Within the Star Trek universe there exists a wide array of nasty diseases, each of which affects their hosts in different ways. From stunted life expectancy, to the literal rotting of living flesh, the writers are not afraid to push the envelope with different ways to bring different cultures to their knees. The majority of these elements are naturally occurring. Others are accidently created, the result of a laboratory failure or an experiment gone wrong. Founder's disease, however, is something entirely different. What exactly is this horrifying illness?
While sharing many of the characteristics of an alien specific disease, the origins of Founder's Disease lie in a far more nefarious, morally ambiguous realm. The disease is in fact man-made, created by Section 31 (Starfleet's not-so-legal special ops' division that operates in the shadows) in an effort to stop the Dominion war before the Founders irradiated all who stood in their way. The Founders, or the ‘Changelings,’ were threatening to invade Earth, systematically wiping out starship after starship. Starfleet sought to uncover as much information as possible to help stop them.
Odo, the DS9 head of security, was a changeling himself (although he himself was not aware of this for a long time). Starfleet requested a throughout examination to understand his biology, and how his species worked. It was, on the surface, a fairly innocent examination to aid the Federation’s chances during the war. However, unknown to almost all, there was a nefarious plan at play.
During the examination, Section 31 secretly infected Odo with their morphogenic disease. The hope was that if he were ever to return to the Great Link, the gigantic space puddle hive mind where the Founders resided when they were in solid form, he would spread the disease to them all. This all happened a short while later when he was forced to return to the Great link for a short time, facing trial for his killing of another changeling. He never actually had the disease; rather, he carried it within him, ready to infect the others all while not being affected himself.
Unfortunately, this all went awry later on. Due to a mutation in his ‘morphogenic matrix’ (the cellular/ quantum structure of a Changeling, the thing that alleged them to change form). Odo ended up suffering from the full on, un-filtered disease. The disease took a long time to show any symptoms, and for a while, everything carried on as usual for the Founders and their Dominion War. They continued to overpower the Federation, killing billions of people along the way, until signs of the infection started to show.
The disease worked in two parts. First, it would eventually wipe the Founders out and thus win the war for the Federation. Second, it had an incredibly helpful symptom that would, in the meantime, stop the Founders' infiltration efforts. One of the best tactical advantages the changelings had during the war was their ability to transform themselves into any living organism. They would commit large scale political espionage, almost bringing the Tribble-fearing Klingon empire to its knees just by replacing their leader. The disease would make their skin flake and fall off, making them unable to maintain a cohesive solid form for long. Furthermore, the symptoms would only get worse the more often the changeling would change. It made their attempts at pretending to be normal people impossible, their skin showing telltale signs of their true identity.
It’s hard to say whether what Section 31 did was right or wrong, but this is exactly what made Deep Space 9 such a great series. They are unable to be the saints in paradise asthe other captains and their crews could be. They were at the very fringes of Federation space, and at the very front lines of a devastating war. They carried this theme through various episodes, including one which changed the franchise forever. The Founders were a nasty, paranoid, iron-fisted a bunch of manipulative dictators who would commit genocide without even a flinch. They genetically altered entire races and cultures to serve them, and would likely have entirely wiped out the Federation and most of the Alpha Quadrant if they were not stopped.
Founder's Disease stopped the war, and gave the Federation the upper hand they desperately needed to survive. The cure they possessed was the only thing able to save the Founders from an agonizing death. Section 31 did not want to commit genocide, but needed the threat of genocide through the incredibly illegal and morally bankrupt biological warfare to win the war, maybe even setting the Changelings on a new path? Whether it was right or wrong is difficult to say, but while the methods were ambiguous, the results can be lived with.
