Bokutou Precinct rarely deals with criminals more nefarious than speeding sportscar drivers. So when Officers Nikaido Yoriko and Aoi Futaba find a cache of illegal firearms in a stolen car, and a rash of traffic control malfunctions snarls traffic along Tokyo's streets, it is up to Tokyo's finest to figure out what's gone wrong. And of course, it'll take the talents of Kobayakawa Miyuki and Tsujimoto Natsumi to crack the case. But will Miyuki's trusty Mini-Pat and Natsumi's fierce determination be enough to stop a devious mastermind from exploiting the weaknesses of the system and crippling Tokyo—and the world—for good?

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.

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 a dark corner of the universe, intergalactic criminal Kain breaks out of prison and destroys the Galaxy Police Headquarters. Basking in the afterglow of the terror and destruction he has caused, Kain sets his sights toward a much bigger prize waiting on Earth. Meanwhile, Tenchi Masaki and his crew are watching some old home videos of his mother, Achika. As the film rolls, Achika slowly starts to vanish. While watching her fade away, Tenchi also begins to disappear. However, thanks to a device created by Washuu Hakubi, Tenchi is not gone for good. The gang soon learns about Kain and deduce that he must have done something to Achika, which has resulted in time being altered. To save himself and maintain the future, Tenchi travels with the girls back in time to protect his mother from her fate.