Jacob Wharton was a colonel in the United States Marine Corps who oversaw a Haitian refugee camp in North Carolina. Several of his troops were found dead under mysterious circumstances, which Wharton pinned on Pierre Bauvais - a known practitioner of voodoo. FBI Special Agents Fox Mulder and Dana Scully questioned Wharton, but concluded that Bauvais could not have been responsible. However, they learned that Wharton himself was practicing voodoo for his own sinister ends; the agents discovered him performing a voodoo ritual over the grave of Bauvais, who was resurrected and seemingly killed Wharton. However, the final scene shows Wharton being buried alive as punishment for his crimes. (TXF: "Fresh Bones")

Jacob Wharton was played by Daniel Benzali.