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The "Class of '89" was a high school class that graduated from a school in Bellefleur, Oregon in 1986. The class included Billy Miles, Theresa Nemman, Peggy O'Dell, Ray Soames, and Karen Swenson. The class also included two other students, who mysteriously died shortly after graduating. Ray Soames confessed to their murders but he shared the same unexplained fate as the two previous students. Karen Swenson and Peggy O'Dell both died in 1992, just before FBI Special Agents assigned to the case, Fox Mulder and Dana Scully, discovered that Billy Miles was apparently responsible for his classmates' deaths and the agents seemingly prevented the death of Theresa Hoese. (TXF: "Pilot")
In the original script of The X-Files' pilot episode, a character named Danny Doty was another member of the "Class of '89". Instead of Ray Soames having admitted to murdering the first two victims, as in the televised version of the episode, Danny Doty had confessed to murdering the first three victims but was only convicted of murdering one as there was virtually no evidence linking him to the deaths. Mulder and Scully visited Doty in prison to question him about the murder of Karen Swenson. It was inferred that Doty had confessed not because he had committed the crime but because he wanted protection that he would be given if he went to prison. After Mulder and Scully learned that Billy Miles was the killer, it was revealed that Doty had felt the same murderous impulses as Billy Miles and Mulder surmised that Doty had confessed because he was scared by what he was capable of. The character's ultimate fate is unclear but he may have been released from prison after Billy Miles confessed to the murders.
Ray Soames still exists in the script. His family is said to have disappeared but Danny Doty tells Mulder and Scully that the Soames family had all been killed. In the televised pilot episode, the Soames family are still alive after Ray's death and it is only members of the Class of '89 that die.