Dr. Leslie Thompkins is kidnapped when crime boss Rupert Thorne requires surgery.

Mulder and Scully head to Ellens Air Force Base to investigate the mysterious case of a military test pilot who disappeared after experiencing strange psychotic behavior. While on the case, Mulder meets a mysterious man dubbed "Deep Throat" who claims to have classified information about his investigations into the paranormal.

It is a busy day for the staff of Holby A&E when joyriders cause a train to crash.