Two years have passed since the end of the Martian Successor Nadesico. Akito and Yurika have disappeared. The Jovians and the Earthlings have joined forces and Ruri is now captain of Nadesico B. As the popularity of Boson Jumping grows, a vast transportation network has been developed. Dubbed the Hisago Plan, this network of Chulip portals holds the answers to the mysteries behind Bose particles and their power. If those secrets should fall into the wrong hands, it could mean big trouble. And big trouble there is. A Martian splinter group has launched an offensive, leaving the United Forces befuddled and desperate. So much so, in fact, that the former crew of the Nadesico is called back to active duty for a special unsanctioned mission-to save us all. Does this menagerie of misfits have what it takes? Who will win the race for the Boson technology? And what the heck happened to Akito and Yurika?

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.

In a near future, an illness called Cagaster made ​​its appearance. It turns humans into insects. The story begins 30 years after the onset of the illness, in 2125. It follows the adventures of Kidou, a boy who fights insects. (Source: MAL News)

In the immediate aftermath of the mana calamity, Sylphiette finds herself teleported to the heart of the Asura Kingdom: the royal palace. Her sudden appearance accidentally saves the life of second princess Ariel Anemoi Asura, who has her sights set on becoming the ruler of the realm. Witnessing Sylphiette's talent with combat magic firsthand, Ariel recruits her as her bodyguard and right-hand woman, commencing their journey to power—which proves far more treacherous than first imagined.