The mysterious flying creatures known as Zai suddenly appear, and in order to fight the creatures, mankind creates fighter aircraft called "Daughters," as well as the automatic fighting mechanism "Anima," which are shaped like human girls. The story centers on a young man named Narutani Kei, who yearns to fly in the sky, and an Anima considered to be humanity's trump card, a girl name Gripen.
The test flight is delayed due to problems. Kei hears that Gripen is to be scrapped and sneaks into the base. But then, the Xi launch another attack. Gripen needs Kei near her to be able to fly, so he heads up into the sky with her.
Gripen continues to lose to Eagle in mock battles, and it's starting tog et to her. Kei tries to improve the mood between the two of them when a new girl, Phantom, comes to the base. Yashirodoori explains that they're forming a new unit for the Anima, the "Independent Mixed Test Unit".
The Xi: unidentified flying objects that are vastly more powerful than humanity's best fighters. Kei Narutani is fleeing Shanghai on an evacuation ship when he's attacked by the Xi, but a mysterious red fighter jet saves him. One day in his new home in Komatsu, he sees the same jet. It's being carried to a nearby Japanese air-force base.
Kei meets Gripen, the fighter jet who saved him. The plane itself is called a "Daughter", and it's piloted by an artificial life form called an Anima. That was the young girl that Kei met. Yashirodoori tells Kei to spend time with Gripen. As they walk through the city, the bond between them begins to deepen.
Gripen's condition stabilizes when she's near Kei, but nobody knows why. The two of them train for the upcoming test flight using the simulator. If they can pass the test flight and Gripen can fight again, she'll be able to wipe out the Xi before long. But one day, Kei learns the truth about the Anima and the Daughters from an unexpected source.