More on the Backstory
The Phoenix Project.
The Phoenix Project was started over forty years ago (From the start of the Game), It was a low priority study on how humanity could avoid extinction in the worst case scenario. During the time moral was still quite high, Earth's fleet had fought and won several pitched battles in nearby systems, and while those systems were lost a year or so later when Machine reinforcements came. The Republic's leadership was confident that with the time they had that they would come up with a proper response and be able to defeat the Machines. The Leadership of the Phoenix Project thought differently. Going through old data they found a hundred and thirty-year-old predictive algorithm that charted the Machines advance, after a year of fine tuning they successfully charted the war from the very beginning. The algorithm only needed information from the first quarter of the war, and predicted every attack and fleet movement from then on, nearly perfectly. the Algorithm's data was originally discarded as ridiculous because it charted the Machines fleet strength in the millions, something thought impossible or at least really unlikely in its original time, but recent reports from space telescopes and deep space scanning technology reported that it had been accurate. This had the Phoenix Project leaders worried. the predicted fleet strength was over six million ships for the Machines final attack, and it would happen in around forty-five years from then and Sol would be the last to fall.
They began exploring their options and when the conventional failed they began digging into the unconventional. Meanwhile, the war continued to worsen, as system after system was lost. soon the FTL Comm could only connect to half-dozen colonies. When the discovery of an FTL drive was announced by one of the colonies, Moral rose once again, with an FTL drive the combined fleet of earth could descend on any system that needed help and wipe out the Machines in detail. Testing began immediately and initial tests were promising. But when they tried to scale it up massive problems surfaced, in the end, the project was abandoned, to move a starship would take more energy then the solar system could produce in a year. The Phoenix Project gained control of the prototypes and data believing that should the energy problem be solved it would save humanity.
Around thirty years ago the Project faded from the hierarchy in the Republic's military, its members dispersing to other jobs and other roles. This was not truly the case. The Phoenix Project created a plan to create the seed ships, the scientists in charge of the FTL project were told to find the energy to launch even one ship, "Blow up the Sun if you have to" were the extract words used, and So they succeeded in creating an engine that would propel the ship into FTL, in fact, the delivery system could be scaled up to send hundreds if not thousands of ships into FTL. The Project leaders realized that for the Project to succeed they needed the resources of the entire Republic and the only way to get it was to take it in secret, one does not simply "Blow up the Sun", so they Officially disbanded the Project and worked in secret to acquire the resources needed. Eventually, they moved high enough in the Republic to ensure the ships could be built (and paid for) and that the resources were in place to build the Launch device in Mercury's Darkside.
While the Captains of the Seed ships are informed about the nature of their FTL drives, they were all carefully chosen because they would be able to keep the secret. Sol's economy would collapse if the public was ever informed that Earth Command knew it was going to lose, even if Humanities extinction was going to be tempory. No one wants to die. They were chosen because their evaluations showed they would pour every available resource into these crafts and then steal more if they had too. They come from all corners of the solar system, and from nearly every space going field, some are Techs and Farmers, some are Generals and Captains of industry, and even if only half answered the call, the Project stood at greater than 73% chance to succeed.
The FTL launch device would be built on time and would be hidden as part of a Steller laser system. A project that has been suggested in the past but discarded time and time again.
All that is left is to inform the "Captains" of their new mission.