An unseen evil lurks in the streets of Paris. Unless something is done, the darkness will unleash its destruction and consume all that is good. The City of Love will be lost to her people forever. All hope rests within the hearts of five young ladies. The only problem is, they don't even know it yet. But will an apprenticed nun, a reserved aristocrat, a hardened criminal, a traveling circus emcee and a Japanese girl experiencing loss set aside their unique differences and come together as one for the defense of many. The Paris Fighting Troup is born.

Sakura travels to the capital with aspirations of defending the city from the demonic forces of the Black Sanctum Council like her father before her. However, things are not as she imagined as in addition to using her great spiritual energy to pilot a mech called a Kobu, she must also perform on stage as an actor as The Imperial Flower Division's cover is an art theater. Making a fool of herself and ruining a production gets her on everyone's bad side and somehow she must learn to work with them as well as prevent the enemy from destroying several shrines which protect the city.

New York City, the late 1920s. The battle with Nobunaga is over, the city restored to peace...until the owner of Little Lip Theater informs Shinjiro... "This time, the leading lady will be...you." Thus Shinjiro, disguised as the actress Petitmint, is forced into the role of "Cleopatra." The Star Division members set out to persuade a reluctant Shinjiro, beginning a chase across the five boroughs. Meanwhile, a dark-skinned youth and his servant have appeared unexpectedly in the midst of the flourishing city. His eyes, concealing a silent wrath, are fixed upon nothing less than the Statue of Liberty. Now Shinjiro and company must protect this city of hopes and dreams from a new menace while safely raising the curtain on a new show.

Despite the destruction of the mechanization home world Andromeda, the machine empire is still swept across the galaxy and Earth has become a battleground. Having returned from his journey aboard the train Galaxy Express 999, Tetsurou Hoshino joins the resistance and fights alongside others who have retained their humanity. When the 999 returns to Earth, Tetsurou receives an enigmatic recorded message from his former traveling companion Maetel, telling him to board the train once more. Fighting his way to Megalopolis station, he makes it onto the train just as it departs. This time, however, Tetsurou is met with several mysteries: Maetel is nowhere to be seen, an ominous "Ghost Train" has appeared, and the ultimate destination of the 999 is unknown. Amid all this, Tetsurou finds himself confronted by the mysterious black knight Faust and soon discovers the machine empire's darkest secret.