In an old, migrant worker's shantytown, Eladio Buente is trying to flirt with Maria Dorantes while Soledad, his brother watches over at them with a burning jealousy as Eladio seems to be winning her over. The flirting is cut short though when suddenly two loud booms come out of nowhere followed by a very bright flash and then it begins raining hot yellow rain. Later, one of the neighbours, Flakita finds the mutilated corpses of Maria with her face having been eaten away. Eladio's whereabouts though are unknown.

Mulder is very interested with this case so he gets Scully to investigate it with him as he recognizes the events that precluded the finding of Maria as he calls them Fortean events. Scully though is obviously skeptical. They decide to interview Flakita who tells them that he believes Maria was mutilated by the legendary goat-sucker called El Chupacabra which is supposed to be a small, hairless creature with big bulging eyes (Alien similarities anyone?). They then talk to Soledad who disagrees with the story and just thinks that Eladio killed Maria out of jealousy. Scully agrees with this story until she takes a look at Maria's remains which seems to have grown some kind of fungus in fact showing that she had been infected to a massive fungal infection.

Mulder meanwhile locates Eladio who denies that he killed Maria and says that he believes something unknown killed Maria during the downpour of rain. The agents both agree on this (for once!). But later, Eladio escapes from INS custody and kills a man who also develops a fungus. With the help of an immigration agent, Mulder manages to track Eladio to a construction site but Soledad is also on his brother's trail and they both escape before Mulder can capture them. They find the site foreman has also been killed with the fungus. Scully warns Mulder that touching the fungi causes that person to be infected with what is an enzyme that causes accelerated fungal growth.

Scully claims that Eladio is killing his victims by spreading the enzyme he is infected with so Mulder thinks that the enzyme is actually extra-terrestrial which causes Scully to lose her patience. Meanwhile, a sick Eladio begs Gabrielle, his cousin for money which she reluctantly gives him. Flakita tells them that Soledad is planning to kill his brother so the immigration agent that helped Mulder arrests Soledad but Eladio escapes. Eladio looks at himself in the mirror for the first time and realizes that he has actually turned into the El Chupucubra. Gabrielle, covering for Eladio, tells Mulder and Scully that he has gone to Mexico but Mulder is too smart to be outwitted so he travels to the shantytown where the incident happened as he believes this is where Eladio has gone. This is where the two brothers will have it out.

What now follows are different versions of what they all claim happened. Flakita claims that the immigration agent, Lozano brought Soledad to the town and told him to face Eladio like a man. Eladio though has now turned into the El Chupucabra so lots of them fall from the sky and kill everyone while Soledad is taken up into the sky.

Gabrielle's version is that Lozano did indeed bring Soledad to the camp where he tells Eladio to face him. Soledad realizes his brother is now El Chupucabra so he doesn't shoot him but instead struggles with Eladio. Lozano gets shot though and Soledad has now turned into the same creature so they both run away to Mexico.

Mulder and Scully report to Skinner what they know. They found at the site that Lozano was dead by being shot and also because of the fungus and the two brothers are gone. Meanwhile we see the two brothers, now looking both disfigured and probably both El Chupucabras going off into the night sky ready to kill again.....