After witnessing someone die, 13-year-old Rachel "Ray" Gardner is brought to the hospital for counseling. However, she instead wakes up in the sixth basement of an abandoned building with no other memories. While blindly wandering around, she is branded a "sacrifice" and encounters a cowled figure covered in bandages from head to toe, wielding a scythe at her.

At first, the hooded man, Isaac "Zack" Foster, desires to kill Ray. But upon deeming her boring, Zack changes his mind and instead cooperates with her to escape the dilapidated structure.

Adapted from the Japanese horror adventure game of the same name, Satsuriku no Tenshi follows Ray and Zack as they evade numerous barriers, traps, and guards all while unraveling both of their dark pasts.