Twenty years after the climactic final battle that decided the fate of the world, legendary mercenary Sousuke Sagara is married to Kaname Chidori. They live far from a peaceful life with their two extraordinary children. Their daughter Natsumi is a high school girl who inherited her father's full combat prowess. Their son Yasuto is an elementary school student and a skilled hacker.

The family's new mission is to peacefully raise a family, but the word peace is not in their dictionary. The story begins when Sousuke calmly states that he needs a weapon from the closet. Natsumi asks if he wants his usual carbine and grenade. Kaname is exasperated to discover her husband still hides a weapons stash despite always insisting he does not need them. As enemies approach, Kaname is told she can complain later.

The family constantly moves to new towns in Japan to stay ahead of threats. Although the terrorist organization Amalgam was shattered by the events of the previous story, its remnants and new forces who have obtained dangerous information continue to pursue the family. They specifically target Kaname because of her Whispered abilities. The Sagara family fights back against these enemies each time they appear, but Sousuke now insists on using non-lethal means because killing is bad for the children's education. The family generally overwhelms their enemies with Sousuke's experience, Kaname's resources as the president of several companies, and their children's natural talents.

Beyond the constant battles, the narrative focuses on the family's struggle to fit into normal society. Sousuke remains unable to fully adapt to civilian life after two decades. He deeply worries about whether raising his children in this environment is correct, especially as he sees them display their combat talents. Meanwhile, they must hide their true nature from neighbors and classmates while dealing with situations like being very camera shy.

Notable narrative arcs involve the family settling into a new home, including a detached house with three bedrooms in Saitama Prefecture, a high-rise apartment in Tokyo, and a seaside mansion in Kamakura. The story also features the return of beloved supporting characters from the original series. Melissa Mao and Kurz Weber appear with their daughter Clara, who works as an Arm Slave engineer. Other former classmates from Jindai High School also reappear, including Atsunobu Hayashimizu and his wife Ren, Kyoko Onodera, and Shinji Kazama. The story connects to Full Metal Panic! Another through Clara Mao and the introduction of a new Arm Slave called the Azur Raven.