The Candidate for Goddess takes place a millennium after Star Year 4084, when a cataclysmic event called "Crisis of Systems" resulted in the annihilation of four planetary systems. With Zion being the one planet left with the ability to sustain human life, humanity must cling to life in space colonies.^[1][2] Now in Star Year 5030, Zion is under constant threat of invasion by extraterrestrial life forms dubbed "Victim" (犠牲者 Giseisha^?). In order to combat their alien foes, humans have developed a quintet of giant,mechanized weapons called "Ingrids", or "Goddesses" due to their female, humanoid resemblance.^[2] A school called the "Goddess Operation Academy (G.O.A.)" is established to train the specific few which have the capability of piloting the Ingrids.^[1] They are typically young men and must meet several requirements: They must be in good health, must be 14 to 16 years of age, must have an EO blood type, and must possess the potential for "EX", superhuman abilities which secondarily link the pilot's nerves to the Ingrid's interface.^[1][2] As EX puts such a physical and mental strain on the pilot, replacements must be turned out by the G.O.A. within a reasonable amount of time.^[3] Each pilot is also partnered with a female repairer, who maintains the Ingrid and manually blocks painful feedback from the Ingrid to the pilot during missions.^[1][2]

The plot of The Candidate for Goddess primarily focuses on Zero Enna, a brash trainee who has recently left colony homelife with his mother in order to pursue his dream of becoming an Ingrid pilot.^[2] Shortly after arriving at the G.O.A., Zero becomes lost and is subconsciously called to a hangar by a mysterious voice, suddenly finding himself within the cockpit of one of the Ingrids.^[3] As each Ingrid is specifically calibrated for their pilot, this would normally mean death. However, the Goddess instead links with Zero's nervous system and physically shows itself to him in a vision.^[3] After a few moments, Zero is pulled free by the Ingrid's pilot, who then takes it into battle with the Victim. Zero is rushed to the academy's sick bay.