Buddy Daddies centers on a family of three who are not related to each other: Kazuki Kurusu and Rei Suwa, assassins who live under one roof; and a little girl, Miri. She is the daughter of Kazuki and Rei's assassination target who ends up being picked up by Kazuki. After killing their target, Kazuki tells Miri that he is her father, to protect Miri from the truth.