Tetsurou Hoshino is a boy bent on obtaining an immortal mechanical body in order to take revenge against his mother's murderer, the machine man Count Mecha. However, due to the incredible cost of obtaining what he seeks, his only hope is to steal a boarding pass for the Galaxy Express 999, a space train that travels across the galaxy and whose final stop is a planet where the metal replacements are provided for free. After swiping a pass, Tetsurou is pursued by the police and ends up collapsing into the arms of a mysterious woman named Maetel, who closely resembles his mother. Once he awakens, she tells the boy that she will provide him entry onto the 999 as long as he agrees to travel with her. Accepting her proposition, Tetsurou boards the cosmic railway with Maetel and begins a journey across the galaxy.

[Written by MAL Rewrite]

For centuries, a god named Celestin has been imprisoned on the moon for betraying the kingdom of Yggdrasil. Released by the fairy Morgan Le Fey, Celestin travels to Earth to reunite with his former pupil, the goddess Belldandy. Things go awry as Celestin erases Belldandy's memories of her boyfriend Keiichi and uses her as a catalyst to wreak havoc on Earth and Yggdrasil.

Hiroki Fujisawa and Takuya Shirakawa harbor admiration for two things in their life: their classmate Sayuri Sawatari and the vast Ezo Tower that stands boundlessly across the Tsugaru Strait. Fascinated by the limitless structure beyond their reach, Hiroki and Takuya begin constructing an aeroplane from a fallen drone they discovered—naming it the Bella Ciela—to fulfill their dream of one day reaching the sky-scraping top of the tower. Later joined by the girl they love, Hiroki and Takuya promise Sayuri to fly with her to the seemingly otherworldly top together. However, Japan has suffered a North-South partitioning that has fueled conflict near the base of the tower, which marks the border between the America-controlled Southern islands and the Northern lands occupied by the Soviet Union.

Further along, Sayuri suddenly disappears, and Hiroki and Takuya never see her again. Unbeknownst to them, she fell victim to a sleeping disorder that left her comatose for the past three years. Although Hiroki and Takuya later learn about Sayuri's condition, they also discover that the girl's unconscious state is oddly linked to the same tower the trio had promised to conquer together.

[Written by MAL Rewrite]

In desperation, Edward Elric sacrificed his body and soul to rescue his brother Alphonse, and is now displaced in the heart of Munich, Germany. He struggles to adapt to a world completely foreign to him in the wake of the economic crisis that followed the end of World War I. Isolated and unable to return home with his alchemy skills, Edward continues to research other methods of escaping the prison alongside colleagues who bear striking resemblances to many of the people he left behind. As dissent brews among the German citizenry, its neighbors also feel the unrest of the humiliated nation. Meanwhile, Alphonse continues to investigate Edward's disappearance, delving into the science of alchemy in the hopes of finally reuniting with his older brother. [Written by MAL Rewrite]