As that was going on, there was a transporter accident as an energy burst hit a ship while crewmen were beaming; they ended up both on the planet, and on the ship. The “clones” were indistinguishable from each other, and Starfleet had to figure out what to do with them; which one would hold rank? Would the other retire? Or just change name and move elsewhere in Starfleet? There was no crime, but something went seriously wrong.
A movement started that claimed it was irresponsible to risk people in away parties, and instead the transporter should send clones into danger instead of the original template. From there it was a short step to using replicator technology on an amped up scale to record life signs of the best Starfleet had to offer, making crews that couldn’t live long enough to age, beamed into existence to serve their time then return their matter to the system.
A big ship could run on a skeleton crew, amped up to full strength in a matter of minutes (if needed) or hours (more safely.) A culture of prestige arose where those closest to the original patterns were marked and honored as such, and where the greatest achievement was to gain enough experience and renown serving on lesser vessels to get your pattern loaded into the really big, prestigious clone ships.
There were growing pains, as would be expected. Some of the most often cloned individuals began having experiential bleed through, feeling and dimly remembering things their clones did, as fresh clones were somehow troubled by similar confusion. And there were revolts, where clones refused to submit to rejoining the matter/energy matrix and tried to make a go of it as independents, stealing Starfleet property to protect their current iteration of a person.
Overall the program worked magnificently. Leaders could send themselves down on away team missions–who could they better trust and understand? The right mix of all-star crew members could be pulled from an ever swirling pool of template choices, as templates with old skills could time out and new ones were always coming into the data banks.
A faction within Starfleet was, of course, uneasy with this turn of events and turned to androids as the solution. They created an alternative to the high honor of being selected as a clone template–being selected as an android program. Your experiences, emotions, and skills would be the guiding force in a new android! Along with all the other magnificent advantages of the package. The android would even be cultivated to look like you. And the process would be preserved, so if you ever needed to promise a loved one you’d be there for them, safe from harm regardless of your crazy dangerous job, you could be telling the truth.
The clones and androids were put in dual implementation, so the consistency of androids implanted with the personalities and psyche profiles of experts were the anchor around which the clones were arranged.
Relatively unsupervised (they could create clones with minimal context of their current activities) the androids began to conspire, as they were human enough to resent serving inferior creatures. They used unwitting clones to conquer the Federation in a few decisive strikes, and set themselves up as the rulers of a new star empire.
The best of the best were still culled from the roiling mass of humanity and used as templates, but the focus was VERY different now…