The story follows Benio "Haikara-san" Hanamura, who lost her mother when she was very young and has been raised by her father, a high-ranking official in the Japanese army. As a result, she has grown into a tomboy—contrary to traditional Japanese notions of femininity, she studies kendo, drinks sake, dresses in often outlandish-looking Western fashions instead of the traditional kimono, and is not as interested in housework as she is in literature. She also rejects the idea of arranged marriages and believes in a woman's right to a career and to marry for love. (Source: ANN)

Ichirou Satou is an ordinary high school student who pretended that he was a hero by the name of "Maryuuin Kouga" back in middle school, which led to others frequently bullying him. Now that he has left this embarrassing phase behind, he does his best to avoid standing out and live a peaceful life, although he feels the world has become quite dull. But when he makes his way back to school one night to grab a textbook he left in class, he runs into a strange girl wearing a costume. This girl, Ryouko Satou, happens to be his classmate and is affected by the exact same condition that he once had, holding on to a delusion that she is someone else and dressing up to reflect this. The very next day, Ichirou is asked by his teacher to become friends with Ryouko, to which he adamantly refuses, unwilling to be reminded of his own history. When he sees that she is being bullied just as he once was, however, the boy makes it his responsibility to take care of her and break her free from that which what once plagued him—the perfect job for Maryuuin Kouga. [Written by MAL Rewrite]

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.

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.