Samurai Champloo opens in a small town where Fuu, working as a tea waitress, is harassed by the son of the town's corrupt prefect. The outlaw Mugen arrives in town, and Fuu begs him for protection, which he gives in exchange for food. Meanwhile, the ronin Jin, also a new arrival, kills the prefect's bodyguards when they abuse a peasant, ending up in conflict with Mugen when the latter mistakes him for one of the prefect's men. The two's fight ends up destroying the teahouse. The pair are captured and sentenced to death, but Fuu saves them. The pair attempt to restart their battle, but Fuu tosses a coin, saying if it lands on heads then the pair can continue their battle, but if it lands on tails they postpone their battle to help her find a samurai who smells of sunflowers, whom she has sought for years. She wins the toss, and they embark on a series of adventures alongside Fuu's quest.

During the closing stories, the three finally arrive at the town of Ikitsuki, with each ending up in conflict with a group of assassins sent by the government to kill the "sunflower samurai", Fuu's father Seizo Kasumi. Fuu finds Kasumi, having wanted revenge for him abandoning her and her mother, but she relents as he is already dying from an illness. One of the assassins kills Kasumi before he is defeated by Jin. Mugen and Jin then have their duel, their swords shattering, but choose not to kill each other as they now consider each other friends. Fuu learns her father played a part in the Shimabara Rebellion and went away to protect her. Fuu also reveals she lied about the coin toss result, which briefly annoys Mugen and Jin. Recovered from their final fight, the three part ways grateful for their shared adventure.