450 years prior to the present, an extraterrestrial force called Efi Dorg invades Earth; the people of Sengoku era Japan dub their mecha and robotic drones as oni. The Washiba Clan falls victim to them, but clan heir Yukihime and her samurai retainer Kennosuke Tokisada Ouma fight back with a stolen Efi Dorg mecha, which they dub the "Black Relic" (黒骸, Kuromukuro). They succeed in vanquishing their foes, but when the Black Relic is caught in an enemy explosion, Yukihime disappears.
60 years ago, the Black Relic is unearthed during the construction of the Kurobe Dam. In the present day, the United Nations Kurobe Laboratory is researching it when Efi Dorg returns. Yukina Shirahane, daughter of the United Nations Kurobe Laboratory director, accidentally reactivates the cockpit module of the Black Relic, releasing Kennosuke from cryostasis. Aided by Yukina's family and the United Nations Kurobe Laboratory in adjusting to life in the 21st century, he stands against Efi Dorg's invasion of Earth just as he did in his home era. As the Black Relic is the most effective weapon the United Nations Kurobe Laboratory has against Efi Dorg technology, Kennosuke becomes one of their most valuable assets. Due to an accident, Yukina is biometrically synchronized with the Black Relic, and as it requires a pilot and a navigator, Yukina thus becomes Kennosuke's combat partner.