The Third: Aoi Hitomi no Shoujo takes place in a future where an interplanetary war has devastated the planet, leaving only a fifth of the population alive. As a result of this war, a new breed of humans, known as the Third, has emerged, characterized by a third eye with oval-shaped red pupils, referred to as "space eyes." This third eye grants them control over advanced technology, effectively making them the dominant force in the world. Honoka, a skilled sellsword, becomes entangled in the lives of the Third, including Ikus, whom she rescues from the desert.