In 1973, in the wake of the brutal six-year Lunar War, Earth was invaded by the hostile alien race known as the BETA—Beings of Extra Terrestrial origin which are Adversary of the human race. They killed billions and devastated Eurasia. Although BETA can be destroyed by conventional weapons, their laser-class units are capable of wiping out entire aircraft fleets, compelling humanity to develop giant combat suits called Tactical Surface Fighters (TSF) to fight them. When the BETA reached Japan in 1998, Yui Takamura, a military school student and TSF pilot—or eishi—was ordered to defend Kyoto's last line of defense alongside her classmates. At the cost of countless human lives and the sacrifice of Yui's friends, the Japanese Imperial Army managed to repel the invaders, leaving destruction in its wake. However, this encounter left Yui determined to never again allow something like this to occur. Three years later, now a lieutenant, Yui joins the XFJ project, a Japan-American TSF development program based in Alaska. 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.