The happy-go-lucky Michi Sonoda announces to her teammate, Sanae Takigawa, that she will quit judo for good after her final middle school tournament. This leaves Sanae in disbelief; after all, it was Michi's passion toward the sport that reeled Sanae into judo in the first place. Michi claims that a well-spent youth should be associated with things such as getting a boyfriend rather than sweaty tatami mats. However, Michi's plan to end her fledgling judo career with a bang is spoiled after experiencing an embarrassing defeat at the hands of the talented Towa Hiura. Later, her plan is further derailed when she finds out that Towa has enrolled in the same high school as herself and Sanae. With the sudden appearance of her past foe, Michi may soon realize that she still has lingering feelings for the sport of judo.

The year is AD 2225. Kouji Aiba and Aoi Housen are serving as astronauts in-training in Liebe Delta which is located on the edge of the Geduld Sea. When saboteurs with unknown intents suddenly strike during a routine dive procedure, the space station plummets into the Geduld, a plasma field that links all the planets like a nervous system and crushes any ship that strays too far into it. With all the adults onboard killed, the young astronauts will have to survive this long journey home in midst of the growing tension amongst each other. Meanwhile the organizers of the sabotage look on and prepare to attack once more.

A menace of huge monster-like insects is plaguing the land of Edo. Too powerful to be subdued by ordinary folks, the creatures are hunted by the Insect Magistrates—a group of warriors who specialize in various secret arts and combat styles. To bolster their strength, they summon Genjuurou Tsukishima, the master swordsman from the Tsugaru Province. Due to an unfortunate incident, however, Genjuurou is incapable of answering the call and sends his son, Jinbee, to serve in his stead. Determined to atone for the incident caused by his own cowardice, Jinbee agrees to travel to Edo and join the Insect Magistrates. Armed with his fiery spirit and unwavering resolve, Jinbee vows to become a stronger samurai and rid Edo of the insect threat once and for all.

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?