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San Joaquin Valley, California: In a migrant workers' shantytown, Eladio Buente is flirting with pretty Maria Dorantes while his brother Soledad watches jealously. Flakita, a nosy neighbour, bemoans the age-old story: "Two brothers. Ome woman. Trouble." When some goats escapes, Maria and Eladio run after them. Suddenly, a bright flash comes from the sky, followed of a downpour of hot, yellow rain. After the rain, Flakita discovers the mutilated corpses of Maria and one of the goats, their faces partially eaten away. Eladio has disappeared.

Mulder and Scully investigates the deaths. According to Mulder, the strange occurences 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 is as usual skeptical, but she agrees to do an autopsy on Maria's body.

According to Flakita, Maria was killed by El Chupacabra. El Chupacabra is a gray, hairless creature from Puerto Rican folk tales with a small body, large head and big black eyes. Scully notes the amazing similarity between the descriptions of El Chupacabra and a gray alien. Soledad, Eladio's brother, angrily refuses Flakita's story. He accuses Eladio of killing Maria out of jealousy because Maria loved Soledad and not Eladio. This convinces Scully that Eladio is the killer. But when she travels to the morgue to perform an autopsy on Maria, she changes her mind. Maria's body is hardly visible beneath mounds of greenish fungal growth.

Meanwhile, Mulder has located Eladio with the help of the cynical immigration agent Conrad Lozano. Eladio is in INS custody, where he is segregated from the other prisoners who thinks he is El Chupacabra. Eladio denies killing Maria, claiming that he was blinded by a great flash and when he was able to see again, something had eaten of Maria's face. But she was still alive, and died in his arms. Then he ran away. Mulder believes he didn't kill Maria, and Scully have to agree with him. Scully's autopsy of her body revealed that Maria succumbed to a massive fungal infection.

When the prisoners, included Eladio, is to be transported to another place, the car they drove in is found crashed in a tree. The prisoners have escaped, and only the driver is left, dead from a different fungal infection. Mulder thinks there may be a connection between the fungi and the missing immigrants. Lozano and Mulder track Eladio to a construction site where he has found work, but that has also Soledad. Both brothers escape before they can be taken into custody. The site's foreman is dead, killed by a fungus infection as usual. Scully calls Mulder to warn 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 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's spreading it.

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

When Eladio sees his face for the first time, he cant believe what he sees. He no longer looks human, he has turned into El Chupacabra. Gabrielle tells Mulder and Scully 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 began, and where it will end. Where the two brothers finally will settle their dispute over Maria.

What really happened next? 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. Then, many Chupacabras come to the village in a UFO. They kill Lozano, and take Soledad up in the sky with them.

But Gabrielle has another story. Lozano orders Eladio to face Soledad. In the horror of realizing his brother is El Chupacabra, Soledad can't kill him. He and Lozano struggle over the gun, and Lozano gets killed. Soledad and Eladio, now both Chupacabras, run away to Mexico.

The story Mulder and Scully reports to Skinner isn't much clearer. All they know is that by the time they got to the camp, both brothers were gone, and Lozano was killed by two bullets and the fungus. And Los Chupacabras? The brothers have disappeared, they may have hitchhiked into the Mexican night.

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