The LouCipher Rebellion
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People are at the core of most stories and this one holds to form. There are the large picture events, rebellion in the colonies, and the paranoid over-reaction of the threatened government. Central Authority is a faceless force which values stability above all else. Their chosen path is absolute orthodoxy, in thought and deed. Layers of enforcement bureaucracy are added to insure that custom is followed.
Mary is now the head of The Science Academy, an agency under fire from the autocratic Government; Jake is the prosecuting attorney, and he needs to win to keep his job.
Central Administration sees this as an opportunity to rid itself of the Scientists of the Academy, who are constantly coming up with new discoveries that threaten orthodoxy. Prosecuting them with the rebels will discredit them and their science forever. Change will not be tolerated!