Mirai, an improved Kongou-class Aegis guided missile destroyer, is one of the newest and most advanced ships in the entire Japanese Self Defense Force (SDF). Her crew, also one of the newest, is lead by Capt. Umezu Saburo and Executive Officer Kadomatsu Yosuke. While running scheduled training exercises one day, Mirai encounters a fierce storm that throws their navigation systems into temporary disarray. After a few minutes of recovery, the crew is shocked to discover that they've been transported back in time to June 4, 1942—The Battle of Midway, during World War II. Letting history take its course for this battle, they manage to avoid the conflict firsthand and make a vow to remain anonymous, changing history as little as possible. However, when the crew comes across the dying Lt. Commander Kusaka Takumi, XO. Kadomatsu's instincts to save lives takes over, changing the course of history more than he could've imagined.

Hundreds of years ago, the borders between the worlds of humans and youkai temporarily overlapped, resulting in many residents of both crossing over to the other side. In the years since this event, the city of Sakurashin has become a central hub for all inter-dimensional affairs—a result of both the sacred Seven Pillars around the city serving as a beacon for the youkai, and the efforts of the Hiizumi Life Counseling Office in keeping the townsfolk happy. This office is composed of Hime Yarizakura, the young mayor of the city; satori Ao Nanami, who can read people's minds; half-youkai Kotoha Isone, who can summon anything by speaking a word; oni siblings, Kyousuke and Touka Kishi; and the office director Akina Hiizumi, who inherited his family's ability to force youkai back to their world. Besides volunteer and arbitration work, the Life Counseling Office also suppresses any Strikes: rare occurrences where humans are suddenly infused with youkai powers and go on a rampage. But the appearance of a sinister man signals trouble as Strikes become increasingly common, political rivals make their moves, and malicious individuals descend upon the city. As the self-appointed defenders of Sakurashin, it's up to the Life Counseling Office to protect the idyllic city they call home! [Written by MAL Rewrite]

Earth has been conquered by the evil Illumidus Empire, with parallels drawn to the U.S. post World War II occupation of Japan. Captain Harlock with a group that will become his life long friends begin their fight against this tyranny visited upon the planet Earth, with no regard to the costs the struggle will have on them, caring only for the ideal of restoring freedom to the people of Earth.

The story follows a boy named Quon and others who suddenly wake up with supernatural powers.