Tomoru Shindo is a City 5 college student nearing graduation, initially uncertain about his future while considering the Earth Defense Force. He experiences recurring dreams of protecting a woman from mechanical threats and witnessing the mecha Orgun battling others on the moon—dreams revealed as premonitions.

When an alien mecha attacks City 5, Tomoru encounters Professor Michi Kanzaki and becomes trapped. Orgun, a rogue Evoluder mecha that traveled 260 million years to reach Earth, intervenes. It merges with Tomoru, enabling them to defeat the invaders. Through this fusion, Tomoru accesses Orgun's memories, learning the attackers are Evoluders. This cybernetic species descended from the lost human Cygnus space probe mission, evolving over millennia due to relativistic time dilation.

Tomoru initially resists further cooperation with Orgun, fearing permanent assimilation and distrusting the Earth Defense Force's motives. However, witnessing civilian endangerment compels him to continue piloting, solidifying his role as Earth's defender. His ancestral link to the Cygnus mission crew—who became the Evoluders—explains his psychic resonance with both Orgun and Evoluder leader Lady Mhiku.

During the final confrontation with Evoluder Commander Zoa, Tomoru rejects Zoa's nihilistic declaration that "the heart is NOTHING!" and instead harnesses the "power of love" to fuel Orgun. Orgun sacrifices itself to stop Zoa's anti-matter cannon using a sunlight-powered "Grand Cross Attack," requiring a telekinetically induced premature sunrise. Orgun is destroyed, but Tomoru survives unharmed.

Standing beside Orgun's remains, Tomoru explains its mission was not only to save Earth but to redeem the Evoluders by restoring their lost humanity through Mhiku's rediscovered compassion. He then walks away with Michi, his journey reflecting a transition from aimlessness to self-defined purpose.