To Disappear Into The Dark Places

12 To Disappear Into The Dark Places



Two and a half days of frantic packing, endless Jumper flights, last minute innovations and never-ending worry later, Atlantis and her citizens were as ready to leave Lantea as they ever would be. The freshwater tanks where Atlantis stored desalinated sea water were full and the waste treatment facility had been given a quick inspection since there was no guarantee that their new world would have potable water. The mainland settlement had been broken down and everything that could be moved was being stored in storerooms scattered throughout the City. All the perishable foods that had been at the settlement were packed into the refrigerators and freezers that had been deemed suitable for food storage and more had been cobbled together at the last minute to handle the influx. As an added precaution the hunters among the Athosians had taken the time to go out for meat and had brought in enough to keep everyone fed for a few weeks at least.

Sitting in the conference room where the decision had been made to leave, Elizabeth went over her lists a final time. Except for the final walk-through of the Da Vinci and the flyover of the crash site, they were finished. And it had all been completed before their absolute deadline of four days. As one of the final tasks on the list, John and Rodney had gone out to retrieve the science detachment stationed aboard the space station and do the final inspection. Meanwhile O’Neill and Jackson were on their way to examine the remains of the Daedalus. Each team was expected to arrive at their destination, do their inspection and then head back to Atlantis as soon as possible.

Hearing her radio chirp for attention, Elizabeth reached up absently and tapped her earpiece to activate the link, “Weir here.” And with most of her attention firmly on her lists, she dimly heard Chuck give the news that they all had been dreading. “Sergeant, could you repeat that?”

“Dr. Weir, we have a ship on the long range sensors that matches the profile we have on file for the Odyssey. At present speed, she has eighteen hours before she reaches the edges of our system. Also, the energy profile we are getting matches the information we have on what an Odyssey class ship looks like when she is trying to come quietly.” The words were quiet, and Elizabeth could hear Chuck taking deep breaths as he tried to stay calm.

“Chuck I need you to dial the Da Vinci and let Colonel Sheppard and his team know what you just told me and that they have three hours to round up the science team and return to Atlantis. Confirm with Major Lorne that there are no teams out on the Mainland and if there are, have him recall them immediately. Once that is done, I need you to call all section heads together for an emergency meeting after all the teams are back. Have housekeeping get the main conference room set up with coffee and tea.” Elizabeth knew that if she gave Chuck enough to do, he wouldn’t have time to panic and his calm would spread through the rest of the staff on the command deck. One thing that they did not need was for people to start spreading wild rumors all over the place.

“Right Dr. Weir, I’ll get started on that now,” and sounding far calmer than he had after he had let her know about the Odyssey, Chuck signed off.

Staring at the blank walls of the conference room, Elizabeth could only wish she was as calm and as in control as Chuck had sounded.


“Roger that, Atlantis. We’ll be back in two hours and will relay this transmission to Lt. O’Neill and his team. Please let Dr. Weir know that the Da Vinci is ready for the power down sequence and we are packing everything up as we speak,” and tapping his radio’s transmit key, John stayed on the line for any further information from Atlantis.

“That sounds good, Colonel. We will be waiting for your gear. Atlantis, out.” And with a sharp click, the transmission ended and the wormhole connecting Atlantis to the Da Vinci was severed. Turning to look at Rodney, John wasn’t surprised to find him at the communications array, repeating everything they had just been told to O’Neill and his team. After all, time was of the essence and while there really wasn’t anything left to strip from the remains of the Daedalus, the idea had been that it never hurt to look. Snorting to himself at the thought, John moved over to the console that housed the interior communications array, they needed to get the scientists to move quickly.

Tapping out his request on the console, John quickly patched his radio into the system. “This is Colonel Sheppard. Due to news from home, we are moving our time table for the shutdown of the station up by three hours. Everyone finish what you are doing and report to the Gateroom in an hour and a half. This means everyone and if you are late, well I hope that you don’t mind the cold and a serious lack of oxygen. Sheppard out.”

“Very funny, Colonel. Was that aimed at me?” it always amazed John how much acid Rodney could imbue into his voice and still have it come out sounding like he was pouting.

“Not really, Rodney. But if you want it to be, please take it as a given.” And hiding a grin at his friends’ habitual irritation with him, John turned around. “What do you say we go and do a final check on the power relays?”

Muttering to himself, Rodney made sure to correctly disconnect his laptop from the command console. John knew that once all his equipment had been put away, he would hear some comment on his thinly veiled suggestion. He wasn’t disappointed. Raising his voice slightly, Rodney said, “I suppose I had better go with you. Otherwise, you will end up locked in a storage locker and we will all forget you. Again.”

Pulling the obligatory offended face out, John tried to come up with a snappy reply that didn’t sound like another in a long line of excuses, “Hey! I was all turned around. Besides, that was on Atlantis. And that was three years ago!

“Some things Colonel are remembered forever. That’s one of them,” and smiling the smile of the smug, Rodney turned to go. “We are going on a walk, right?”

“Yes, we are leaving. So what’ve you guys found on this thing?”

The smug grin that Rodney had been wearing as he teased John seemed to get wider at the question, “Lots of empty rooms, labs that were actually closed up properly and surprise, surprise, the database has a search function that actually makes sense and is easy to use.”

Hearing that the holy grail of anyone who had ever had to try to mine the database on Atlantis actually existed, John shot an incredulous look at his best friend. “Please tell me this program is one that we can download to a laptop and bring back? And that it will actually work with Atlantis and her computers?” Begging wasn’t exactly condoned when you were the military commander of a base, but John had spent some of his on duty hours trying to tickle desperately needed information out of the database and more often than not coming up dry.

Nodding swiftly, Rodney gave John the good news, “We can and have it on a laptop and the software engineers back home are reviewing the coding to see if we can even interface it with Atlantis. Hopefully, this won’t be a case of incompatible software.”


Walking down the hallways of the Da Vinci was nothing like the halls of Atlantis. For one thing, the station was nowhere near as alive feeling as the City, which might have been a function of the limited power available to him. Then there was the artwork gracing the walls. Atlantis was very easy to get lost in because most of her hallways looked remarkably similar, here there was no chance of that happening. Every hallway was different and there seemed to be whole artistic themes going on, plus there was the lack of windows. Atlantis was constantly bathed in multicolored light from the hundreds of stained glass windows studding her walls. Here on the Da Vinci, the only light available was from artificial sources and while it was full spectrum, it never changed.

One thing that was good about how the Da Vinci was constructed was how close the main power room was to the command deck. When John and Rodney had first arrived on the station they had discovered that there was a ZPM that had reached entropy and the attack on the Daedalus had been the equivalent of a last hurrah. Making sure the naquadah generators had been tied in quickly and correctly had been more than just convenience, it had been a matter of life or death. Right after they had dialed Atlantis, they had gotten an alert stating that they had less than three hours worth of power left in the ZPM and the replacement needed to be found.

Given that the only ZPM Atlantis possessed was currently plugged into the main power hub and thus not readily available, it had been decided that naquadah generators were the only way to go. And they would have to leave them behind so the station could power down correctly and when the expedition was able to come back, they would be able to power him back up.

Walking into the room that housed another depleted ZPM was always a bit depressing to John. They had found so many of the devices, and yet so few were usable. Moving around the room as Rodney fussed over his generators; John ran his fingers over the rows of the script the Ancients had carved into the walls. While he wasn’t reading at the same level as Jackson or even Rodney, some words leaped out at him. The letters of the Ancient alphabet crawled over the walls, spelling out potenta, navitas, origo and vita in endless, repeating patterns. “Rodney has anyone been in here to find out what these walls are saying?”

“Gee, let me think. We have six walls full of Ancient text, all talking about ZPM’s and maybe the clues on how to make more. What do you think I did Colonel? Hold a séance in here? Of course I got Jackson and his soft science morons to look in here. The only thing the walls say is nothing. Well, nothing immediately useful at any rate. Jackson and his people spent a few hours recording everything and all we can hope is that they find something useful and not the Ancient version of a battery commercial!”

John had just confirmed to himself that his plan of annoying Rodney was one of his best ideas ever. Deciding that pushing his luck was the way to go, John glanced over at his friend and commented, “So I am guessing that there is nothing useful to be found here?”

Listening to the sputters and half formed words tumble out of the other man’s mouth, John kept moving around the room. There seemed to be something nagging at him, something that was vitally important and he knew that he had to pay attention to what that nagging feeling was trying to tell him. Moving over to the hub that was the main power relay for the station, John started running his hands over that too. There was something here…

“Really, you don’t think that I haven’t tried that? We had a full scan done of this room and the ones surrounding it. Nothing has shown up. Nothing is in here but another Ancient monument to their short sightedness and arrogance.”

Not really paying attention to what was being said to him; John stopped moving around the central pillar. Whatever was nagging him was strongest right about here. Moving away from the pillar towards the wall increased the sensation and running his hands over the wall in front of him got him to an area where the feeling was strongest. “Rodney, shut up. I need you here. Now. With your scanner.”

“John? What did you find?”

“I have no idea. But I think Da Vinci is trying to let me know something,” John murmured.

Bitching was something that Rodney had learned how to do while still managing to get his job done, so his hands were pulling his scanning equipment out while his mouth was running, “How can the Da Vinci tell you anything? There is barely enough power for life support, let alone enough to really activate the ATA network!”

Shaking his head slightly at the buzzing of his nerves, John kept moving his hands over the area that was keeping his attention. “I know something is here, Rodney. And whatever it is, it’s important.”

“Well, there is something here now. I scanned this area myself when we got here and there was nothing. No energy readings, no blips, no spikes, nothing. And now? Thanks to Mr. Super Gene, I have a blip, a spike and a reading,” and tapping the screen of his scanner, Rodney moved it over the wall. “Okay. I need you to touch this area,” and waving a hand at an area the size of a piece of paper, he looked over at John.

“I think I already figured that part out, McKay. Here goes nothing,” and placing his hands on the area indicated John tried to make himself as receptive as possible. For five nerve wracking heartbeats nothing happened. And then the wall cracked open and a drawer slid out.


“Atlantis this is the Da Vinci. We have all personnel aboard and are ready to start transport. Please lower the shield.”

Tapping the key for the external communications array, Chuck started to reach for the shield controls. “Da Vinci this is control. We have your IDC and the shield is down. Come on home.”

“Thanks, control. We have some good news for everyone. Before we get into that, make sure that the Gate stays up until Dr. McKay gives the all clear.”

“Roger that, Da Vinci. We are getting personnel in now. How many Jumpers should we be expecting?”

“Only the one. I’ll be signing off now and heading through the Gate. See you in two. Da Vinci out.”

Deciding that moving out of his chair was better than having it jerked out from under him, Chuck watched Dr. McKay hurry up the staircase to the command level. Instead of his usual computer case, it looked as if Dr. McKay was clutching a large sample case like the one Botany department used. When he got to Chucks station he set the case on the floor between his feet, like the case was too precious to let out of his control for any length of time.

Deciding that the case was a mystery that he really didn’t need to worry over, Chuck turned his attention to the Gateroom floor. All members of the science detachment and away teams were back and Colonel Sheppard had just exited the wormhole. “Dr. McKay, Colonel Sheppard has stepped through the wormhole and the Jumper is through.”

“Right, time to send the shut down sequence,” and Dr. McKay began tapping a series of commands into the Ancient console before him. Almost immediately there was an acknowledgment from the space station and the Gate shut down. “Sergeant, do you know where Elizabeth is?”

“She went down to the mess for something, sir. She should be back any moment now.”

“Let her know that we are going to be in medical and that Colonel Sheppard and I need to talk to her as soon as possible,” and grabbing his sample case, Dr. McKay trotted down the stairs and out the door towards medical.


Walking into medical was always a bit of a disconcerting affair. There was so much that had gone wrong in these rooms, so many times that she had walked through the doors not knowing if her friends would be alive on the other side or if they were still alive, they were injured beyond the ability of Carson to completely heal. So although she knew that there was nothing wrong with any of her people this time, she still felt a chill as she walked in the room.

Glancing around quickly, Elizabeth made sure to stay out of the way of all the corpsman and nurses as they moved from person to person and from room to room. The sheer number of people in these rooms was unusual, but she could see that the numbers were already thinning as returning expedition members were processed and released. Catching sight of Rodney as he expressed his displeasure over his blood draw, Elizabeth made her way over, wondering why she was meeting him in the sickbay of all places.

“Rodney? You wanted to see me?”

“Ow! Do you have to be so rough every time you poke me? Right, go away now and play vampire with some other poor bastard,” and flapping his hands at the nurse who had just taken his blood, Rodney waited until she had actually left before turning to speak to Elizabeth. “John and I found something on the station that needs to be dealt with immediately. The station is in shut down mode and he has sufficient power to keep his current orbit stable for the next hundred years or so. I need to get to my lab before the meeting to do a few tests and then I need Radek to meet me in the ZPM room. John will explain the rest. Gotta go.”

Watching as Rodney grabbed the specimen case that had been on the gurney beside him and run out the door, Elizabeth could only nod and feel like she had just been run over by a bulldozer. Taking a few seconds to think over what Rodney had just said to her, she felt a wild hope start to rise in her heart. If she was right, if what Rodney had implied was correct and everything worked, they were safe. Turning quickly she scanned the room for Sheppard. When she found him, she rushed over, eager to see if her suspicions were correct.

“John, Rodney just ran out of here clutching at a sample case and saying something about tests, Radek and the ZPM room. What happened on the Da Vinci?”

“We found ZPM’s, Elizabeth. Two of them. And from the initial scans, they are half to three-quarters full. Which means we now have enough power to fly the City and hide her where the SGC can’t find us.”


Smiling down at the objects on the surface, Rodney tried not to gloat. Speaking over his shoulder to the man behind him, he said, “To look at them, you would never know how much power is stored in such small objects. We have three ZPM’s in the City and we get to keep them. Finally.”

“Yes Rodney, we get to keep them. But only if we get the testing done fast enough to hook them into the power grid.”

Releasing a put upon sigh, Rodney turned away from the comforting sight of two more ZPM’s standing on the table in the main lab. “I know we have to get the tests done, Radek. But it’s nice to see that things aren’t going to be as desperate as we thought they would. What do your instruments say?”

“ZPM on the left is showing as 65% charged and the one on the right shows as 67%. And I never said it wasn’t nice, I just think we need to move faster since the Odyssey is on her way in. It would be very bad for us if they watched us leave,” muttered Radek as he continued to take sensor readings.

“Yes, I know that. My tests show that there’s nothing on the outsides of the ZPM to cause them to overload and all indicators are green for insertion,” and rubbing his hands in glee, Rodney began removing all the testing equipment attached to and placed around their two power sources. “Want to come with me to the power room?”

“Really must you ask?” Radek snapped back. As Rodney finished removing the equipment from the second ZPM, he set the first into the sample case. Carefully moving the second over to its temporary resting place beside the first, Rodney nodded. Tapping his radio, Radek made sure that the command deck knew they were leaving the main lab and headed to the main power room. Chuck would ensure that everyone was routed well away from them and the way would be clear.


“How in the world did Rodney miss the energy signature of two ZPM’s? Wouldn’t they have lit up the Jumpers scanners as soon as you got near the Da Vinci?” Elizabeth asked.

Leaning back in his chair, John sighed. “You would think that would be the case. But the space where they were stored was heavily shielded. The only reason I knew it was there was because something on the Da Vinci started nudging me to look in that area. Even with that nudge, it took Rodney a good ten minutes to open the access panel. Once we had the drawer open the energy readings were obvious, and after we removed them there was still a residual level from the compartment that pinged the scanner. When we closed everything back up though, there were no energy traces at all. Or at least none that Rodney’s handheld could find. He keeps muttering things like ‘If he missed something like this, what else did he miss?’ I’m betting he is going to want to head back when it is safe so he can go over the whole facility with a fine toothed comb.”

Nodding her head in agreement, Elizabeth sighed. “And I’ll let him go with my blessing. Rodney did say that the station was properly mothballed by the Ancients, right?”

“Oh yeah, it was. Someone who actually knew what they were doing made sure he would be able to be brought back up. Did Rodney mention that his geeks found a search program and that they downloaded it to a laptop for analysis? If the code is compatible, the word is that it will be uploaded to the database and we may actually be able to find stuff now!” John said smugly. Watching the genuine shock move over Elizabeth’s face was always fun. And being able to do it while giving her good news was even better.

“What? A reliable search engine written by the Ancients? I thought there was no such thing!”

“Yeah, the programmers have it in the lab, and as soon as they give the go ahead, it will be uploaded. After that, we’ll have to see what it can turn up. And well, given what we saw when we originally arrived here on Atlantis, I don’t think the Ancients ever really intended on coming back. Especially after I saw how careful they were to shut the station down correctly. Nothing against your counterpart, Elizabeth, but she just didn’t know how to correctly mothball the City. And it showed,” and giving his friend a look of apology, John shrugged. He knew that there were really only a few people in the new colony that had the skills to do a proper shut down, and Elizabeth wasn’t one of them.

Waving off the apology, Elizabeth nodded. “Oh, I agree. Are we ready to go?”

“Once Rodney and Radek get the ZPMs tested, installed and the power grid is initialized, we should be able to send Caldwell and his crew home and be on our way. Has Carson cleared everyone?”

Sighing at the thought of leaving their friends to the ‘mercy’ of the new SGC, she nodded. “They’re starting to stage the more mobile members of the crew on the edges of the Gateroom. Carson is making sure that everyone who isn’t mobile has enough support to be able to last at least twelve hours and his people will bring them up when we are ready to gate them out. Once we have the all clear from Rodney, we’ll send them through to Cimmeria, with enough supplies to feed them all for a few days.”

“Good,” and reaching up to open his radio to a shared command channel, John decided to check up on his favorite geek. “Rodney? Are we ready to get this show on the road?”

“Yes Colonel, we are good to go. We have run the ZPM’s through every test we could think of, and they’re clean. They are currently at a combined 66% power level, and with the one we have, should be more than we need to send the Daedalus crew home, and get us off Lantea. Which we need to do sooner rather than later.”

Nodding his head in agreement even though Rodney couldn’t see, John pressed one more time. He had to make sure. “Right. So everything is good to go? No surprises waiting for me when I fire up the engines?”

Hearing Rodney huffing out an angry breath, John had to smile. And then grin as he got blasted by a wave of condescending wit, “Gee Colonel. When I said we were good to go I meant next week, not now. So why don’t you get out of Elizabeth’s office and get your skinny ass down to the chair room and get us off this rock?”

Snickering lightly as he nodded good-bye at Elizabeth, they traded a look of shared amusement at Rodney’s expense. He was funny, especially when he wasn’t really trying. “On my way. Meet you there?”

“Yes, yes. I am on my way there now. Chop, chop Colonel. We don’t have all day. McKay out,” and with his usual lack of grace, Rodney dropped out off of the command channel.

Making his way down the stairs to the Gateroom floor, John looked at the people waiting to go home. So many of these people had helped them out over the years, had been a part of the Atlantis family that it would be a wrench when they were gone. Stopping by Caldwell, John held out his hand, “Good luck, Steven. If we ever get back, we will stop by to let you know how things are going.”

Laughing lightly at the thought, Steven took Johns’ hand and shook it firmly, “Yeah, I bet you will. We’ll be fine, John. Good luck and smooth sailing.”

Flashing the man a quick grin, John nodded. “Thanks. Elizabeth will be out in a few minutes to say her piece and send you all home. I am sorry about what happened to your ship.”

“Shit happens, Colonel. You didn’t put us on that heading. And you sure as hell didn’t tell us to drop out of hyper there either. Most of us made it, and we accounted for everyone else. Plus we’re still going to go home. Thank you for that.”

“It’s what we do, Steven. And for what it is worth, thank you again. For everything, you have done. Now I need to get moving before McKay comes up here and fetches me himself!” and with a final handshake, the two men parted.

Moving quickly through the crowd, John made his way over to the nearest transporter. Tapping in his desired location on the map, he waited for the flash of light that told him he had been moved from one location in the City to another. No matter how many times he had been in one of these things, it was still cool. Normal now, but still cool. Dropping into a light jog, John headed towards the Chair room. Rounding the corner he saw Rodney staring at his watch and tapping a toe, practically oozing impatience.

“Relax Rodney; I stopped to say good-bye to Caldwell. We still have plenty of time before Odyssey gets here.”

Huffing out a breath in disgust, Rodney waved his hands in a ‘hurry up’ motion, “We have forty-five minutes before the Odyssey gets us within her sensor range. I would like to be off the planet and in hyper before then, Colonel. Move faster,” and turning away, he moved over to the monitoring equipment behind the chair.

Sitting down in the chair had always felt weird to John, and this time was no different. Atlantis wasn’t really alive, at least not in any true sense. There was no AI, nor was there any evidence that there had ever been one, but there were layer upon layer of programs that were dedicated to looking after the inhabitants of the City. After the last few years the feel of them no longer bothered him, actually, he was at the point where they felt like a normal part of his daily life. But the programs that came into action when the Chair was used were different. Closing his eyes only blocked out the visual cues of the room around him and brought into sharper focus the various command trees and decision points that he had to choose from. Thankfully they were in something that he could read, even if it wasn’t technically English.

“Rodney, the City says that we have green lights across the board, we are ready to initialize the Star Drive and move out. Please let Elizabeth know that now is the time to send our guests home.”

With his hearing was mostly tuned to what was going on in his head, John only faintly heard his order being passed on. Moving through the command trees, he reached the area where the star drive was located. With most of his attention on what was ahead of him, he stopped noticing everything outside but he did notice when the ‘Gate opened. There was a bright flare on the power grid and he grimaced. That was going to eat a noticeable amount of power. Moving his attention to the relevant graph, he saw the power levels drop from 66% to 65.8% and holding steady. Checking the readouts for the engines, he nodded to himself. They had more than enough power to get off-world and into hyper with the shields at full strength.

Feeling the ‘Gate close, John started the pre-flight checks for this. It had been a long time since the City had been flown, and while everything had been checked out by the engineers, this was now the real thing and they couldn’t afford mistakes. Tapping into the City-wide communications grid, John made the final announcement, “Everyone brace yourselves, we are taking off in three, two, one. Lift off.”

The feeling of flight, of freedom, was overwhelming. Flying the Jumpers was more than John had ever thought he would have and yet, flying the City was even more so. She was huge, powerful and more than ready to escape gravity’s grip. Reaching space felt like popping to the surface of a deep pool, and taking a deep breath, John brought up the first set of hyper coordinates. Here went nothing.


When the Odyssey reached Lantea there were only fading traces in space of a hyper window. And on the sea below where Atlantis had rested, there wasn’t even a ripple left to mark her passing.


  1. Yeah !!! ZPMs ! The ancient devices are really sluts for John’ s gene lol !

    It’s excellent !

  2. They do like giving their all for him, yes!


  3. ahhhhhh very good, bookmarked 🙂 keep it up, JusyKassy.

  4. yay! They found ZPM’s and got out of town in the nick of time.

  5. Woo hoo! What an escape. here’s a little hint about the search pattern, but did Caldwell ever get asked about it? Hmmmmm.

    Ancient tech just loves John–2 count’em 2 ZPMs. Also, a very nice escape.


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