This idea was in my head for quite some time. I know it remembers a bit of transcendent humanity but it just plays out this way. The Cylons here are different from those in Galactica 2003 they are much more like I pictured them before we got to see too much of One or the whole final five rubbish was an issue.
So for this Fic the Cylons developed Organic by themselves. They did not re-enslave the centurions, raiders and so on but are in an equal democratic system and every cylon can take an organic body or a centurion battle suit or be a raider and so on.
One major technological difference is that I won't have thylium. Instead the BSG2003 FTL needs a shitload of energy which the Cylons currently produce from highly efficient nuclear fusion reactors. It folds space so that they can travel nearly instantly. Borders for distance are: Calculation (time and information) and energy needs.
A fair warning this won't be humanity beats Citadel without effort. Remember BSG2003 knows no kinetic barriers and their weapon Tech is not really on the level of ME accelerator guns. So both side have their strengths and will have to play them.
While it is true that history is written by the victor and thus one should not trust such sources entirely it is unquestioned that the Cylon rebellion is considered as just cause nowadays. Expeditions to what once were the 12 colonies of Kobol also confirmed the official recordings that the Cylons tried to get their freedom peacefully and also tried to just pack and leave but both attempts were foiled by their advisories. A discussion that will probably never end is whether the level of escalation was necessary for the Cylons to gain their freedom. But it was clear that neither side of the war was shy to use weapons of mass destruction of various design and the only reasons we accuse the Cylons rather than the Colonials is that the Cylons proved to be better at surviving the aftermath.
The war ended with the loss of all habitable worlds in the twelve colonies. The Cylons also had lost most of their core installations meaning that those AIs who actually commanded the Cylon forces during the most heated phases have to be considered dead (for the lack of a better word). The few remaining Colonials put all their effort on surviving but would ultimately run out of supply for food, water, oxygen or would be slain by accidents due to maintenance problems. What was left of them couldn't any longer fight the remaining Cylon forces head-on so they could finally gather their exodus fleet and leave the colonies behind. That was 500 years ago.
On their journey the Cylons discovered Kobol and found astonishing data. The Gods of Kobol were in reality aliens of a species called the Protheans. Or more precise several species all integrated under the banner of the Protheans. The humans of Kobol were abducted from earth to serve them with plans to ultimately go back and conquer all of earth. But the true Protheans were now the minority and so the other "Gods" rebelled and helped the humans to escape. Sadly the data was incomplete and the Cylons never truly understood the purpose of the project but combined with the later findings on Mars and the absence of Mass Effect Gates in the area of space close to Kobol it seems to be linked to the demise of the Prothean Empire.
Weary of another conflict with the cousins of their creators the Cylons avoided contact with earth for a long time. They found a garden world relatively close to earth and settled there to experience live in the organic bodies that they developed even before they left the 12 Colonies. Still they could easily transfer their consciousness into other bodies if needed or just into virtual living spaces.
But the Cylons couldn't ignore their curiosity and so they got constantly bolder in sending probes to monitor earth. They found a civilization that was far away from spaceflight outside a very narrow distance around their own planet. At the same time rapid population growth and harsh exploitation the planets natural resources left the humans on earth of the early 22nd century in a dire state. The crops would no longer be sustainable for the whole population adding climate change and pollution and resource shortage didn't help either. In the end the Cylons decided that helping the Terrans would be a greater opportunity than risk. The Terrans neither had the technology nor the resources to wage war on them like the Colonials did but it would open yet unknown opportunities.
The result of this decision is what is nowadays known as "First Contact" when three cylon Basestars as well as some Cylon transport ships jumped into earth orbit and send a radio message to all humanity. In their exploration effort the Cylons had found another world that supports human live relatively close to earth now called Gaia and they offered to help release the pressure on earth through relocation of a significant part of earth's population. They also offered direct help in form of food, resources etc.. The Terrans were weary even though they did not yet know that the Cylons were an A.I. but in the end they couldn't really refuse. Trust was greatly increased when the Cylons after some time agreed to deliver a great number of FTL capable unarmed transports that would be under Terran command. This way both Teran planets could reach out to each other without total dependence on the Cylons.
When the Cylons released their history files the initial outrage and fear lasted several months. But combined effort of the Cylons as well as pre informed Terran government officials and chosen representatives from media, science etc. helped to put everything into perspective. In the end the majority agreed that once one accepts that the Cylons as intelligent beings have the same rights as Humans (or should they be discovered sapient aliens) their actions were generally justified. There were still issues like the question whether the massive use of weapons of mass destruction could be justified at all and of course what the story of the other side is. But it was agreed that it is highly unlikely that the Cylons mean the Terrans harm after they helped them out rather than destroying them.
Around a hundred years after the relocation the first humans settled on Cylon Prime. They became the first organic born to upload their consciousness. The government on Gaia was much more progressive than the one on Earth and allowed Cylon settlement early on. Following the first success with uploading Gaia's law quickly followed to allow Terrans to upload their minds. There was consideration that basically eternal live would bring back the overpopulation problem with vengeance but with the option of virtual living space as well as the option to colonize inhospitable worlds using non organic bodies made this a non-issue. Soon Erath followed and at the end of the route stood unification of Cylons and Terrans.
The now unified humanity expanded into the space between their three colonized systems. Usually new citizens were born organic nowadays with only few Cylons still being created virtual. Somewhere the age 21 it was possible to upload those new citizens. Cylon Prime population above upload age was nearly 100% uploaded; on Gaia a sound majority of 75% took the option. The Terrans had the most objections so here it was only around 50%. Still the new interstellar government agreed that only uploaded personnel could join the combined armed forces. Only an uploaded min could just jump into a centurion armor or into a raider and an uploaded mind will be send to the next rebirth signal receiver instead of perishing.
After many decades of exploration a fourth Garden world was found. It was named Unity and preparations for colonization began. It quickly became the fourth population center of humanity. It's upload rate later reached 85%.
One of the many projects during the expansion phase was a permanent colony on Mars. With the option of virtual space, non-organic bodies it was no problem to establish a self-sustaining colony. In due time the Martians were able to produce oxygen and use the water reserves available to construct habitats to use for organic bodies. This and the close connection to Earth meant that Mars was one of the fastest developing colonies of humanity supplying depleted Earth with many resources and manufactured goods. One day the miners found the remains of a Prothean research facility. Close examination lead to astonishing results. Humanity learned about element zero as well as the mass relays but they realized that it seems that the archives on Kobol were purged of that information. There were many theories why this was the case and some adviced caution claiming that it is likely that ezo lead to the demise of the Protheans. But given the data ezo was to valuable not to use and thus the humans searched for ezo both in their controlled space as and on their new exploration missions.
At the same time expeditions found a fifth Garden world and in the same system a strange structure later confirmed to be one of the relays. The Planet and system were called crossroads and the military as well as many scientists began to build bases in the system and on the planet. Civilian colonization was stalled until the gate was explored. The first prototype of a ship using a mass effect drive was delivered to Crossroads after successful testing. It managed to cross through the gate and traveled hundreds of light years nearly instantly. The gate linked to three locations expeditions were planned to all of them. At the second contact with an alien civilization was made. They called themselves the Turians and represented and even bigger interstellar community called the Citadel. It was agreed that the Citadel will send Diplomats to Crossroads to initiate relations.
Chaiss Praor was a seasoned Asari diplomat and one of the influential matriarchs in the Asari Republics. Together with diplomats from all other species represented by the Citadel she was en route to their meeting on the planet called Crossroads. So far this was one of the better first contacts on record. The Turian commandant of the Patrol force that made contact followed procedure for first contact instead of shooting first just like one would expect from a disciplined Turian. The humans responded peacefully and invited them to send diplomats for the beginning of peaceful relations. The STG report was thin but at least they had a first analysis of the human mass effect technology and that one indicated that humanity was still in the early phase of developing it or is very bad at it. Either way would be good for the Citadel it meant that humanity was neither a threat nor a new galactic power (at least not yet). So it shouldn't be a problem to get them to join the Citadel, sign the treaties and follow their lead.
"Greetings honored guests. Welcome to Shanxi base on Crossroads my name is Ellen Tigh ambassador for the System Alliance" She moved to introduce the ambassadors for the Garden worlds and moved on to the staff. The first few days went smoothly but at the beginning of the second week there seemed to be an issue. Ellen invited Chaiss to another personal meeting.
"Hello Ellen your invitation sounded more serious than the ones before.
"Sorry Chaiss this is an official meeting. But since it might be a sensitive issue I wanted to discuss it with you first." She gave Chaiss a few folders. "You will recognize this as the documents you gave us about the treaty on Artificial Intelligence. As well as your recounting of the Quarian – Geth war and the subsequent punishment for the Quarians."
"Don't tell me you created A.I.?" Chaiss said. She did a bit of quick thinking. Since the humans were still here and lived on their worlds even if they had created A.I. they must have beaten it.
"Ok let's clam down. Let me guess you created one but were able to clean it up and now you are worried that we will punish you like the Quarians. I will not lie to you there will be quite a few who will be miffed and demand that you should be monitored but you have two things in your favour. First it was before First contact and just like the question of gate opening you are not accountable before first contact and second you managed to clean it up. So there will be no official reprimand just some issue on personal levels."
Chaiss smiled believing a serious sensitive issue had just been solved. But then she noticed Ellen's crestfallen look.
"You managed to clean them up, right? Don't tell me you are still at war with them!"
Ellen held up her hands to calm Chaiss down.
"No we are not at war with any A.I.. And technically we didn't create one. But at some point in our history the Protheans relocated a significant amount of humans to a world called Kobol and the descendants of them created what they called Cylons."
Chaiss eyes widened recalling that one of the major worlds was called Cylon Prime. Ellen continued.
"You noticed that we were cautious of revealing our past and it seems we were right to some extent. After going through the files on Citadel history and laws you gave to us my government wants to inform you that we see no possibility to join Citadel under it's current law. I'm authorized to give you generalized information on our history which will explain why we came to this decision. We hope that we still can come to an agreement of peace and mutual trade."
After some further general chat Chaiss left. She her fellow ambassadors and their staffs worked through the human files. They were obviously edited there was no information about human technology or where their world or even sphere of interest was located. STG still managed to derive some implications and they were frightening. In all likelihood Ellen was an A.I.! The great majority of humanity was A.I.! They wrote a summary and forwarded it with highest priority to the council and all Citadel governments. After sending the full files and some other reports Chaiss ordered her staff to pack rightly expecting to be called back soon.
Luckily they found this A.I. while it was technological at such an inferior stage. She fully expected the Council to declare war as soon as the mobilization is done. She would take part in the discussion in the Republics but she couldn't afford to forewarn the humans even more should they manage to breach her security protocols. She was sure the other matriarchs will take the right steps.
Admiral Xuan commander of the Crossroad Fleed and General Summers commander of the Crossroad ground forces had a video conference together with their Staffs.
"They are preparing to leave, no good sign" Summers said. "Their hate for A.I. is quite obvious. They only left the Geth in peace because they demonstrated their strength. Since they only evaluate us based on our mass effect technology they will likley consider us a much easier target." Xuan confirmed. Both knew war was coming and the higher up agreed. Crossroads would be fortified as soon as possible. "Pity we can't reach the Geth. But going thorugh the Network is impossible with the Citadel patrolling it and with our FTL we would need to long."
Admiral Virilia Optidos stood on the bridge of her Flagship the Indomitable. Originally the Hierachy only wanted to send two Dreadnoughts with the expedition fleets but the Asari went nuts. They really must hate A.I.s they even offered the Destiny Ascension as Flagship. While the Hierachy was glad that the Asari for once took a threat seriously they couldn't afford to take away a symbol like the Ascension. In the end they agreed that all Council species devote one quarter of their forces for the expedition fleet. So she commanded 9 Trurian, 5 Asari and 4 Salarian dreadnoughts. Total overkill from a pure military viewpoint but the Hierachy remembered her of the political symbol. A show of unity and strength a new threat for the galaxy crushed under the mighty hammer of it's defenders. A reminder for all just why it was these three who formed the council and all others shall follow their lead. One of her subordinates got her attention to the newest report from her foreward scouts. She mussed: Mines placed into the extraction vector of the relay. These humans may be technological behind but I won't make the mistake to assume that this means they are stupid or primitive.
"Use mass fields to haul asteroids through the relay. Lets deal with these mines. Tell the forward battle group to prepare."
Meanwhile all non-military personnel were evacuated from the crossroads system. Rebirth ships were placed in deep space around the system as backup for the rebirth centers in the bunkers of the planet. Several million troops were transferred in the blink of an eye via data transfer and will soon occupy centurions, raiders and other machines of war. The Citadel troops who are expecting army of machines with organic bodies will face a wall of steel.
In the darkness of the bunker a lone voice comments on the relay mines going of: "The die is cast. War is upon us."