The BETA, an alien race who had waged a brutal war on the Moon in 1973, invaded Earth and left billions dead, with the Eurasian continent in ruins. Conventional weapons were ineffective against their laser-class weaponry, resulting in humanity creating giant fighting suits called Tactical Surface Fighters (TSF) to combat the BETA. In 1998, Yui Takamura, a TSF pilot and military school student, was called upon to defend Kyoto's final line of defense against the alien invasion. Despite the loss of many lives, Yui and her classmates successfully repelled the threat, but Yui was left with a desire to prevent such devastation from occurring again. Three years later, Yui was promoted to lieutenant and tasked with working alongside Japanese-American test pilot, Yuuya Bridges, to develop the new Japanese TSF, the Shiranui, in Alaska. Yui faced political tensions from the Cold War, while also working with eishi from countries who had faced defeat against the BETA. In Muv-Luv Alternative: Total Eclipse, the story follows Yui on her delicate mission and Yuuya's journey to confront his troubled past.