Mitsuha Yamano could not have had it worse. After failing to enter her university of choice and losing her entire family in an accident, she finds herself plummeting off a cliff due to an especially fragile guardrail. Through what seems to be the only bit of the fortune left in her life, Mitsuha's firm unwillingness to die allows her to be transported to another world, where she ends up surviving. In this foreign land, Mitsuha wanders around for days before collapsing from exhaustion and being rescued by a little girl named Colette. Not long after, she finds herself in yet another life-threatening situation, and her indomitable will shines once more, granting her an audience with a divine cosmic being. The entity reveals to Mitsuha that she has acquired not only superhuman regeneration but also the ability to transport between worlds at will. Armed with this new information, Mitsuha brainstorms ways to utilize her newfound power to its full potential. Realizing that she can take goods from Earth and resell them to the other world at a higher price, she resolves to save up eighty thousand gold coins to be able to retire comfortably.

In the year 1999, humanity begins to advance beyond the solar system. The planet Gishin, led by the Emperor Zule, which aims to conquer the galaxy, runs into conflict with Earth. He targets Earth for elimination and to do this, he sends a baby called Mars to live among humanity. Accompanying the baby is a giant robot named Gaia, which utilizes a new power source strong enough to destroy an entire planet. As planned, Mars is expected to grow up, where he will activate the bomb within Gaia to fulfill the mission of destroying the Earth. However, when Mars arrives on Earth his is adopted into a Japanese family and given the name Takeru. Seventeen years later, Takeru would grow up with a love for humanity and refuses to detonate the bomb as ordered by Zule. However, if Takeru was to die, the bomb within Gaia would explode destroying the earth. Takeru possesses psychic powers ( ESP ) and decides to join the Earth defense forces and becomes a member of the Crasher Squad (an elite space defense force) where he and his friends take a last stand against the Gishin's attack. The relationship of Takeru with his brother Maag, which fate would have it, pitted the two against each other in the war. Unknown to the Gishin five other robots were created in secrecy along side Gaia by Takeru's father and sent with Gaia to protect Takeru. Whenever Earth is in danger, Takeru is able to summon the five other robots to combine with Gaia form the giant robot Godmars. The five other robots are Sphinx, Uranus, Titan, Shin and Ra.

Two mad scientists, Professor Hiiragi and Count Collection, simultaneously manage to open a dream hole to an alternate world where myths are real, the Sixgate world. Professor Hiiragi recruits his daughter Rokuna and her friend Mondo to be the Mon Colle Knights and help him in obtaining six magical items before Count Collection does. These items which can alter the barriers of dimensions when combined, allowing them to be used to either peacefully have the magic of the Sixgate world cross over in the human world, take over the minds of all monsters, or worse, reformat reality. While this entry only has details based on the Japanese version, it also includes the version aired on Jetix.

As the story of Rozen Maiden closes, a new chapter begins in Rozen Maiden: Träumend. Shinku and the other sentient dolls of the Rozen Maiden collection are living life as usual at Jun Sakurada's house. Having settled into his role as Shinku's partner in the deadly Alice Game, Jun overcomes his former fears and prepares to return to school. And although Shinku and the other dolls idly pass the days by in the comfort of Jun's home, dark times lie ahead as a new foe presents herself: Barasuishou, the seventh Rozen Maiden. But Barasuishou is a mystery even to her sisters, none of whom have ever laid eyes on her until now. Shinku considers this a sign that the Alice Game is coming to an end, meaning the dolls will soon be forced to fight one another. Haunted by the upcoming battle and nightmares concerning another doll, Shinku begins distancing herself from the others. If she wishes to claim victory, it will come at a high cost—the lives of her sisters.