Based on the game by Age, sequel to MuvLuv Unlimited, taking place in an alternate universe where the Earth is invaded by aliens. In Alternative, Takeru wakes up three years after the end of Unlimited to find himself back in his room. Although he first thinks that everything that had happened to him was a dream, he soon feels that something is wrong, and leaves the house to find that he has been sent back in time to the beginning of the events in Unlimited. Unwilling to accept something like Alternative V, he decides to help professor Kouduki to complete Alternative IV and save mankind.

One day Shirogane Takeru wakes up late, wondering why Sumika or Meiya didn't wake him up that morning. Not seeing any signs of them he gets a bit worried, and goes out of his house only to see the town he lived all his life in ruins, and that, to his joy, there are real life giant robots. After getting past the initial shock he convinces himself that it must be a dream and decides to enjoy it as much as he can. Takeru, still skeptical about his situation, decides to join the military in order to pilot a mech. Soon he finds out the terrible truth behind the reason the world is in ruins, and meets people that look exactly like his friends from his original world.

Total Eclipse is set in the same world as MuvLuv Alternative, at Alaska's Yukon base, test site 18, where first-class staff from all over the world regardless of country gather to work on new Tactical Surface Fighters (TSFs). The main characters are engineers and pilots and it features many TSFs that failed to show up in Alternative.