The Abyss—a gaping chasm stretching down into the depths of the earth, filled with mysterious creatures and relics from a time long past. How did it come to be? What lies at the bottom? Countless brave individuals, known as Divers, have sought to solve these mysteries of the Abyss, fearlessly descending into its darkest realms. The best and bravest of the Divers, the White Whistles, are hailed as legends by those who remain on the surface. Riko, daughter of the missing White Whistle Lyza the Annihilator, aspires to become like her mother and explore the furthest reaches of the Abyss. However, just a novice Red Whistle herself, she is only permitted to roam its most upper layer. Even so, Riko has a chance encounter with a mysterious robot with the appearance of an ordinary young boy. She comes to name him Reg, and he has no recollection of the events preceding his discovery. Certain that the technology to create Reg must come from deep within the Abyss, the two decide to venture forth into the chasm to recover his memories and see the bottom of the great pit with their own eyes. However, they know not of the harsh reality that is the true existence of the Abyss. [Written by MAL Rewrite]

Despite their differences in position, three men—the youngest senior executive of the Port Mafia, Osamu Dazai; the lowest ranking member, Sakunosuke Oda; and the intelligence agent, Angou Sakaguchi—gather at the Lupin Bar at the end of the day to relax and take delight in the company of friends. However, one night, Ango disappears. A photograph taken at the bar is all that is left of the three together. Fast forward to the present, and Dazai is now a member of the Armed Detective Agency. The Guild, an American gifted organization, has entered the fray and is intent on taking the Agency's work permit. They must now divide their attention between the two groups, the Guild and the Port Mafia, who oppose their very existence. [Written by MAL Rewrite]

Sweet and naïve Hanato Kobato came to Earth on a mission to collect and fill a bottle with "konpeito," which appear after healing a person's heart that is suffering. Kobato collects these because it is her wish to go to a certain place. Despite her strangeness, Kobato turns out to be well-suited for this mission as her heartfelt sincerity in helping others earns her the love and admiration of everyone she meets. However, she is not allowed to fall in love with anyone whose heart she heals. [Written by MAL Rewrite]

In the distant future, humanity has found a way to live forever by purchasing mechanical bodies, but this way to immortality is extraordinarily expensive. An impoverished boy, Tetsurou Hoshino, desires to purchase a pass on the Galaxy Express 999—a train that travels throughout the universe—because it is said that at the end of the line, those aboard can obtain a mechanical body for free. When Tetsurou's mother is gunned down by the villainous machine-man hybrid Count Mecha, however, all seems lost. Tetsurou is then saved from certain death by the mysterious Maetel, a tall woman with blonde hair and a striking resemblance to his mother. She gives him a pass to the Galaxy Express under one condition: that they travel together. Thus, Tetsurou begins his journey across the universe to many unique planets and thrilling adventures, in hopes of being able to attain that which he most desires. [Written by MAL Rewrite]