2199 AD. Yamato tried to leave behind the Large Magellanic Cloud galaxy, after receiving a "Cosmo Reverse System" at its destination, Iscandar. However, suddenly, it encounters a mysterious group at the edge of the Large Magellanic Cloud. The crew finds out that the group is called the "Gatlantis," and that its leader is the Gutaba expeditionary force commander who calls himself "Goran Dagaamu of Thunder." The commander demands that Yamato be handed over to him. Yamato, wanting to hurry to Earth, escapes the fray. However, Yamato is attacked by a devastating beam weapon called the "Flame Direct Attack Cannon" that can transcend space. Yamato was able to retreat, but ends up getting lost, and finds itself in a strangely colored irregular dimension. The crew decides to turn off the engine on the ship, and explore a mysterious planet. In order to collect information, Kodai, Kiryū, Sawamura, Niimi, and Aihara land on the planet. What they saw when they arrived was a ship that was not supposed to be there. Dagaamu chases after the traces of Yamato's warp, and also reaches the strangely colored space. The planet on which Yamato landed was in fact what Dagaamu had been looking for all along.

Beautiful sisters Ai, Mai, Mii, their android maid Mea and slippery pet ferret Unagi make an amazing journey together through time and space without ever leaving their beloved mansion behind! Following the clues of the strange dandelion-like "Popotan," the girls are theoretically seeking the person who has the answers to their most personal questions, but they seem to have more than enough time to take side trips, meet new friends, visit hot springs and occasionally operate the X-mas shop they keep in the house along the way! Yet, the girls' ultimate destiny holds more than a few surprises of its own, and not every moment is filled with hilarity, as moving through time means having to leave friends behind as well.

Kouichi Sanada and Kazuki Aihara's childhood friend Mao Mizusawa has returned after living in France for a couple of years. Kouichi is surprised to learn that, since her parents are remaining overseas for the time being, his mother has agreed to let Mao stay with them. The three friends help each other deal with the ups and downs of high school romance.

Years of political tension and mistrust between the two rival nations of Zafran and Revillia escalate to the point of war. Each nations solution: to gain possession of Decimators, the same ancient robots of war that nearly ended all life on the planet 200 years before. As the war ensues and the leaders of both nations become reluctant to surrender, only the desperate plan of Lean, a young cadet, and Nataruma, a psychically gifted young woman, to alter the timeline of events 200 years before stands the chance between humanity's survival or absolute destruction.