Tenchi runs off into the woods to spend some time alone after his friends have another argument. While lost in thought, he hears a voice coming from a camellia tree. Tenchi approaches it and vanishes through a portal. Six months later, Tenchi still has not returned home. Though most have given up the idea of ever finding him, his friends refuse to lose hope and have split up into two teams. Aeka and Ryoukou remain on Earth to investigate while Washuu, Sasami, Kiyone, and Mihoshi comb the rest of the galaxy in search. Their efforts eventually pay off when Tenchi's energy is picked up on their radar. However, the happy reunion will have to wait as the girls gear up for their biggest challenge yet—Tenchi seems to have completely forgotten them and is living happily with another woman. Instead of solving their problems, finding Tenchi has left them with even more questions.

Tenchi Masaki gets the surprise of his life when a teenage girl approaches him and calls him "Daddy." Believing that the girl is mistaking him for someone else, Tenchi brings her home to figure out what is going on, which turns out to be a big mistake. When the girl introduces herself as Mayuka Masaki, Tenchi's daughter, the Masaki household is thrown into yet another frenzy. Thinking that Mayuka is just taking advantage of Tenchi, the girls refuse to believe that she is really his child. However, when DNA testing reveals that Tenchi is indeed her father, Washuu comes to the conclusion that Mayuka is his daughter from the future, the result of a recent time distortion. With this new revelation, everyone tries to welcome Mayuka into their lives with the sole exception being Ryouko Hakubi, who senses something sinister lurking beneath Mayuka's charm.

Sakura Nankyoku is a total otaku. Due to a fluke, she gets elected as her class' Student Council President. Everything takes off from there into a series of crazy misadventures revolving around Sakura, her family, and her classmates. (Source: ANN)

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.