Ethan Waber, the main character, and his younger sister, Lumia Waber, are at the celebration of the 100th anniversary of the Alliance Space Fleet on the GUARDIANS Space station. The celebration is interrupted when a mysterious meteor shower almost destroys the entire fleet. During an evacuation, Ethan and Lumia divert from the main evacuation route; collapsing rubble separates Lumia from Ethan. Ethan then meets up with a GUARDIAN named Leo, but they are attacked by a strange creature that paralyzes Leo. Ethan kills the creature. After killing multiple creatures and saving people, Ethan finds Lumia and they leave the station. Ethan reveals that he dislikes the GUARDIANS organization because his father died on a mission. Leo, impressed with Ethan's abilities, persuades Ethan to join the GUARDIANS.
Ethan and his classmate Hyuga Ryght are trained by a GUARDIAN named Karen Erra, who leads them against the S.E.E.D, the monsters that came from the meteors. After being hired to accompany a scientist to a RELICS site of an ancient, long-dead civilization, they find out that the SEED are attracted to a power source A-Photons, which the ancients used and that the solar system has just rediscovered. Karen discovers she is the sister of the Divine Maiden, the prophet of the Holy Light, and takes over that role when her sister dies at the hands of her estranged father who intended to kill Karen to increase the power of the original Divine Maiden (Mirei). After befriending Rogues, Guardians, and CASTs alike, Ethan angers Magashi, a CAST who heads the Endrum Collective and has been kidnapping scientists who know about the ancient power source.
Ethan and a Rogue named Alfort Tylor kill Magashi. Ethan helps activate an ancient weapon the prior civilization used to survive the S.E.E.D before they were almost completely wiped out. Ethan gathers allies against GUARDIAN orders to attack the last S.E.E.D outpost, where two of his friends and the scientists are being held. In the outpost, Magashi claims to have been resurrected by the S.E.E.D, but he is actually a CAST incarnation of Dark Force, who controls the S.E.E.D and whatever they infect. With the help of Karen, Leo, and Tonnio, Ethan defeats Magashi.