In a migrant workers' shantytown in California's San Joaquin Valley, Eladio Buente flirts with pretty Maria Dorantes while his brother Soledad watches jealously. Flakita, a nosy neighbor, bemoans the age-old story: "Two brothers. One woman. Trouble." Suddenly, three ear-splitting booms come from the sky, followed by a painfully bright flash, and a brief but torrential downpour of hot yellow rain. In its aftermath, Flakita discovers the mutilated corpses of Maria and one of her goats, their faces partially eaten away. Eladio is missing.

Mulder and Scully investigate the deaths. According to Mulder, the strange occurrences preceding Maria's death are called Fortean events, "An unusual or highly infrequent meteorological phenomenon...Fortean events have been linked to alien encounters, and cattle mutilations..." Scully greets Mulder's information with her usual skepticism. She can't tell much from the goat's corpse, and Maria's body is at the morgue.

According to Flakita, Maria was killed by El Chupacabra--the Goatsucker)--a gray hairless creature out of Puerto Rican folk tales with a small body, large head and bulging black eyes. Scully notes the amazing similarity between the descriptions of El Chupacabra and a gray alien. Soledad angrily refutes Flakita's story. He accuses his brother, Eladio, of killing Maria out of jealousy. This lover's triangle convinces Scully that Eladio is the killer, until she examines Maria's remains. The state of Maria's corpse shocks even Scully. It's hardly visible beneath mounds of greenish fungal growth. Meanwhile, Mulder locates Eladio with the help of Conrad Lozano, a cynical Immigration agent. Eladio is in INS custody, segregated from fearful prisoners who think he's El Chupacabra. Eladio denies killing Maria, claiming something or someone unknown mutilated Maria during the yellow rain. Mulder believes Eladio did not kill Maria, and Scully must agree. Scully's autopsy of the body revealed that Maria succumbed to a massive fungal infection--no one, she says, could deliberately do such a thing.

Eladio escapes from INS custody, and the agents discover the driver of the INS deportation bus dead from a different fungal infection. Mulder thinks there may be a connection between the fungi and the missing immigrant. Lozano and Mulder track Eladio to a construction site where he has found work, but the vengeful Soledad is also on Eladio's trail. Both brothers escape before Lozano and Mulder can take them into custody. The site's foreman is dead, his body ravaged by a myriad of fungi. Scully calls Mulder and warns him against touching or inhaling the lethal lichen. A mycology professor has isolated an enzyme that acts as a catalyst, accelerating fungal growth. If it escapes into the environment, there could be a biological hazard of frightening proportions.

Scully believes that Eladio is inadvertently responsible for deaths by spreading the enzyme which he somehow is carrying. Mulder now thinks the Fortean events could have been caused by something falling from space...which would mean the enzyme is alien. Scully,on the verge of losing patience with Mulder's theories, just wants to find the man who seems to be spreading it.

Now quite ill, Eladio begs his cousin Gabrielle for help. She reluctantly agrees to lend him money. Flakita, the village gossip, warns the agents that Soledad is planning to kill Eladio. Eladio eludes them again, but Lozano arrests Soledad.

When Eladio sees his own face for the first time, he can't believe the horror of it. He no longer looks human--Eladio has indeed transformed into El Chupacabra. Gabrielle tells Scully and Mulder that Eladio has run away to Mexico. But Mulder realizes it's a lie. Speeding on their way, he alerts a hazmat team to meet them at the shantytown...where it all began. Where the two brothers will finally settle their dispute over Maria.

What really happened that night? According to Flakita, Lozano brings Soledad to the camp, and orders Eladio to face his brother like a man. But Eladio is no longer a man...he is El Chupacabra. Flakita hides as gray aliens-- whom she calls Chupacabras--descend on the village. They kill Lozano, and take Soledad up in the sky with them.

Gabrielle weaves another tale. Lozano orders Eladio to face Soledad. In the horror of realizing his brother is El Chupacabra, Soledad can't shoot. He and Lozano struggle over the gun, and Lozano takes a bullet. The two brothers, now both Chupacabras, run away to Mexico.

The story Mulder and Scully report to Skinner isn't much clearer. All they know is that by the time they got to the camp, both the brothers were gone. Lozano was dead...brought down by two bullets and the fungus. And Los Chupacabras? The Buente brothers, their faces luridly disfigured, may have hitchhiked off into the Mexican night.