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The story takes place in Edo (known today as Tokyo because of the name change in 1868), Japan, which has been taken over by aliens called Amanto since the late Edo period. The samurai of Japan have fallen, and the Amanto placed a ban on carrying swords in public. The story focuses on an eccentric samurai, Gintoki Sakata, his (partial) apprentice Shinpachi Shimura, and a teenage alien girl: Kagura. All three are "free-lancers" who search for work in order to pay the monthly rent, which usually goes unpaid anyway.

Gintoki Sakata is the main character of the story. He has naturally permed hair, which he blames for his lacking love-life. He rides a motor scooter and wields a bokuto, which has "Lake Toya" inscribed onto it. His job, as is written on his business card, is a "free-lancer", meaning he'll take any job for nearly any price. He enjoys reading Shonen Jump comics and he has a sweet tooth and will go into crazed combat if he does not have his sweets (he has glycosuria). In the past, he was a Joi, known as Shiroyasha, or the white demon (someone who attempted to overthrow Amanto to protect the government). The reason Gintoki does not join Kotaro Katsura again to fight the aliens is that he does not like to fight alongside "gloomy terrorists".

Shinpachi works under Gintoki to learn the ways of the samurai. However, it seems more like he is just trying to help Gintoki pay the rent than to learn. Shinpachi is the captain of the "Otsu Imperial Guard," a pop-singer's fan club. Shinpachi first met Gintoki after he was tripped by an alien ambassador. Gintoki beats up the ambassador and his guards to get revenge for his spilled parfait. Soon after, Gintoki framed Shinpachi for the crime, which somehow led to him saving Shimura Tae (Otae), Shinpachi's sister, from being added to a brothel.

Kagura is an alien from the "Yato Clan," one of the strongest races in existence. Despite her alien heritage, she looks like a normal human and talks with a Chinese accent. She can stop Gintoki's motor scooter single-handedly and has an umbrella that is bullet-proof and can fire bullets from the tip. Her stomach knows no bounds and she apparently loves to eat sukonbu. She originally came to Earth to earn money to help her parents' financial situation. Because of her immense strength, she took to fighting for a gang. After she was told to kill a few people, she tried to escape from the gang and was almost run over by Gintoki's motor scooter. He liberated her, and she forced him to let her join his free-lancer business. She sleeps in the closet of Gintoki's home. Kagura has a giant dog-like creature called Sadaharu as a pet, which she had found. Sadaharu has a habit of often biting most characters, with the exception of Kagura.