A high school girl, Izumi Gojo, who has been found guilty of murder, falls into the sea and disappears when running away from the police. However, a mysterious group rescues her and had her undertake training to transform her into an assassin. Years later, Izumi seeks to escape the group.

The Waller Empire destroys the planet Clin in search of water for its deity. Two Clinian children, Spielban and Diana, escape to Earth aboard the Grand Nasca. The two grow up during the long journey and don High Tech Crystal Suits to defeat the Waller who have come to Earth in search of more water. Spielban must avenge his dead mother Anna and his homeworld, and find his missing father Ben and older sister Helen. Unknown to Spielban at the start of the series his father and sister have been made members of the Waller against their will.

In 1945, Dr. Ryuichiro Koga designed Metalder as a top-secret weapon for the Japanese Imperial Army for use in the Pacific War, modeling it after his late son, Second Sub-lieutenant Tatsuo Koga. However, the pacifistic Dr. Koga puts him to sleep in the Silver Carcass base and left for America to work for NASA. During the 42 years, Dr. Koga's former colleague Major Muraki became the evil God Neros and sends out his massive armies to kill Dr. Koga, who learned of their organization and returned to Japan to activate Metalder. Koga desperately tries to activate his android creation, who he named Ryusei Tsurugi, but the android is unable to understand what to do. In order to give Ryusei a "purpose", Koga runs out of the Silver Carcass base, allowing Neros' troops to kill him. Suddenly seeing his creator die, Ryusei becomes shocked and fueled with rage, evoking the conversion to his 'true' form, the android known as Metalder.