Buddy Complex revolves around the main character, Aoba Watase, an ordinary high school boy. He lived an average, everyday life commuting to high school in the city. On the first day back after summer break, Aoba is attacked by a giant robot that appears out of the sky. As he's pursued through the city, his classmate Hina Yumihara appears in a giant robot of her own. She rescues him, and tells him cryptically that "Dio is waiting," before she sends Aoba into the future and then disappears. When Aoba wakes up, he finds himself over seventy years into the future, where the Free Pact Alliance and the Zogilia Republic are at war with each other, and there he meets a young pilot named Dio Jyunyou Weinberg. This begins Aoba's new life as a pilot of the Free Pact Alliance, and together with Dio, they would change the fate of the world.