Brandon Teena is a young trans man whose birth name was Teena Renae Brandon. When Brandon is discovered to be transgender by a former girlfriend’s brother, he receives death threats. Soon after, he is involved in a bar fight and is evicted from his cousin’s trailer. Brandon moves to Falls City, Nebraska, where he befriends ex-convicts John Lotter and Tom Nissen, and their friends Candace and Lana Tisdel. Brandon becomes romantically involved with Lana, who is initially unaware both of his actual anatomy and his troubled past. The two make plans to move to Memphis, where Brandon will manage Lana’s karaoke singing career. Eventually, during a date night which ends with them having sex, Lana discovers that Brandon is trans, but continues to be intimate with him.
The police detain Brandon on charges that arose prior to his relocation; they place him in the women’s section of the Falls City prison. Lana bails Brandon out and asks why he was placed in a women’s prison. Brandon attempts to lie to her, saying he was born intersex (in the movie said “hermaphrodite”) and will soon receive genital reconstruction surgery, but Lana stops him, declaring her love for Brandon regardless of his gender. However, while Brandon is in prison, Candace finds a number of documents listing Brandon’s birth name, Teena Brandon, and she and her friends react to this news with shock and disgust. They enter Brandon’s room, search among Brandon’s things, and discover some transgender literature that confirms their suspicions. Tom and John violently confront Brandon, forcing him to remove his pants and reveal his genitals. They try to make Lana look, but she shields her eyes and turns away. After this confrontation, Tom and John drag Brandon into John’s car and drive to an isolated location, where they brutally beat and gang rape him. Afterwards, they take Brandon to Tom’s house. Though injured, Brandon escapes through a bathroom window. Although his assailants threaten Brandon and warn him not to report the attack to the police, Lana persuades him to do so. However, the police chief proves to be less concerned with the crime than with Brandon’s ‘sexual identity crisis’.
Later, John and Tom get drunk and decide to kill Brandon. Lana attempts to stop them, but the pair drive to Candace’s remote house where they find Brandon, who has been hiding in a nearby shed. John shoots Brandon under the chin, killing him instantly. Tom shoots Candace in the head as Lana fights with them, begging them to stop. Tom stabs Brandon’s lifeless body and tries to shoot Lana but John stops him. John and Tom flee the scene while a crying Lana lies with Brandon’s body. The next morning, Lana awakens next to Brandon’s corpse. Her mother arrives and takes her away from the scene. As Lana leaves Falls City, a letter Brandon wrote to her is heard in a voiceover.