A long time ago, in a galaxy far, far away...
The Jedi studied The Force through meditation and contemplation. It was a mystical force that only a disciplined mind could wield and master. It was known that force-potential was often an inheritable trait passed on from mothers and fathers to their offspring. This prompted one Jedi, a former scientist, to seek scientific explanations for The Force. He discovered midi-chlorians and their relation to The Force. He postulated that at one time, the midi-chlorians were a virus that infected living cells. Eventually, mutations occurred and they became a part of living cells that were copied as each cell divided (like the mitochondria of our galaxy). The Jedi of the time viewed his findings with disdain. "Science is not the way to The Force", they said. Fearing that this particular jedi would unlock powerful secrets of The Force through midi-chlorian research instead of practiced and disciplined spiritual study, the council banned further study of the midi-chlorians. The science-jedi took offense to this and left the order with many other jedi following him.
This group would later go on to become the Sith. It's leader would one day take the name Darth Plagueis. It is said that he possessed such wisdom that he could influence the midi-chlorians to prevent those he cared for from dying. Well, who does a Sith care for? Himself. Plagueis mastered the ability to transfer his consciousness from one body to another. He lived for thousands of years this way, taking the names of his victims and sometimes using various new Sith names. When his apprentice, Palpatine learned that his master planned to one day possess his body, he attempted to kill Plagueis. He succeeded in killing Plagueis' body but Plagueis took possession of Palpatine as he delivered the final blow. Snokes is Palpatine is Plagueis.
While Plagueis had great knowledge of the midi-chlorians, he never managed to increase his own midi-chlorian count or the midi-chlorian count of other living beings. He eventually took a different tack and it payed off. He was able to use the midi-chlorians to cause parthenogenesis and, in the process, boost the number of midi-chlorians in the fetus. There are Sith legends that he first performed these experiments on animals - which created some rather nasty force-immune and force-wielding creatures. He eventually learned how to do this with humans - which proved very useful for creating new, powerful hosts for himself. Each time, he was able improve the midi-chlorian counts in the midi-chlorian conceived offspring.
If the Jedi had such contempt for midi-chlorians and using science to study The Force, why were they using it to test for force-potential during the time of the Prequel Trilogies? The Jedi originally existed as a cloistered order. As the Republic grew, the Jedi were called upon for aid more and more often. Eventually, the Jedi became very intertwined in the political workings of the Republic. The Republic continued to grow and so did the Jedi responsibilities within the Republic. Eventually, the Jedi were spread very thin and too busy to send Jedi out looking for new jedi recruits. They acquiesced and allowed the use of midi-chlorian testing to identify potential candidates. While they allowed midi-chlorian testing, study and discussion of the midi-chlorians were always discordant and controversial. Thus, midi-chlorians were still a rather taboo topic of conversation. By the time of the Clone Wars, the Jedi had already fallen from their pure, spiritual grace without even realizing it. Through Luke Skywalker, with Obi-wan and Yoda as his guides, the Jedi Order regained its integrity and its spiritual roots.
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