Zion is the only planet left in the year 4084. Humanity struggles to defend Zion from the alien race known as Victim. In order for humans to have a place to call home, they deploy something called a Goddess, a gigantic spacecraft/robot, to fight the Victim. Special children are trained in a space academy known as GOA to qualify as pilots for Goddess. Among the new recruits is Zero, an exuberant kid that makes piloting his ultimate goal. But he soon finds out that his learning experience has just begun.

Something goes wrong, as Zero is taken into a Goddess by accident. Inside he experiences a flashback to when he saw a Goddess for the first time, an image that has haunted him for some awhile. The past continues to unravel its convolutions to the young recruit, while a battle with a Victim commences outside. The Goddess forces are short one fighter, as Zero cannot break from his internal conflict.

Once Zero is removed from the robot's body, the Goddess forces are at full strength. As the battle rages outside, inside fellow recruits Hiead and Clay are learning about the harsh realities of combat casualties. They also find Zero as he wakes from his coma. Once he awakes he shows that he is at full potential. It is also revealed that Zero and Hiead both exhibit a power known as EX, and that it is important to not only possess this power, but to control it to become a true Goddess pilot.

Mitsuro Hongo's Pilot Candidate, takes you to the distant realms of outer space in a traditional human vs. alien war. Little is known about the alien race known as Victim and about the last planet Zion. People live on space colonies, not on planets, so this makes the protection of the last existing natural ecosystem vital. That's about all that is given. The vagueness is enough for the viewer to ask questions as the humans battle Victim. Hints of the past are revealed when Zero has a flashback to when a Victim attacked his home colony. This anticipates many answers in episodes to come.

In the tradition of Evangelion, the fate of humanity rests on the actions of young teenagers. The mind and spirit of the youthful characters gives the anime life. The thought process that each character goes through during a time of crisis, gives it a true-to-life appeal. Rather than having the protagonist destroy 20 monsters all on his own, the story reminds you that each character is only a kid, each having issues of their own. Which is true for the new candidates: Zero and Hiead. Each one exhibits different stigmas of a kid growing up. Zero is the hyperactive, eager type, whereas Hiead is the conservative, strict type. These personalities create a rivalry between the two, thus motivating them more to become Goddess pilots even more. The story has depth.