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.

Now in 2001, with the nations of Eurasia having fallen to the BETA, their survivors race to develop a new tactical surface fighter at a base in Alaska. Yuuya, an ace pilot with a bad attitude, is reassigned from the US army to the joint US/Japan TSF development project. There, he meets the imperial soldier Yui. They start off as constantly bickering enemies, but gradually begin to develop a relationship of trust... 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.