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.

Kouichi Sanada and Kazuki Aihara's childhood friend Mao Mizusawa has returned after living in France for a couple of years. Kouichi is surprised to learn that, since her parents are remaining overseas for the time being, his mother has agreed to let Mao stay with them. The three friends help each other deal with the ups and downs of high school romance.

Seiya Kanie, a smart and extremely narcissistic high school student, believes that the beautiful but reserved Isuzu Sento has invited him on a date at an amusement park called Amagi Brilliant Park. Much to his chagrin, not only is the location a run-down facility, the supposed date is merely a recruitment tour where Sento and Princess Latifa Fleuranza, the owner of the theme park, ask him to become the park's new manager. Their cause for desperation? As stipulated in a land-use contract, Amagi has less than three months to meet a quota of 500,000 guests, or the park will be closed for good and the land redeveloped by a greedy real-estate company. Seiya is won over by the revelation that Amagi is no ordinary amusement park; many of its employees are Maple Landers—mysterious magical beings who live in the human world and are nourished by the energy created by people having fun. Entrusted with the hopes and dreams of this far-off enchanted land, Seiya must now use his many skills to bring Amagi back on its feet, or watch it crumble before his eyes.