Weetzie Bat is a young woman living in a magical version of 1980s Los Angeles. Obsessed with the glamour of 1950s Hollywood, Weetzie dresses the part. She’s thrilled to meet a classmate, Dirk, who shares her style and love of the time period. The inseparable pair often hangs out with Dirk’s congenial grandmother, Fifi.
When Dirk admits he’s gay, Weetzie is unfazed and says they will help each other find true love. Fifi gives Weetzie a magic lamp with a genie inside who offers her three wishes. Weetzie asks for a “duck” (a perfect boyfriend) for Dirk and a true love for herself whom she calls “My Secret Agent Lover Man.” Finally, she requests a beautiful house in which they can all live happily ever after.
Her wishes begin to come true. Fifi dies and leaves her house to Weetzie and Dirk. Dirk meets a surfer named Duck, who moves in with them. A man flirts with Weetzie at the diner where she works and says he wants to put her in his movie. She balks, until he says his name is My Secret Agent Lover Man. Yes, it’s a weird name, he admits. But Weetzie knows her wish has come true.
My Secret Agent Lover Man moves in with the others. The four go out on the town and make several films together and seem to have their happily ever after. Then Weetzie realizes she wants a baby.
My Secret Agent Lover Man argues there is too much pain in the world to have a child. When Weetzie can’t convince him to impregnate her, Duck and Dirk offer their services. One night, when My Secret Agent Lover Man is out of town, Weetzie, Duck and Dirk get drunk and all have sex together, so they won’t know who has fathered the child. When Weetzie gets pregnant and admits everything, My Secret Agent Lover Man packs his bags and leaves.
Weetzie is heartbroken. Dirk and Duck support their friend and are thrilled when their little girl, Cherokee, is born. Shortly after her birth, My Secret Agent Lover Man returns. He says the baby is perfect, and Weetzie says Cherokee has features of each of the three men she loves. My Secret Agent Lover Man moves back in, and everyone is happy again.
A mysterious woman comes to see My Secret Agent Lover Man. He admits to Weetzie he used drugs and alcohol to help him forget her when he left. He slept with a woman at a party who now claims to be carrying his child. The woman is a witch who has put a voodoo spell on him to make him sick. She says she’ll do the same to Weetzie if My Secret Agent Lover Man doesn’t give her money for an abortion. They pay her off, but she leaves a baby on their doorstep months later anyway. They decide to keep the child and call her Witch Baby.
Weetzie’s dad dies of a drug overdose. Then Duck learns one of his friends is very sick (presumably with AIDS). Duck runs away, leaving a note that says he doesn’t want to kill Dirk just by loving him too much. Dirk hunts for him for days and finally convinces him to come home.
As Weetzie enjoys time with her patchwork family, she contemplates that people can live in fear or in love. Happiness may not be ever after, but she chooses happiness anyway.