The film begins with Brandon Teena (Hilary Swank) driving through the night alongside his cousin, Lonny (Matt McGrath), who is an older gay man. As they head to a skating rink, Lonny cautions Brandon to be careful and avoid recklessness. Ignoring this advice, Brandon enters the rink, enchanted by its atmosphere. There, he meets a girl and later shares a kiss outside her home, where he gallantly assures her that he won't leave until she is safely inside.
However, things take a dark turn when Brandon is pursued by a group of young men, including a relative of the girl, who hurl insults and threats at him. Seeking refuge in Lonny's trailer, the audience learns through their conversation that Brandon is actually a girl aspiring to live as a boy. Lonny expresses his concern, asking Brandon to find alternative accommodations. It's evident that Brandon has a complicated past, having faced legal troubles and rejection from his family.
In search of comfort, Brandon frequents a bar, where he flirts with Candace (Alicia Goranson). In a show of bravery, he intervenes when a large man harasses Candace, leading to a brawl where John Lotter (Peter Sarsgaard) steps in to help. This encounter marks a turning point for Brandon, as he suddenly feels he has allies. Brandon eventually relocates to Falls City, Nebraska, where he stays with Candace, who has developed a crush on him.
As Brandon spends time with Lotter, Nissen (Brendan Sexton III), and Candace, he becomes infatuated with Lana Tisdel (Chloë Sevigny), especially after witnessing her sing karaoke. Although initially indifferent, Lana becomes intrigued by Brandon, who is completely smitten. While Brandon enjoys his vibrant new life and friendships, he struggles with unresolved issues back home, including a missed court date as he grapples with the reality of his identity. He carries a court summons revealing his true name: Teena Brandon, and faces a situation that forces him to confront his biological identity.
Amidst these challenges, a humorous yet tense encounter occurs when Brandon steals tampons at a gas station while trying to hide his reality from Lana, with whom he shares an increasingly intimate connection. Lana, growing up in an unstable environment, finds solace in Brandon, who has spun a web of lies about his family to gain acceptance.
The dynamic grows more complex as Lotter exhibits erratic behavior, oscillating between affectionate and harsh towards Brandon, who he sometimes treats as a younger brother. An intense bond develops between Brandon and Lana, culminating in a passionate encounter during a break at Lana's work. However, tension escalates when Brandon’s mounting legal troubles surface, leading him to commit a desperate act: stealing Candace's check to pay off his fines.
Ultimately, Brandon is captured and placed in the women’s section of the Falls City prison, triggering a chain of revelations that devastate the people around him. Candace discovers evidence of Brandon's true identity, leading to heartbreak and confusion as she confides in Lotter and Nissen about her findings. In this whirlwind of emotions, Brandon writes to Lana, insisting he is a hermaphrodite awaiting surgery, prompting Lana’s declaration of love for Brandon irrespective of his identity.
However, the situation spirals into tragedy when Nissen and Lotter, enraged by Brandon's secret, confront him and commit violent acts. Despite Brandon's attempts to escape and seek justice, the outcome is haunting. The film concludes with the heart-wrenching aftermath, as Lana reads a letter from Brandon before he tragically passes away, leaving her to navigate the painful void left in his absence.
