. Now on to start on the next one 🙂

  4. Very, very interesting and very detailed. I’m looking forward to see what comes next.


  5. I get the feeling that the Ancients filed things using the following system: surgical stuff and purple things, triangular like objects, guess where I’m hiding today (for files that move themselves around the database), and then all the Jeopardy categories ever used to date all the labels of their own files, and then a two year old ancient child went through all the organized (hah) bits and threw them about like papers just as a mini tornado went through to blow every thing around, until the ancient database became the perfect comparison to total chaos.

    That said, well done. I like how nothings perfect on Atlantis and how nothing is truly settled on earth either. *heads off to bed for the night*

  6. Hey there! So fun to see you at BASCon. I really enjoyed this story and will eagerly be getting in line behind all the other people waiting for a sequel. LOL. I’m off to read your Sentinel one. Yay!!

  7. greywolfthewanderer

    awesome story, yo! Onward 2 tha sequel!

  8. This is amazing.
    Such a complex, but not too complicated to read easily, story with all the elements from political machinations to the details of food on the Da Vinci.
    And the undercurrents of personal relationships which can finally progress is delicious.
    Going straight on with the sequel, as I can’t help but want to know more.

  9. I loved how you wrote the tension and emotions in this. I think it’s some of your best writing. Well done!

  10. greywolfthewanderer

    second read, stands up well! off to read tha next 1 now…

  11. What a great story, I like how every one had a plan for the worst but still where a little heartbroken when they had to use them. Thank you for sharing 🙂

  12. That was simply LOVELY! Thank you for this! My mind and my spirit both thank you for the calm this had brought. 🙂

  13. Just re-reading after the fanfic rec on Facebook.

    It’s still awesome. I still love it!

  14. Loved this fic, and how they planned for being abandoned/seceding from Earth!

    Going to look for the sequel mentioned above now!

  15. Both these series are really excellent! The characters and relationships, group/political dynamics, plans/action, and tech are all well developed, canon-appropriate, and plausible.
    I actually read AUC first, not realizing until I was far enough in to be reluctant to stop that it was the wrong order, giving myself some spoilers for TSSoI, but (not being especially spoiler-averse) that didn’t bother me. This story-arc and TSSoI’s ending were satisfying and even sweet.

  16. I was so excited when I found this! I’ve read the next part already and you did such a good job covering what happened before that part that I really didn’t think that you had written about the events that caused the break from Earth. Love this series and I hope you’ll write about Atlantis negotiating with Earth and expand on the Epilogue from the next part.

  17. Loved it!

  18. I don’t know how i missed this, but it was a lovely read. Thanks for sharing.

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