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.

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

New episode included with the 10th blu-ray volume. The episode will adapt the true ending from the original PS2 game.