The Goddess Gambit by B. Michael Stevens

Something is wrong in the Ziggurat. A city-state-fortress, built to be a shining beacon of hope for the surviving remnants of the human race. The last bastion against the swirling forces of chaos. Home to Jon 310-257, a super soldier, born and bred to fight for the purity of the planet, to keep Home safe, and to help bring about a brighter tomorrow under the honorable Chairman Accoba Warbak.
A shadow now crawls across the land, a wrongness that runs deeper than the Ziggurat’s vaunted goals. Esoterrorists have infiltrated the capitols surrounding Shanty. They are traitors, criminals, sworn enemies of Home and the safety it offers… or are they?
When Jon is contacted in the most surprising way by one of the enemy, he is unwittingly set upon a path that will challenge all his assumptions and beliefs, and will teach him what it truly means to be a hero for humanity.