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According to Jesse, they met when they were still in elementary school. Jesse mentions that Saul Goodman provided Emilio legal representation on at least two occasions, getting him acquitted both times despite much evidence against him.
Emilio is arrested during a raid on a house in which the DEA is looking for meth supplier who goes by the street name "Captain Cook". Emilio makes bail and suspects that his partner, Jesse Pinkman, ratted him out to the police (which turned out to have been Krazy 8 as a DEA informant) and forces Jesse to lead him and Krazy 8, in Emilio's 1980 Buick Regal, to his new partner, Walter White. Emilio recognizes Walt from the time of his arrest and suggests killing both Walt and Jesse. Walt convinces them to spare their lives if he teaches them his meth formula.
While the three are in the The RV in the desert, Walt deliberately causes a chemical explosion and flees, trapping Emilio and Krazy 8 inside the RV with deadly phosphine gas and leading to Emilio's death.
Emilio's corpse subsequently disposed of by being dissolved in hydrofluoric acid in Jesse's bathtub. However, the corrosive acid eats through the bathub and the floor, splattering Emilio's bloody, liquified remains on the floor. Walt and Jesse later clean up the mess.