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The plot of Samurai Champloo largely revolves around Fuu's quest to find the samurai who smells of sunflowers and the unfinished duel between Mugen and Jin. Mugen meets Fuu when he enters a tea house where she is a waitress and offers to take care of some ruffians in exchange for food. Fuu agrees, but Mugen characteristically overreacts and the scene erupts into a brawl. As the situation progresses, he and Jin end up in a duel that remains unfinished as they literally bring the tea house down on themselves and are arrested and sentenced to death.

Fuu recruits the two to help her in a quest to find the Sunflower Samurai in exchange for helping them escape from prison. Mugen and Jin, however, are intent on completing their duel first. Fuu gets them to agree to a coin flip: heads, they continue their duel; tails, they travel with her and put their duel on hold until the journey is over. Mugen flips the coin and Fuu tells them it is tails: Mugen and Jin are thus obligated to hold off on their duel and journey with her. At various times, however, they try to abandon Fuu, and they also intermittently confront one another each vowing to kill the other by journey's end.

Throughout the journey the trio are often broke and starving. They are also forced to face many elements of their pasts. In the two-part "Misguided Miscreants" (a.k.a. "Dark Night's Road"), Mugen encounters his old pirate gang and becomes involved in a looting scheme with his old partner Mukuro. The situation quickly turns into a backstabbing contest resulting in much bloodshed. It is revealed that Jin killed his master, Mariya Enshirou, and in a number of episodes ("The Art of Altercation"; "Lullabies of the Lost") he is pursued by students of his former dojo who wish to exact revenge. Jin is reluctant to kill these pursuers.

In the final three-episode arc, "Evanescent Encounter" (a.k.a. "Circle of Transmigration"), all three must confront their unresolved pasts. Fuu finally meets and confronts the Sunflower Samurai. Jin is challenged by a master swordsman, named Kariya Kagetoki, who is revealed as the primary antagonist of the series, although he has remained behind the scenes until this story arc. It is revealed that Kariya attempted to gain control of Jin's dojo and train its adepts for the purposes of assassination. Mariya Enshirou was ordered to kill Jin because of his opposition to the plan, and in the ensuing fight Jin killed his master in self-defense and was forced to flee the dojo. It also turns out that Kariya had the group tracked so that he could find and kill the Sunflower Samurai, Kasumi Seizou, as punishment for his role in the Shimabara Rebellion. In the course of the story, Mugen is also forced to confront three brothers seeking revenge because Mugen crippled one of them during his days of piracy. (Source: Wikipedia)

- Mugen: A brash vagabond from the Ryukyu Islands, Mugen is a wandering sword for hire with a wildly unconventional fighting style that resembles breakdancing and capoeira. Approximately 19 years of age. He wears metal-soled geta and carries a katana on his back, although, historically, the Tokugawa government prohibited unsanctioned men from carrying daishor any of its components. In Japanese, the word "mugen" means "infinite" or "endless."

- Jin: Jin is a mild-mannered ronin who carries himself in the conventionally stoic manner of a samurai of the Tokugawa era. Approximately 20 years of age. Using his waist-strung daishhe fights in the traditional kenjutsu style of a samurai trained in a prominent, sanctioned dojo. Jin wears glasses, an available but uncommon accessory in Edo era Japan. Spectacles -- called "Dutch glass merchandise" ("Oranda gyoku shinajina" in Japanese) at the time -- were imported from Holland early in the Tokugawa period and became more widely available as the 17th century progressed.

- Fuu: A young, somewhat ditzy girl of approximately 15 years of age, Fuu recruits Mugen and Jin to help her find a sparsely-described man she calls "the samurai who smells of sunflowers." Fuu seems to disapprove of the size of her breasts, which she displays after seeing the breasts of Sakonshougen Nagamitsu's wife. A flying squirrel named "Momo" (meaning "peach" in Japanese and also short for "momonga," meaning "flying squirrel") accompanies her along the way, inhabiting her kimono and frequently leaping out to her rescue when she encounters trouble. She is often hired as a prostitute in the TV series.