The inhabitants of a certain wealthy town think nothing of throwing objects away. However, their waste is priceless to Rudo, a resident of the town's slums. Despite the constant warnings from his adoptive father Regto, Rudo spends his days searching for reusable materials that would otherwise be sent to the giant disposal area known as the Pit. Due to its vastness, the Pit doubles as a means of criminal punishment; those dropped in are never to return again. When Regto is murdered by a mysterious assailant, Rudo is falsely accused of the crime and thrown into the Pit. To his surprise, he awakens in a trash-filled area inhabited by enormous monsters formed from the junk. As the toxic air and Trash Beasts push Rudo to the brink of death, he is saved by Enjin, one of the Cleaners who wield weapons known as Vital Instruments to fight the monstrosities. Having gained his own Vital Instrument, Rudo soon joins the Cleaners in the hopes of finding a way to escape the Pit and avenge his father.

Under the capital city of Tokyo, Japan, there exists a large, vast, and unknown world known as Underground. There, people known as Elemental Users exist; people who have the ability to control the elements: Fire, Water, Lightning, Magnetism, Freeze, etc. Meet Rumina Asagi and his best friend Ginnosuke Isuzu, two average high school freshmen who reside in Tokyo. When they meet Gravity User, Chelsea Rorec, and the Miko of Life, Ruri Sarasa, their whole lives change into one big adventure.

A squid-like creature, known as a Happian, leaves his home planet with the desire to spread happiness across the universe. He lands on Earth, but quickly finds himself in danger of captivity by its inhabitants. Fortunately, he is found by an unsmiling little girl named Shizuka Kuze, who feeds him and names him Takopii. Feeling indebted, Takopii decides to do everything in his power to bring a smile to her face. The task is easier said than done, however. Shizuka is bullied by her classmates, she does not have a father, and her mother is never home—though the gravity of these issues flies over the naive Takopii's head. Even so, Shizuka does have one source of happiness: her dog Chappy. The connection Shizuka and Chappy share only increases Takopii's desire to make the girl smile. While Takopii's attempts to lift Shizuka's spirits lead to unintended consequences, he is determined to take things into his own tentacles, test his understanding of human beings, and achieve his goal of spreading happiness.

Though he grew up as an orphan, Nio Chirinu finds a place to belong: being a waiter at his adoptive grandmother's restaurant. But this peace does not last long; Nio and his sister Iroha are used as bait to arrest child abductors by Toshizou Hijikata and Souji Okita—two members of an infamous ronin group called Miburo. After the ordeal, Toshizou proposes that Nio join the ranks of Miburo and protect the people of Kyoto. Frustrated by his own weakness, Nio trains to match the swordsmanship of his new comrades. Even so, he struggles to be accepted by Tarou Tanaka and Hajime Saitou, the other Miburo members of his age. Determined to befriend them, Nio must discover his own sense of justice and become strong enough to prevail against all his enemies.