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The story takes place after 90 percent of humanity wiped out due to an invasion. Survivors live in a shelter where their lives are monitored, and memories of the invasion erased. Three teenagers from the shelter are chosen to pilot three machines that combine to form the Musashi robot, made out of a material named Megatronium alloy.
Mars is discovered on a forming volcano island, Heisei; a man with no memory. In reality, Mars is from outer space, and is supposed to gather information to decide whether Earth should be destroyed or not. Along with the giant robot Gaia, and his mysterious images of a woman urging him not to destroy the world, Mars decides to fight for Earth rather than destroy it, even if it means fighting his own kind. But if Mars is killed, Gaia will explode, destroying Earth along with it.
In the year 2050 the world population is crazy about the "Metal Fight", a competition where people compete in battles featuring giant robots. An organiation called Iron Mask is planning on transforming Metal Fight competitors and their robots into weapons, and tries to kidnap Shoko Saeba, a robot programmer who created the Red Baron, which uses a feedback system. Ken Kurenai is able to protect Sally and the Red Baron, and becomes Metal Fight World Champion in the process. Iron Mask then decides to send out their forces to take Ken and the Red Baron out forever.
Many years ago, Duke Fleed fled to Earth with the mighty Grandizer robot to prevent it from falling into the hands of the Vegan Empire. Hiding the robot and taking on an Earthian persona, he vowed never to pilot Grandizer again. Fast forward to the present, and a group of UFOs led by his childhood sweetheart have tracked down Duke Fleed once more. Demanding Fleed turn himself over, they give him a choice: return the Grandizer or watch Earth be destroyed! Will Duke Fleed stand by and watch his adopted home be obliterated, or will he break his vow, pilot Grandizer, and face off against the combined Vegan UFO Fleet?
The official music video for Koukyoushihen: Eureka Seven - Hi-Evolution's first movie's ending theme, performed by Hiroya Ozaki.