Mr. Y and Erika are part of a mysterious organisation, who oppose the Cigarette Smoking Man and his plans for depopulation of the human race. They attempt to get Fox Mulder to join their cause and want him to kill the Smoking Man, claiming that they are planning space colonization and have the means to create dyson spheres. However Mulder doesn't believe them and comes to the solution they are just as bad as the Smoking Man, and no doubt have their own secret agenda. (TXF: "My Struggle III)
He is later shot in the head by Mulder, who came purposefully to find the whereabouts of his son. After not being told what he wanted, Mr. Y attempts to shoot Mulder, but his adversary reacted far more quicker.