The story is set on Okinawa's isolated island of Iwado, which has seen a growing movement advocating a return to an autonomous government. Ao Fukai, a 12-year-old boy with a missing father, lives on the island with an old doctor named Toshio and is about to enter middle school. Ao's mother was taken away a decade ago by unknown individuals. Naru Arata, Ao's 12-year-old childhood friend and the story's heroine, lives with her father, older sister, and grandmother. She has a Yuta power awakened within her due to an incident when she was young. A mysterious entity called Secret suddenly appears and launches an attack on the Scub Coral lifeform on the island. Ao launches a certain military FP called Nirvash aboard a Japanese military transport in his fervent desire to protect the island. (Source: FUNimation)

The second movie of Sora no Otoshimono that concludes the anime series.

In 1973, following the ruthless six-year-long Lunar War, the hostile alien species known as the BETA—Beings of Extra Terrestrial origin which are Adversary of the human race—invaded Earth, killing billions and decimating Eurasia. While BETA can be destroyed with conventional weapons, their laser-class is able to wipe out entire aircraft fleets, forcing mankind to develop giant combat suits called Tactical Surface Fighters (TSF) to combat them. When the BETA reach Japan in 1998, military school student and TSF pilot—or eishi—Yui Takamura is ordered to defend Kyoto's last line of defense with her fellow classmates. At the cost of countless human lives and the sacrifice of Yui's friends, the Japanese Imperial Army manages to repel the invaders, leaving destruction in its wake. However, this encounter leaves Yui determined to never again allow something like this to occur. Three years later, now a lieutenant, Yui joins the XFJ project, an Alaska-based Japan-American TSF development program. In an international team composed of the uncooperative Japanese-American test pilot Yuuya Bridges and various eishi from countries lost to the BETA, Yui's task is to help develop the new Japanese TSF Shiranui. Amidst political tensions inherited from the Cold War, Muv-Luv Alternative: Total Eclipse follows Yui's delicate mission and Yuuya's journey to overcome the demons of the past that still haunt him.

Cool-headed and rational, Koujirou Shindou is a government official and master negotiator with a well-earned reputation. While departing on a business trip, a giant cube materializes and his plane is taken undamaged into the mysterious, indestructible structure. As Japanese authorities attempt to identify the cube's properties and origins, Shindou encounters an otherworldly entity known as Yaha-kui zaShunina, who materializes in the form of a human man. He assures Shindou that the passengers are not in any danger and requests help in negotiations with the human world. Hailing from a higher dimensional universe known as Novo, Yaha-kui zaShunina is able to transfer information between Novo and Shindou's universe through a cube called Kado. Despite having these unfathomable abilities, he does not appear hostile. Instead, he announces that he has come to this world with only one intention: to advance humanity—starting with Japan.