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.

Kenshi Masaki has been kidnapped and brought to the world of Geminar by a mysterious group. To get back home, he agrees to help them assassinate the newly crowned empress of the Shtrayu Empire, Lashara Aasu XXVIII, using a giant robot called a Sacred Mechanoid. As her army fights them off, Lashara takes note of Kenshi's abilities and demands that her attacker be captured alive, only to find out that the pilot is male which is extremely rare on Geminar. Believing it to be a waste to kill him, she makes Kenshi her attendant. As the empress' new servant, Kenshi is required to accompany Lashara to the Holy Land, an academy where Sacred Mechanoid pilots hone their skills. His arrival attracts attention, but Kenshi is unaware that something sinister is brewing within the academy and it could plunge the entire world into war.

The streets of Treasure Town are said to belong to The Cats. They know everything that goes on in the city, and no one can stir up trouble without going through them first. In reality, The Cats are a pair of orphan boys called Black and White, who aren’t afraid of anything or anyone. But their rule of the streets is challenged when the Yakuza come to town and start making changes. The wild Black and the carefree White have no one to rely on but themselves to get their Treasure Town back to the way it was. But their bond is tested as they quickly realize going back to how things were may no longer be an option.

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.