Now aboard the mysterious train, Mulder locates the car containing the scientific equipment and what appears to be the autopsy room he saw in the video he purchased. There is also an assassin on board who claims to work for the NSA. When they are locked in, he reveals that there is a bomb aboard which is set to go off and destroy any evidence on the train. Scully meanwhile traces her implant to a medical research facility in West Virginia which she feels provides a logical explanation for what has been happening - rogue medical research by a Japanese scientist working without authority. Mulder remains convinced the work was to create a human-alien hybrid.

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