Mulder and Scully swap roles as they pursue a man killing priests that claim to have the wounds of Christ. The agents find and must protect a young boy who may be a real stigmatic. While Scully's faith draws her close to the boy, Mulder is convinced of another explanation.

A rare planetary alignment causes strange behavior in the residents of a small town, but particularly in two teenage girls who were born at the exact same moment on that date. While investigating the strange occurrences Mulder's interest in the local female detective makes Scully jealous.

A French salvage ship searching for a lost WWII fighter plane unknowingly surfaces an alien which appears in the form of black oil and has the ability to jump hosts. Mulder heads to Hong Kong to investigate the salvage broker who sold the information to the French and he encounters Krycek, who has been selling information from the MJ documents. As Mulder prepares to take Krycek back to the US, the alien makes its way to Hong Kong and takes control of Krycek.