Twenty years after the final battle that decided the fate of the world, Sousuke Sagara and Kaname Chidori are married and trying to live a peaceful life. Their new mission, it seems, is to peacefully raise a family. However, the word peace does not appear to be in the Sagara family dictionary. Sousuke still instinctively asks where the weapons are, much to Kaname's exasperation. Their daughter, Nami, is a high school girl who has inherited her father's combat prowess and often sleeps in the closet next to the entrance out of caution, while their son, Yasuto, is an elementary school student and a skilled hacker with a large social media following.

Despite the defeat of the Amalgam organization, its remnants or new forces seeking the power of the Whispered continue to target Kaname, forcing the family to move frequently and fight back. The Sagara family, including the exceptionally talented children, often ends up unilaterally dealing with these threats, with Sousuke even insisting on non-lethal means for the sake of his childrens education. The narrative balances action with the familys daily struggles, such as Sousuke finally grappling with a career and the family trying to fit into a new town while being very camera shy.

The story is structured around the family relocating to various residences, including a detached house in Saitama, a high-rise apartment in Tokyo, and a seaside mansion in Kamakura. The series also catches up with many characters from the past. Melissa Mao and Kurz Weber are now married and have a daughter, Clara Mao, who works as an Arm Slave engineer. Other alumni from Jindai High School, such as Hayashimizu and his wife Ren, as well as Shinji Kazama and Kyoko Onodera, also make appearances. The narrative blends the serious consequences of their past with the comedic chaos of family life, exploring Sousuke's lingering difficulty in adapting to a society he no longer needs to fight.