The story of "Appleseed Alpha" is set in a post-apocalyptic world where humans coexist with advanced artificial intelligence. The plot revolves around Deeno, a young and extraordinary individual with superhuman abilities, and his companions, who embark on a perilous journey to uncover the secrets behind a mysterious project known as "Appleseed." Along the way, they confront various factions vying for power and survival in a world fraught with danger and deception.