Mysterious flying creatures known as the Zai suddenly appear in the skies, possessing highly advanced weapon systems that far surpass any existing human military technology. In response to this overwhelming threat, humanity develops special fighter aircraft called Daughters, which are existing jets retrofitted with reverse-engineered Zai technology. These Daughters require a unique autonomous interface unit to function properly, a cyborg-like being known as an Anima, which is grown from salvaged Zai parts and takes the form of a human girl.

The story centers on Kei Narutani, a young Chinese-Japanese teenager who lost his mother, an air show pilot, to a Zai attack. While evacuating from Shanghai to Japan with his childhood friend Minghua Song, their ship comes under attack by Zai fighters. A strange fighter plane appears and drives off the attackers before crashing into the sea. Kei rushes to help the pilot, only to discover a pink-haired girl at the controls. This girl is Gripen, an Anima unit assigned to a JAS 39 Gripen fighter. After arriving in Japan, Kei is brought into the Anima project by Haruka Yashirodori, the lead scientist who developed the system. Yashirodori discovers that Keis presence stabilizes Gripens erratic behavior and emotional defects, which threaten to get her scrapped. Kei agrees to become Gripens partner, serving as her weapon systems officer and emotional anchor as they take to the skies together.

The story is set primarily at Komatsu Air Base in Japan, where Kei and the Anima units operate under the Japan Air Self-Defense Force. As the series progresses, Kei and Gripen are joined by other Anima characters. Eagle is a blonde, perky Anima flying an F-15J Eagle who adores Yashirodori as a father figure. Phantom, flying an F-4 Phantom II, is the first Anima ever created, serving as a tactical reconnaissance specialist with a condescending attitude toward her counterparts. Viper Zero flies an F-2 but has the unusual property of appearing as whatever person the viewer most thinks about. Rhino is an American Anima flying an F/A-18 Super Hornet who becomes corrupted and destroyed by the Zai after falling into a trap. Minghua remains a significant presence as Keis forceful childhood friend who considers herself his girlfriend, though Kei sees her more as an older sister.

The manga covers several major narrative arcs from the light novel series. An early arc focuses on Gripen facing potential scrapping due to her instability, with Keis involvement proving essential to saving her. The Komatsu base comes under direct Zai attack, forcing Kei to sortie with Gripen for the first real combat mission, successfully shooting down the enemy. A later arc involves the Battle of Seabird Island, where Phantom suggests Kei formally become Gripens pilot, a role he accepts. The Shanghai Landing Operation sees Kei, Gripen, and Rhino become separated from their unit, forced to land at a deserted Pudong Airport, where Rhino reveals her true nature as a corrupted Anima and is shot down. Another arc follows a Russian Anima named Berkut, flying a Su-47, who defects to Japan as part of a mysterious plan using high-powered EPCM technology to attract Zai. The manga also introduces international Anima units including Frances Rafale and Russias Zhuravlik, Pakfa, and Lastochka.

The manga adaptation, illustrated by Takahiro Seguchi, was serialized in Kadokawas Monthly Shōnen Ace magazine from October 26, 2018, to May 26, 2019, and compiled into two complete volumes. The story follows Keis journey from a civilian teenager mourning his mother to becoming an integral part of the fight against the Zai, developing deep bonds with Gripen and the other Anima as they struggle to protect humanity from an enemy that remains largely mysterious throughout the series.