The title is based on the Gnostic notion of an Æon – emanations of God – specifically the Valentinian notion of a syzygy, a sexually complementary pair of emanations, here the two main characters. The Gnostic influence is also present in the use of a demiurge in one episode.
Makes sense, right? Yeah I have no idea what it means, but we’ll try and give you some background on the title character and her polar opposite just the same (via Wikipedia).
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The title character is a tall, leather-clad secret agent from the nation of Monica, skilled in assassination and acrobatics. Her mission is to infiltrate the strongholds of the neighboring country of Bregna, which is led by her sometimes-nemesis and sometimes-lover Trevor Goodchild.
Monica represents a dynamic anarchist society, while Bregna embodies a police state—referred to on one occasion as a Republic by Goodchild. The names of their respective characters reflect this: Flux as the self-directed agent from Monica and Goodchild as the technocratic leader of Bregna. Although Bregna is shown to be repressive, in the first full-length episode, “Utopia or Deuteranopia?”, Clavius, the president deposed by Goodchild, is described by a questioning journalist as having been democratically elected. In the same episode, an upper house of parliament is also mentioned by the character Gildemere.