Rito Yuuki remains unsuccessful and indecisive with his love for his crush, Haruna Sairenji, and the alien princess, Lala Satalin Deviluke. Meanwhile, Lala's little sister Momo also falls in love with Rito and works on building a harem for him in hopes of giving herself a place in Rito's love life.

To do so she enrolls in his school to secretly support all of Rito's love interests and even attempts to find him more, including the recently enrolled alien assassin Konjiki no Yami, also known as "Yami," who puts off her next bounty because of him. However, Kurosaki Mea, Yami's little sister, intends for Yami to return to being an assassin.

To LOVE-Ru Darkness continues from the events of To LOVE-Ru with new girls, new foes, and even more lewd moments.