In the year 2167, a wave of radiation released by the supernova of the nearby star Hydrus Beta caused cataclysmic damage on Earth, leaving millions dead. Now, it is the year 2356. United to rebuild Earth, humanity prepares for the supernova's second wave of destruction. In order to protect the planet from future harm, massive space colonies called Foundations have been built throughout the Solar System. Acting as centers for both knowledge and exploration, it is at one of these Foundations—the Stellvia—that Shima Katase applies to be a preparatory student against her mother's wishes, aspiring to see space directly with her own eyes. At the Stellvia, Katase trains to become a pilot and hopes to be selected for the Great Mission to shield Earth from the second wave. While she struggles with both her pilot classes and her tumultuous social life, she slowly grows into someone who might just be able to protect humanity.

Unbeknownst to most humans, a bizarre tournament is held to decide the next ruler of the Heavenly World. In this tournament, 100 Heavenly Beings known as the God Candidates are required to search among the middle school students on Earth, and transfer their powers to a student of their choice. The chosen ones will then battle each other, representing their God Candidates. The victor of this tournament will be awarded the Blank Talent—allowing them to choose any one unique ability they so desire—while the God Candidate they represent will obtain the position of God and become the king of the Heavenly World. Participating in this grand tournament is Kousuke Ueki, a middle school student who is given the power to turn trash into trees by his homeroom teacher, Kobayashi. Despite the concerns of his classmate, Ai Mori, Ueki embarks on a journey to pursue his own sense of justice after witnessing the people around him misusing their powers for selfish purposes. But as he encounters talented power users such as Seiichirou Sano, Rinko Jerrard, Robert Haydn, and Hideyoshi Soya, he realizes that achieving his goal might be harder than it seems.

Akira Yuki has spent years honing his Bajiquan skills under the guidance of his grandfather. He yearns to see the constellation of the eight stars of heaven, which are only revealed to those with real strength. This burning desire urges him to embark on travels, so as to learn more about how to see the stars. Meanwhile, a nefarious robotics scientist, Eva Durix, desires to create the perfect soldier. Eva's group, Judgment 6, tracks down and kidnaps Sarah Bryant, a college student and close acquaintance of Akira who is investigating a mysterious accident concerning her brother. Akira must now fight his way to Sarah to save her from the clutches of Judgement 6, a perilous path sure to be paved with countless challenges.