The Ancients arrived in a new galaxy, forced away from home by their brothers and sisters. Unable to go back to their old home they built a new one, one that could travel amongst the stars. They built it to last for millennia, and it has stood the test of time. When the Tau'ri awaken the city it provides them with much more than they expected, and an enemy far worse than they hoped.

Alternative Title: The ancients aren't idiots this time! Atlantis was made with longevity in mind, designed from the ground up to outlive its creators. What would happen if the Ancients thought a bit more long term? AU, modified ship/Atlantis design and some tweaks to the history of the ancients. Starts at S1E20: Siege part 2. May/May not contain minor crossover elements such as ship names/designs or weapons.

So, This is new for me. This is going to be my attempt at retelling Atlantis with some minor tweaks here and there to spice things up a little. Some people will die, others will stay alive but most of the main characters will stay as is. Some of the things I've changed involve episodes being left out such as The Defiant One and Before I Sleep as they won't fit well with the changes I've made. Season 2 is still up in the air for what is removed and what is added but feel free to give your suggestions.

And here, we, GO!

Speech - "Wraith!"

Radio/comms - "Zelenka still hasn't fixed this thing"

Atlantis City-wide - "Attention. This is Dr. Weir speaking…"

Telepathy/Wraith mind speak - "What do you call your world?"

Stargate SG-1 and Stargate Atlantis are the property of MGM

Chapter 1: "Oh look! A big red button!"

Earth, Several million years ago

Atlantis

The city was finished, after centuries of scientific and engineering breakthroughs the final home of the Ancients was complete.

The towers rose high above the snowflake base, gleaming in the afternoon sun. Systems were being initialized and the final checks were run. Moments later a hum could be heard, followed by the faint applause of the thousands of people that put their all into the project.

Many hardships were encountered, analyzed and eventually overcome, leaving only a sense of accomplishment for the Ancients. But it was not for the reasons one might suspect.

A great plague was spreading, decimating the inhabitants of the galaxy, started by the ones they once considered family, now there were less than 20,000 of them left. This was the last chance they had at survival and it had to go right.

As they were leaving, they seeded the galaxy with the beginnings of life, using the doorways they invented and a failed experiment to give the galaxy a chance at rebuilding. Planets across the galaxy were terraformed in an instant, destroying the plague and planting the beginnings of life.

The Ancients felt satisfied, leaving the galaxy that they called home for a new one, far away from their old family.

~Break~

In an undisturbed system of eight planets a rift in space was created, ejecting a structure that quickly took up orbit around the second planet.

The occupants of the structure started scanning the system they were in before choosing to settle on the planet beneath them. Within minutes the snowflake patterned superstructure of the city was floating calmly on the surface of the planet's ocean.

They were safe at last.

Years passed and the intergalactic refugees developed into the dominant power of the new galaxy, seeding planets with life much like they did before leaving their previous home.

The results were unpredictable, and a few short decades later a group of scientists were exploring one of those planets only to find a creature they called the Iratus Bug. They set up a research station and a permanent staff to study this insect, believing it to be useful in developing a way to increase their lifespan.

A junior researcher had performed tests on the creatures in captivity but decided that in order to gain more insight on the creatures he needed to see how they lived. He left the outpost in search of a nest so he could observe the creatures in their natural habitat.

On his way there, one of the insects managed to latch itself to his throat. He was paralyzed and unable to return to the outpost, dying shortly after. The Iratus Bug detached itself from the body and returned to the nest, laying its eggs that would eventually create the worst threat that the Ancients had ever seen.

The researcher was eventually found dead by his companions, but by then it was too late. The products of those eggs were ruthless, driven only by the need to feed on living beings. The other personnel were quickly overcome by the creatures and devoured.

The city was quick to order the outpost and its doorway destroyed but by then the creatures had escaped the planet.

Other worlds started to fall prey to the creatures, leaving very few alive. The ones that did survive would tell of phantoms in the trees and shrieking wraiths that could pull the life out of someone with their hand.

The Ancients could not let this stand and sent out ships to destroy these wraiths before more worlds fell.

They failed.

~Break~

Years had passed and still more reports of the creatures came. The Ancients created great warships to destroy the infestation yet they still could not eliminate them. Eventually the enemy created ships of their own to do battle.

Grown instead of built, they were a formidable foe and could overwhelm the Ancient ships with ease. The Ancients responded with more advanced vessels, yet they would still be matched by the enemy's sheer numbers and tenacity.

World after world fell, eventually leaving only a few systems left untainted by the scourge. The Ancients, feeling like they had no choice, started developing more and more sophisticated and dangerous technology.

They created a drone weapon that could destroy ships far easier than before. Fitted to their ships they could cut swathes through the enemy ranks with little effort.

They developed shields that could withstand anything their enemy would attack with. Integrating them into their ships gave the crew a better chance at survival.

And then they developed the Potentia, the pinnacle of energy storage. A device that could hold an incredible amount of vacuum energy extracted from a region of sub-space-time. So powerful that they were eventually used as the main power source for the great city itself.

However a fault was found in the design during the first siege on the city. Even the nigh-invulnerable shields of the city could only last so long when powered by a finite power source. The Potentias were on the brink of depletion when reinforcements arrived from elsewhere in the galaxy. The Ancients realized that the Potentia represented a great leap forward but it was far from perfect.

And so they began their search for a superior power source. Many ideas were debated, designed, built and tested, everything from dyson spheres to the Arcturus project yet everything would fail to meet expectations.

Eventually the answer was found. A research mission on the far side of the galaxy had developed a way to extract energy from alternative universes. The Ancients had been experimenting with the technology for a very long time yet could never find a way to focus the collection in a specific universe. However, this team had not only managed to target an uninhabited universe, but they managed to pull from multiple targets at the same time, making it potentially more powerful than anything in this universe.

The High Council debated for months on the potential for instability and even dangers to causality, yet the tests showed no issues and continued to perform well over the expectations, and eventually it was agreed upon to install The Collector on Atlantis.

The Collector was different from other power sources in that it required an absurd amount of energy to initialize, leaving the Potentias as the only way to initialize it. The team tasked with integrating it into the city had set up a pedestal for three Potentias to be used as a backup power source in the event that the collector had to be taken offline.

However, even with these advantages the war was still drawing closer to an end. Over the course of half a year the Ancients went from controlling hundreds of systems and hundreds of Aurora class destroyers to being hard pressed to defend their last bastion of freedom; Atlantis.

The enemy had thousands of ships and they were swarming the planet, forcing the Ancients to sink the city to the bottom of the ocean in order to protect it from the bombardment.

A few more months passed before the High Council decided that the only course of action was to evacuate to their old home through the doorway.

Only two thousand Ancients remained, making the evacuation a simple procession. A rebellious young man named Janus stayed behind for a few minutes longer, setting a few safeguards in order to ensure the safety of the city in the event that they could not return. As the city was put to sleep the final command sent was to power down The Collector, leaving the city to run on the Potentia Buffers.

When the Ancients returned to Earth they encountered the early stages of Human evolution. Unable to return to Atlantis, they intermingled with the Human population and lived out the rest of their lives in seclusion, occasionally helping to shape the future of their descendants.

And the Great City Atlantis slept at the bottom of the ocean, waiting for the day it would awaken.

~Break~

Ten Thousand years had passed.

The people of what would be called the Pegasus Galaxy had been ravaged by the enemy of the Ancients, eventually known as the Wraith. Over the years the Wraith had lessened in numbers, due to the amount of humans in the galaxy being greatly diminished. Many people have gone decades without seeing a culling, giving many civilizations the chance to grow and spread out among the stars.

In the home galaxy of the Ancients, the descendants of the Ancients had been waging war with a parasitic species known as the Goa'uld. The war was a long one, spanning eight years and over a thousand planets, resulting in hundreds of thousands of casualties on all sides.

Eventually the war ended when the Goa'uld Anubis had attacked Earth. The armada assembled would have overtaken the planet in minutes if it weren't for the intervention of the team SG-1 from the American Stargate Program.

The team leader Colonel Jack O'Neill had the Ancient repository of knowledge downloaded into his brain for the second time. Using the knowledge and with some assistance from his team they managed to recover a Potentia which they used to replace the depleted one in a defense outpost under the ice of Antarctica. However due to the overwhelming amount of information downloaded into his head, O'Neill was on the verge of death. He was placed into stasis in an effort to preserve his life and was later saved by a race of Aliens known as the Asgard.

Once the outpost was further examined they discovered an entry talking about Atlantis, prompting a visit from the now Brigadier General O'Neill. Once he made it to the outpost after a mild incident involving an Ancient drone weapon he authorized the use of the Potentia, also described as a Zero Point Module to dial Atlantis.

Dr. Elizabeth Weir, leader of the expedition, had asked General O'Neill if she could also bring along Major John Sheppard due to his exceptional piloting skills and his near instinctual ability to use Ancient Technology.

As they made their way through the Stargate and started to explore Atlantis they started to power up the systems they had access to in its dormant state. Soon however the power levels dropped too low and the city started to enact its failsafe measure put into place by the Ancient inventor Janus in his final moments in the city.

All of that was unknown to the expedition team and when they saw the diagnostics of the city they quickly attempted to conserve power, however the rising protocol had already been enacted.

A team was sent off world in order to find a fallback location in case they couldn't save the city. On the planet they chose they encountered the Athosian people who informed them about the Wraith. Unfortunately the Wraith attacked in response to an accidental activation of a transmitter.

Both Athosian and Tau'ri were taken and the survivors returned to Atlantis in time to witness the rising of the majestic city. As the power finally hit critical levels the rising program fired the star drive for the briefest of moments, simultaneously disengaging the clamps that held the city to the ocean floor.

As the city rose the new residents all prepared for the worst, believing the city to be lost. However their fears were soon alleviated, as the city came to rest calmly on the surface.

After getting set up, Major Sheppard went on a rescue mission for the people taken by the wraith. Using the Ancient Gate Ship, affectionately nicknamed the Puddle Jumper by Sheppard, the team quickly managed to get to where their people were held. After an encounter with a Wraith queen, Colonel Sumner was killed by Sheppard as an act of mercy after being fed upon by the queen.

Sheppard was then captured and brought before the queen, and was almost fed upon were it not for the timely intervention by Lieutenant Ford.

Managing to land a few good shots, the Queen was killed but in the process the rest of the Wraith had begun to exit stasis and prepare for a culling. Managing a narrow escape, the rescue team and the captured people managed to make their way back to Atlantis.

Over the next year the Atlantis expedition would encounter the wraith at every turn, and their numbers started to grow. Though not every challenge presented was caused by the Wraith.

Their encounters with the Militant Genii had left a deep rift between the two peoples, and had almost ended in disaster. Both times the situation was handled well by the team, if only just.

As time progressed things in the Pegasus galaxy got worse, more Wraith were awakening and even more ships were being grown in preparation to attack Atlantis once more. The Expedition learned of the attack due to the Long Range Sensors coming online in response to the earlier plan to power the city's shield using lightning from a storm. 16 Hive ships and 20 Cruisers were on their way to Atlantis, seeking to use the Stargate there to make their way to earth.

As the ships grew ever nearer the Atlantis personnel were in a mad search for Z.P.M's to power the city but they could not find any. Using their naquadah generators they managed to send a message back to Earth in order to apprise them of the situation.

On the final approach to the city, the wraith ships encountered a dormant Ancient defense satellite that they believed to be inactive but had been reactivated when Atlantis's systems came back online. The satellite managed to take out a single Hive and two Cruisers but was swiftly destroyed by the rest of the ships.

In the final days of the Wraith's approach Dr. Weir ordered the city's self-destruct be armed and the full evacuation of the base. Before the city was destroyed however, the Stargate was activated, sending support from Earth as well as a Z.P.M being transported to them on the Daedalus within two days.

With the support from Earth and the armaments and soldiers led by Colonel Everett the Atlantis team starts to set up the defenses, leaving Dr. McKay to work on powering the Drone weapons platform with the new naquadah generator. As the different plans are set up some tension arises due to Colonel Everett's distaste for both Major Sheppard and Dr. Weir.

When the Wraith arrive in the system, the first wave of Darts is released and immediately the city devolves into chaos. Multiple defense stations were attacked ruthlessly by the Wraith that were beamed down into the city, leaving holes in the defense that were quickly exploited by the other Darts.

Eventually the first wave was defeated, but more Wraith were still in the city and had attempted to damage the generator stations. One of the cruisers descended into the atmosphere and tried to dock with Atlantis but McKay managed to activate the Chair platform in time for Sheppard to use the last remaining drones to destroy the cruiser.

Minutes later the Hive ships start getting into position to bombard the city but luckily the Daedalus managed to arrive just in time and delivered the Z.P.M to Dr. McKay.

And this is where the story begins.

Lantea

Atlantis

23:00

"Rodney! We need those shields now or we're all toast!" John Sheppard yelled over the comms. The Wraith ships were almost in position to begin their bombardment and the Canadian scientist had yet to finish plugging in the Z.P.M.

"Just a second!" Came the snappish reply from the man "This is a very delicate piece of technology and if I rush this we could all explode!"

"Rodney!" Elizabeth shouted at him.

"Fine! Plugging it in now!" The man yelled back.

As the scientist placed the Z.P.M in the pedestal it began to glow, signifying a proper connection had been made.

"Alright, the Z.P.M is in place! Raise the shields!"

In the control room, Dr. Zelenka input the code to raise the shield, only to be met with an error.

"Rodney, it's not working!" He said, trying to find what was interfering with the system.

"What? It should be working! The Z.P.M is in and glowing!" Came the frantic reply as he moved from console to console in the room trying to see what went wrong.

"Nothing up here is powering up!" The Czech responded. "Are you sure you did it right?"

"Of course I did it right! Give me a minute!"

As the Wraith ships finished getting into position the city gave an alarm, indicating that they were about to fire. McKay, hearing the alarm, went back over to the pedestal and tried to find a switch before he gave a small push to the top of the Z.P.M and it began to sink into the receptacle.

"Okay, try it… now!" He gave the command as it sat flush with the surface of the pedestal.

Zelenka retried the Shield subroutine and gave a sigh of relief as the program ran successfully.

The rest of the control room staff quickly went to the balcony, watching as the pale filament of the shield rose in a dome around the great city just in time to intercept the bombardment from the wraith. The city shook under the stress of the weapons fire but the shield held firm.

Back in the control room Zelenka was busy making sure the city's systems wouldn't drain the Z.P.M too fast when he noticed a strange prompt come up on a terminal.

He quickly went for his radio. "Rodney, Elizabeth? Can you please come to the control room? There's something you need to see."

A few minutes later everyone was all watching the two geniuses bicker and type away on their computers.

"What else could it be, Radek? Some sort of water collector?" Rodney snarked.

"I'm simply saying that we still don't know what it could be, there's no indications in the database." The smaller man replied.

Weir interjected, "Hold on, what are you two talking about?"

Both scientists stopped their argument and turned to her and Rodney opened his mouth to speak.

"Shortly after the Z.P.M was installed a new subroutine was activated and displayed an activation request for something called a 'Collector'. There's nothing in the database on it and all we have is the prompt to activate it. I think we should turn whatever it is on, but Sparky over here thinks it could be dangerous."

"I'm just saying that it could be anything from an air collector for life support to the Ancients version of a self-destruct. We should be careful with this."

"There's no way of knowing for sure until we turn it on! Look, as far as I can tell whatever it is will most likely be harmless. Besides, with a name like 'The Collector' it sounds perfectly safe to me."

"But we cannot be sure Rodney."

"Gentlemen, focus." Elizabeth interrupted again, "Rodney, turn it on. Radek, monitor systems and let me know the moment anything happens, We still have the Wraith to worry about."

"Thank you." "Fine." They replied, both beginning their tasks.

"Get me city-wide." she nodded towards Grodin.

"Attention all personnel, This is Doctor Weir speaking."

"As I'm sure you already know, the city's shield has been raised and we are safe from the Wraith for now. However, we are about to activate a new system and we don't know what it may do."

"I ask that you all stand by and prepare to assist should anything go wrong."

"Rodney, go ahead." She motioned.

"Activation in, 3… 2… 1…"

"Now!"

As the command was given, lights across the city went out before quickly coming back online. Terminals went dark before coming alive with new sequences of Ancient text streaming across them. The shield briefly glowed brighter before settling back to its previous intensity. People all over the city were starting to report new programs initializing and new entries in the database.

The control room was a storm of activity, technicians and scientists were running back and forth between terminals, checking new systems and making sure that nothing went wrong. McKay and Zelenka were both absorbed in their stations, frantically going through dozens of windows and reports.

They were snapped out of their trance at the call from Sheppard, "Rodney, what the hell just happened? I'm getting calls from everywhere in the city about weird things happening."

"I don't know, once we turned on whatever that 'Collector' is, the entire city's operating system rebooted. Now there's so many new programs and systems starting up that weren't there before." The pudgy man replied, intent on analyzing every character that crossed his screen.

"Well? Is there something wrong?" Elizabeth questioned.

"I don't know yet, give me five minutes." He responded absently, typing away at his computer.

Atlantis, Lantea

23:40

Briefing Room

"Well, we've gone over the city's logs and so far it looks like whatever happened was supposed to happen." Rodney started, walking over to the display showing a schematic of the city.

"Yes, it seems to be reacting to the activation of this 'Collector', but we still haven't been able to tell what or where it is." Zelenka chimed in, earning him a dirty look from McKay.

"Whatever its purpose is, we've found something a little more interesting than that." The Canadian scientist huffed, bringing the room's attention back to him.

"What kind of interesting Rodney? Are we talking a big gun to get rid of those Hive ships currently bombarding us? Because that would be much appreciated given our current power situation." John snarked at him.

"Well no, but I don't think we'll have to worry about it." Rodney retorted, already showing another screen on the display.

"As you can see here, the Z.P.M is currently at 86%, which at the current drain on the shields means we should have a little over three weeks before it fails and we all die." He started, causing everyone in the room to glance about worriedly.

"Rodney, we know this already, can you please skip to the part where you explain your plan to get us out of this mess?" Elizabeth lightly chastised, already exasperated at the man's childish showboating.

"Ah, well you see, when we first plugged in the Z.P.M it was only at 79%." He declared, smirking as the people watching him leaned forwards, questions barely held back.

"Seriously? How did that happen, I thought we couldn't recharge them?" John asked, eyes wide with curiosity.

"So far we cannot tell for certain but it appears that whatever this 'Collector' is, it's responsible for this." Zalenka interrupted, "We believe it's something like a generator but we haven't been able to find any data or schematics for it."

Rodney cut in "We think that whatever this is, it's in a room near the bottom of the tower but there's no way in or out of it. All the schematics are showing nothing but a large empty space with some walkways." He began. "But with the Daedalus in orbit we can use their asgard beaming tech to get us in there so we can finally figure it out."

"Well then, you better get to it, those Hive ships aren't going to leave on their own." Elizabeth said, dismissing them.

As they all started to pack up and begin their tasks, Sheppard stumbled a bit and grabbed his head, momentarily looking dazed and a little confused before shaking it off.

~Break~

Collaborating with the rather prickly Asgard named Hermiod wasn't on McKay's list of favorite pastimes, but between the two of them with some assistance from Zelenka, they managed to get a lock on one of the walkways in the void. Tapping his earpiece, he reported in to the rest of his team.

"This is McKay, we are ready to go, we have a transporter lock." He said, grabbing his p90 and the rest of his gear.

"Ford is still unaccounted for so it'll just be the three of us, beam us down." Sheppard responded over the radio.

Rolling his eyes at the Major's rather brusque attitude and briefly wondering if the young lieutenant was okay, McKay nodded to Hermiod before his vision was obscured by light. It cleared up in seconds and he marveled at the room he found himself in.

In the center of the room lay a transparent half-dome approximately 60 meters across. Inside, there appeared to be a small point of light, almost too bright to look at. Arcing off of it, blue and gold strands of lightning hit rods placed on the inside of the dome connected by a hexagonal latticework of conduits, funneling whatever energy it was to seven large, light blue conduits coming off of the device, presumably one for each pier and a seventh going up to the control tower. Around the room's walls laid small, glowing orange hexagons arranged in rows, each pulsating in time with the arcs and conduits. The atmosphere around them seemed to crackle with raw energy, making their hair begin to stand up.

In front of them laid a single console with a display lit up showing many different graphs and charts. McKay immediately moved towards it, setting his firearm down and tapping some of the crystal controls. The display flashed through several new screens before settling on a wall of ancient text.

As Rodney began to comb through what was in the console, Sheppard and Teyla began to circle the room, glancing at the hexagons and keeping an eye out for anything potentially dangerous. Stopping at one hexagon, John leaned in for a closer look, noting that it looked remarkably like the top of a Z.P.M. Turning around to get the team's scientists attention, he faltered, falling into a crouch. A sharp pain lanced through his head, quickly spreading to the rest of his body. He heard a faint voice, unable to hear what it said, or even where it came from.

Then, as quickly as it hit, he was back to normal.

Jerking as a hand came to rest on his shoulder, he quickly turned his head to see Teyla giving him a concerned look. "Are you alright?" She asked, helping him up from his crouched position.

He shook his head, trying to clear the fogginess from the experience. "I'm fine, just a small headache." He placated, still trying to figure out what had happened. "It was probably just a small zap from the wall."

She looked unconvinced but didn't push the matter, helping him straighten out his vest. A call from the third member of the team had them walking back to the console to see what he had found.

"It's a generator!" The Canadian exclaimed, "It's what we activated, it appears to extract energy from sub-space-time, similar to a Z.P.M, only way more powerful." He chattered, still scrolling through blocks of Ancient script. "As far as I can tell, it produces hundreds of times more energy than one Z.P.M can hold, powering the city through the Z.P.M pedestal, using it as a sort of buffer for the more delicate systems. With this, we could power the city at full blast and recharge all the depleted modules and still have power to spare!"

Blinking in shock, John and Teyla gave each other a hopeful look before turning back to the scientist. "Does this mean we can go back to Earth?" The Major asked, not wanting to get his hopes up, yet unable to hold back the question.

"That's the easy part, we could dial Earth continuously for as long as we wanted, while powering the shield and literally everything else at the same time!" Rodney explained quickly before reaching up to his earpiece.

"Dr. Weir, we just found out what the collector is and you're gonna have to take a seat for this one." He said, before quickly asking Hermiod to beam them to the control room.

~Break~

The Gateroom team was given very little warning before they were inundated with orders from the head scientist.

"Zelenka, grab the empty Z.P.M's and head down to the pedestal room, once you get there, plug them in and radio me." Yelled McKay as he ran to his workstation.

"Grodin, Dial Earth, I want to have a connection with the SGC as soon as we get the gate open." He commanded, running over to a console near the back of the room dedicated to power management. Grodin nodded, turning back to the DHD and dialing the eight symbols.

As the chevrons engaged, Dr. Weir walked out of her office, having heard their arrival and the subsequent bombardment of orders from McKay.

"What's going on Rodney?" She questioned.

The scientist didn't look up from his laptop, frantically typing away as he explained.

"The collector is Atlantis's main power source, we just couldn't activate it until we had a Z.P.M installed. It pulls energy from sub-space-time much like a Z.P.M does, only instead of it being a contained reality, it pulls it from an alternate space-time. Because of this, we have access to more energy than a hundred Z. and we can recharge any depleted ones using the pedestal down below." He paused as the wormhole opened and the familiar kawoosh dissipated. "This is Atlantis to Stargate Command, are you reading us?"

The surprised voice of Samantha Carter came out over the speakers, "Yes Rodney, we can hear you. We weren't expecting you to dial us for a few more days, is something wrong?"

"Nothing is wrong, I'm just forwarding you some data. Turns out, Atlantis has more than a few secrets we have yet to find."

Back on earth, Sam watched as the compressed files were unpacked and opened on her monitor. Her face slowly morphed from confused to worried to incredulous. "Are you sure this is right, Rodney?"

The annoyed response came fast. "Of course I'm sure, I was in the chamber and I saw it working with my own eyes. The data I pulled off the terminal proves that the Ancients were much more advanced than we expected, and thanks to that, we now have more power than ever. Once we get a couple of Z.P.M's charged, we'll send some back to you guys so we can set up proper travel."

Sam blinked, before looking over the report that detailed the mechanism that allowed the Z.P.M's to be recharged, noting that while they could recharge them, they still had no way of creating the crystal devices. "We'll send you all the dead ones we have once you send one back, anything else you'd like us to have ready?"

The voice of Dr. Weir replaced the Canadians', "Yes, we could use some more medical supplies as well as more security and medical staff. Oh and tell General O'Neill that we have a proposition for him, I think we just might be able to help Doctor Jackson make a trip."

Smirking slightly at the other woman's words, Sam shut down the gate with a parting "Will do".

~Break~

As the Expedition prepared to send the wounded and a Z.P.M back to earth, Rodney and Zelenka were busy trying to catalog all the new systems that were revealed. They had already come across many research programs and their respective sensors, including a log of the Ancients' evolution. However their focus was currently on a new system that they discovered.

It turns out that Atlantis was full of hidden features that didn't appear unless there was power enough to run them. One of those systems just so happened to be a nanite repair system. The nanites would be released in any damaged section of the city and they would quickly work to break down any damaged components and replace them with functional duplicates. They were incredibly advanced, but had a limited lifespan due to them using pure energy-to-matter beams to create the required parts. The power was provided by the Collector and the nanites were created in special chambers across the city.

Another drawback was that they were very hard to program, and the system was immensely complicated, making it tough for the two scientists to get the nanites to start repairing the city. They had some success with repairing the hull of the city and some of the damaged towers but they have yet to figure out how to direct them to fix any of the more complex systems like shields or the Star Drive.

In the meantime, they decided to use another of the new systems to start manufacturing drones, though it was not going well, as the system didn't have enough materials to make more than a few dozen. Until they could get more of the raw materials, the manufacturing facilities were unable to produce anything, causing the nanite repair system and the Drone production to halt.

They had found a schematic for an asteroid mining drone that they might be able to produce, but with the Wraith in orbit, that wouldn't be a good idea. Until they took care of the 33 ships in orbit, they wouldn't be able to do much.

"Hey guys, find anything useful yet?" Came the rather enthusiastic question from Major Sheppard.

"Why are you so cheerful? Do you have any idea how much of a problem we have? Those Ships won't leave, and we have less than a week before the shield fails and we all die." Rodney snapped irritably.

"Wait just a second, I thought you said The Collector produced more than enough energy to power the shield?"

"Yes, we have the power, but sooner or later the emitters will fail. When that happens, we won't be able to protect ourselves from the fleet of Wraith Hive ships bombarding us from orbit." The Canadian snapped, looking very haggard and sleep deprived.

"Well what do we do then? I thought you had an idea already?" Sheppard snarked, walking over and peering over the Scientist's shoulder.

"I'm working on it, don't you have somewhere else to be? Maybe somewhere other than here?" The Canadian turned towards the inquisitive Major, huffing in annoyance at his innocent expression.

"Fine, let me know when you come up with something. In the meantime, I think it's lunchtime." Turning away and whistling lightly, the major left the lab, leaving McKay and Zelenka to keep looking for a solution to their problem.

~Later~

"I got it"

A half asleep Czech was startled out of his dreams by the triumphant shout from the man next to him. "Rodney? What's going on?" He asked as his companion started to collect his computer and other items before walking out of the lab.

The Canadian shouted over his shoulder, "I figured it out! We aren't going to die!" Before turning the corner and leaving a bewildered Dr. Zelenka alone.

~Control Room~

In the Control room sat a motley crew of people watching the recently arrived Scientist hurriedly run from station to station, before beginning to dial the Stargate. Sharing a look with Major Sheppard, Dr. Weir stepped forwards and posed the question on everyone's minds.

"Rodney, you mind explaining your 'master plan' with the rest of us?" She asked, watching as he finished typing on his laptop.

"I figured it out! We aren't going to die!" Rodney exclaimed, before running to the jumper bay.

John and Elizabeth both looked to the recently arrived Radek for an explanation to which the Czech shrugged. "He said the exact same thing to me and then ran all the way here."

Following the (probably) mad scientist into the jumper bay, they found him in one of the jumpers, poking around at the control crystals, muttering under his breath and rapidly tapping away at his tablet. Swapping crystals with such frequency that even Zelenka couldn't tell what his goal was.

"Rodney? What are you doing?" Dr. Weir tentatively asked, unsure if the scientist was aware of them.

"We disappear! That way they'll think we left or they destroyed us! Now I just need to get this interface done so I don't overload the jumper." He chattered, clipping some cables to the crystal tray and leaving the jumper.

Getting fed up by the vague and absent-minded responses, Sheppard stepped in front of the chief scientist. "McKay! What are you talking about? How and why are we supposed to disappear?"

"We cloak the city! With the proper interface, I can get the city to use the jumper's cloaking device to replace the shield, then we just need to get them to stop firing…" He trailed off, as if realizing something important. The others were surprised, and turned to Zelenka with questioning looks.

"It's possible, but we'd be sacrificing the shield and with the amount of weapons fire coming from the wraith in orbit, the city would be destroyed if the shield was off for even a second." He elaborated.

"We get Teyla to connect with them and say we'll blow up the city! That way they'll stop firing!" Rodney exclaimed, turning to the aforementioned woman that had just arrived.

Seeing everyone's eyes on her, Teyla considered if she would be able to make it work, judging from the previous attempts to connect with them. "I would like to try, if it can convince the wraith to leave, then I will take the risk."

"Teyla, no one is forcing you to do this." Dr. Weir said, giving a warning look to Rodney, who looked like he wanted to interrupt.

"It is my choice, I will do it to save all of Atlantis."

Glancing around the room, the expedition leader sighed, before giving the order. "Okay, all of you get to work."

~Break~

The shields went through many hundreds of small changes within the few hours it took for the modification. Everything was ready to be activated, all that remained was Teyla and the Daedalus. Once they received confirmation that the Daedalus was in place, Teyla, with the assistance of Dr. Beckett, began to enter the Wraith mind-meld.

Watching the images play in her mind's eye, Teyla began to send the message, feeling the shock and panic of the Wraith, she smirked and disconnected from the link. Nodding to the doctor, she caught her breath. "The message is away."

In the control room, Dr. McKay began pressing a series of controls on the terminals, getting the shields ready for the final transition to cloak. "Commander Caldwell, ready when you are."

All of the human-made computers were quickly shut off, with technicians unplugging them and stowing them in bags, ready for the EMP from the nuke.

The commander of the Daedalus gave the order and within seconds, the bomb was over the city, detonating almost immediately.

A massive mushroom-cloud rose up off the city shields, distorting the air itself from the intense heat. Every ship in orbit had their sensors blinded by the intense energy of the bomb. Within minutes, the radiation subsided enough for the shields of the mighty city to be replaced with the cloak.

Absolute silence took over the Gate room, nobody wanted to make a sound for fear of breaking their cover. Eventually, Rodney began to type away at his laptop, swapping between every sensor reading they could get on the Wraith ships in orbit.

"Is it working?" Elizabeth whispered, watching the man's face closely.

"I think so, they're scanning us now." He whispered back, continually typing on his laptop.

"Why are you two whispering?" Sheppard whispered, pointedly ignoring the irony.

Embarrassed at being called out on an irrational tick, Rodney stammered out a quick excuse before checking on the sensors one more time. "They're leaving! It worked!"

Everyone in the Gate room broke into cheering, delighted that the enemy had been tricked by their ploy.

~Break~

After a few days, the Z.P.M.'s were fully charged, and one was sent back to the SGC, allowing them to finally send the supplies that the Expedition so desperately needed. Along with them came a surprising visitor, Brigadier General Jack O'Neill had arrived alongside his former teammates Lieutenant Colonel Samantha Carter and Dr. Daniel Jackson.

Greeted by Dr. Weir at the gate, she quickly took them to her office to discuss the next steps for the expedition.

"Well doctor, it's a nice place you got here, even if it's a bit of a fixer-upper." O'Neill commented, taking a seat on the edge of the office, his teammates finding seats beside him.

"It is incredible, there seems to be no limit to the wonders here, and we've only scratched the surface of the city."

Samantha Carter leaned forward, setting up her laptop. "Well, I hope that we'll be able to help with that, the IOA has finally allowed Daniel and I to do some research here."

Smiling at the eager tone, Dr. Weir glanced between the two intellectuals, noting how they both seemed to be barely restraining themselves from running about. "I can arrange for a tour and some assistants if you'd like, we have no shortage of work here and your efforts will go far in reducing it."

A chime sounded, drawing the attention of the room's occupants to the door, where a sheepish-looking duo of Sheppard and McKay stood.

Beckoning them in, the expedition leader smirked again, "In fact, here's the two people I had in mind. Major Sheppard, Rodney, I'm fairly certain you've been acquainted with these three?"

"Yep" "I have" Were the predictably laid-back responses, garnering a chuckle from the General.

"Sheppard! How are things so far, I hear you've all been up to some crazy stuff in the past year."

With a small wince, the Major stepped forward. "They could be worse, luckily the Z.P.M. you sent us was enough to save our asses from the Wraith."

"So I hear, and apparently it was also what you needed in order to use some cool tricks the city has?"

Nudging the scientist behind him forwards, Sheppard looked a little confused and guilty. "Rodney here could explain it better than I could, I wasn't paying much attention to the briefing."

Giving his friend a small glare, the Canadian cleared his throat. "The Z.P.M. was what we needed to finally kickstart Atlantis' real power source. It has a similar premise as the Z.P.M.'s however, it draws its power not from a pocket of sub-space-time, but another dimension entirely. By doing this, it allows the Collector to output an incredible amount of energy with practically zero maintenance." Pausing to take a breath, he noticed the almost cross-eyed look he was getting from the general and the looks of interest from Sam and Daniel. "This means that we have more than enough energy to spare for the many systems we have, and even better, we can recharge the depleted Z.P.M.s we have on hand."

Noticing O'Neill slowly following the conversation less and less, Dr. Weir stepped in. "Why don't you and Colonel Carter go and discuss this in your lab. I think the General might want a tour of the facility, and I have the perfect man for the job." She smiled conspiratorially at the Major.

~Break~

The tour through the city was certainly impressive, and Jack O'Neill was seriously considering finding a way to stay here permanently. It was made even more impressive given it only covered the small fraction of the city that was currently explored, leaving out over 95% of the structure untouched by the expedition.

His tour guide was also impressive. Major Sheppard was certainly knowledgeable about the city he now called home, making the general feel even better about his decision to allow him to be a part of the expedition.

A call broke him out of his musing. "And that concludes the tour, anywhere else you'd like to see?" His guide stood there, looking the part of a perfect soldier if it weren't for the amusement in his eyes.

"Nope, this city is awesome, but as much as I'd love to stay and chat, bureaucracy back home takes precedence." Giving a mental groan at that thought, he started to follow Sheppard back to the Gate room, far from happy to have to cut his trip short.

As they continued back, he felt an odd buzzing feeling run through him, too minor to be anything serious, he ignored it at first. Eventually though, it was impossible to ignore, and just as he was about to ask the Major about it, both of them collapsed. Quickly losing consciousness, the last thought in his mind was: "Why does this always happen?"

And that ends Chapter 1, What do you think?

Things are progressing well so far, and the next few months will be pretty rapid-fire in the timeline. Much of the initial setup will be glossed over in the next chapter and the proper story will probably begin in the later half of chapter 2 or the beginning of chapter 3, so keep your pants on.

Like some of my other upcoming stories, this one is also free for anyone to use to start their own. So long as credit is given, feel free to use any of my stories as a base or just to continue them.

In the meantime, this is Goat, getting ready to eat your hats.

Cheers