Kuromukuro opens at the United Nations Kurobe Research Institute in Japan, a facility built around an ancient artifact uncovered during construction of the Kurobe Dam. Scientists from across the world gather there to study the mysterious object, while their children continue their ordinary school lives at Mt. Tate International Senior High School.
At the center of the story is Yukina Shirahane, a reserved high school girl and the daughter of the institute's head scientist. When she visits her mother at the facility, Yukina manages to solve part of the artifact's puzzle and unexpectedly awakens Kennosuke Tokisada Ouma, a young samurai from the Sengoku era. His sudden arrival draws her into a conflict that stretches across centuries and places the artifact's secret at the heart of her world.
As an extraterrestrial threat closes in on Earth, Yukina and Kennosuke are forced to stand together on the front lines. While fighting invading forces and uncovering the truth behind Kennosuke's presence, Yukina begins to understand why he is determined to protect her and how deeply his past is tied to the danger facing humanity.
