Kei Narutani and his childhood friend, Song Minghua, are Chinese refugees fleeing the Zai, a mysterious organization that terrorizes their country and its people without discrimination. Fortunately, while escaping to Japan, they are rescued by a strange red aircraft. Kei's fascination with the aircraft leads him to meet his savior: a girl who is an "Anima"—the pilot of a unique type of airplane known as a "Daughter." The girl is named Gripen, an adorable JAS-39F fighter aircraft. Kei forms a bond with Gripen and is subsequently recruited by the Japan Self-Defense Force to assist Gripen in overcoming her difficulties with flying. Later joined by Eagle, a carefree F-15J-ANM, and Phantom, a proud RF-4EJ-ANM, the squadron takes up arms, determined to protect humanity. Together, the five individuals battle the invasive Zai, forming the last line of defense against the threatening alien force.