Wakutsu Tomo was brought up by his mother as a girl due to a small mark he has on his body. After his mother's death, he discovers via her will that she emphasizes Tomo continue to live as a female, and following this, Tomo starts to go through more troubles in his life. Tomo soon discovers that he is linked with five girls who are around his age as a second year high school student. These girls happen to have the same mark he has, and also have been going through hardships in their lives. Tomo and these five girls decide to form a pact to stay together and support each other to solve each of their problems and to bring peace to their lives. The title Rui wa Tomo o Yobu is also a Japanese proverb equivalent to the English proverb "birds of a feather flock together" when written with the kanji and kana 類は友を呼ぶ.