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.

There once existed a planet named Beal, until it was wiped out by the mysterious entity known as Gaizok. The few remaining survivors escaped to Earth and split into three families, named Jin, Kamie, and Kamikita respectively. While attempting to start a new life, the collectively known Jin Family prepared for the inevitable Gaizok invasion on Earth and its giant mechanical beasts known as Mecha Boosts. In order to defend their new home, they have built three vehicles which when combined form the mighty Zambot 3. The Jin Family must not only defend against Gaizok attacks, but also harsh criticisms from the very people they protect, who blame the Jin Family for the invasion in the first place. (Source: AniDB)

Souzou Haran was a brilliant scientist that was conducting research on Mars. He created a form of cyborg life with the ability to think for itself. These cyborgs, dubbed the Meganoids, soon ran out of control and killed Dr. Haran along with his whole family, save his youngest son, the 16-year-old Banjou Haran. Banjou escapes from Mars on a rocket with a solar-powered super robot called Daitarn 3, which was built with the special metals of Mars. Now eighteen years old and living on Earth in a luxurious mansion, Banjou fights against the Meganoids with the aid of his faithful butler Garrison and his two gorgeous companions Reika and Beauty. Together they must stop the evil Meganoids which aspire to turn all humans into cyborgs and thus improve the human race. (Source: AniDB)

The world has been engulfed in a desperate, three-decade-long war against the BETA—an alien species that invaded the planet in 1973. Amid this chaos, a high school student named Takeru Shirogane suddenly wakes up from a terrifying nightmare where he sees mankind in utter defeat. Soon after, he realizes that his dream was nothing more than the recollections of his life in an alternative universe. In those memories, the Alternative V project is implemented, sending hundreds of thousands of people into space as a last resort to preserve humanity, while leaving the remaining billion on Earth to suffer a cruel fate. Yearning to change this grim future, Takeru joins a military base in Yokohama, which happens to be his former high school. There, he manages to convince the base's vice-commander and leader of the Alternative IV project, Professor Yuuko Kouzuki, to prevent Alternative V from happening. To ensure the success of Alternative IV, Takeru must pilot the gigantic humanoid machines Tactical Surface Fighters (TSF) alongside his fellow cadets. However, he has only two months to complete his training and exploit his partial knowledge of the future—lest the ensuing tragedy take place.