The film stars Zaide Silvia Gutiérrez and David Villalpando, in their first film roles, as two indigenous youths who flee Guatemala in the early 1980s due to ethnic and political persecution. They head north and travel through Mexico to the United States, arriving in Los Angeles, California, after an arduous journey.
The writing team of Nava and Thomas split the story into three parts:
Arturo Xuncax: The first part takes place in a small rural Guatemalan village and introduces the Xuncax family, a group of indigenous Mayans. Arturo is a coffee picker and his wife a homemaker. Arturo explains to his son, Enrique, his world view and how the indio fares in Guatemalan life, noting that \"to the rich, the peasant is just a pair of strong arms.\" Because of his attempts to form a labor union among the workers, Arturo and the other organizers are murdered when a co-worker is bribed to betray them — Arturo\'s severed head is seen hanging from a tree — and the children\'s mother is \"disappeared\" or abducted by soldiers. So, the two decide to flee Guatemala, the land of their birth, and head north.
Coyote: During the second part of the film the two teenagers flee Guatemala, travel through Mexico, and meet a Mexican coyote who guides them across the border. This section includes various comic scenes relating to mutual stereotyping among different ethnic groups; the two attempt to pass themselves off as indigenous Mexicans, failing to convince one Mexican truck driver after naming the wrong destination, but later succeeding in convincing a Border Patrol officer by copiously peppering their responses with the Mexican word for \"fuck,\" which a neighbor had suggested was how all Mexicans speak. After their first failed attempt to cross the \"frontera\" they have a horrific experience when they finally cross the U.S.-Mexican border through a sewer pipe and run into rats; critic Roger Ebert noted:
The scene is horrifying, not least because it\'s pretty clear these are real rats. Disease-free rats purchased from a laboratory, yes, but real rats all the same, and although Gutierrez was phobic about rats, she insisted on doing her own scenes, and her panic is real.
El Norte: In the final part of the film Rosa and Enrique discover the difficulties of living in the U.S. without official documentation. The brother and sister team find work and a place to live and initially feel good about their decision. However, Rosa nearly is caught up in an immigration raid and must find a new job. Enrique uses a day laborer pool to obtain a job as a busboy and, as his English classes begin to improve his command of the language, he is promoted to a position as a waiter and is approached by a businesswoman who has a better-paying job for him in Chicago, which he initially declines; he too encounters problems when a jealous U.S.-born coworker reports him to immigration, causing him to flee the restaurant and seek out the businesswoman.
He decides to take the position, but when Rosa becomes ill with typhoid contracted from the rat bites she received during their border crossing, he delays leaving for Chicago and loses the position. After Rosa dies, he is shown once again waiting with the other day-labor hopefuls in a parking lot, offering his services to a man looking for \"strong arms\"; reviewer Renee Scolaro Rathke observes, \"It is a bitter realization that Arturo\'s words about the poor being nothing but arms for the rich holds true even in El Norte.\"
The final shot in the film again shows a severed head hanging from a rope, which may be the same image used in Part I of the film; one critic has commented that a hanging, severed head is \"a symbolic device used in some Latin films to signify that the character has committed suicide.\" 
Rosa sums up the film\'s major theme when she says to her brother Enrique near the end:
In our homeland there\'s no place for us, they want to kill us. In Mexico there\'s only poverty. And in the north we aren\'t accepted. When are we going to find a home, maybe only in death?