Mulder met Calderon in a much more confrontational manner, pulling a gun on him and demanding that he do more to save Emily's life. Calderon was thoroughly intimidated and hastily fled back to his house, despite being followed by Mulder. There, Calderon met with a two men from the hybrid police who killed him and took his appearance to confuse Mulder.
Later, with assistance from Frohike, Mulder is able to trace Anna Fugazzi, Emily Sim's surrogate mother and a patient of Dr. Calderon, to a San Diego nursing home. At the nursing home, Mulder learns that several other elderly women have ben treated with hormone therapy by Dr. Calderon and have beared children between the years 1994-1996.
A while later, still in the guise of Calderon, one of the hybrids incapacitated Detective John Kresge via exposure to his toxic blood but allowed Mulder to escape by posing as Kresge. When the pseudo-Kresge fled in Calderon's car, Mulder realized the deception (TXF: "Emily").
A man identical to Doctor Calderon is seen arresting Jeremiah Smith at the Social Security Administration office in Washington, D.C. in 1996 (TXF: "Talitha Cumi"). This seems to imply that Calderon was part of a clone series doing various tasks for the Syndicate.