Dolls takes puppeteering as its overriding motif, which relates thematically to the action provided by the live characters. Chief among those tales is the story of Matsumoto and Sawako, a young couple whose relationship is about to be broken apart by the former's parents, who have insisted their son take part in an arranged marriage to his boss' daughter.

When the mobster Iwaida Nishikawi is executed by the hit man Takeshi, his family chases the killer. Takeshi's brothers Takashi and Hideshi Miwa try to find Takeshi, who is hidden with the nurse Rie Ishibashi, to protect him and Hideshi discovers that Takeshi was secretly sent by their Yakuza boss to eliminate Iwaida. Meanwhile, the mobster Kenmoshi abducts Takashi's wife Mariko and rapes her, trying to force Takashi to deliver his brother to him.

A Japanese Yakuza gangster's deadly existence in his homeland gets him exiled to Los Angeles, where he is taken in by his little brother and his brother's gang.

Focusing on the search for Sayaka, a young girl whose mother has recently died. Sayaka’s father, an undercover F.B.I. agent, has had a rough relationship with his daughter since the death of her mother and feels that her kidnapping by the evil Neo-Guild is his fault. Sayaka has been angry at her father because he was away in America while her mother died, leaving her feeling abandoned. Aiding Sayaka's father in the search is Tokusou Robo Janperson! The two don’t get along at first, but things between them go smoother as they continue the search.