The name God refers to the deity held by monotheists to be the supreme reality. God is generally regarded as the sole creator of the universe and is the central figure in Christianity, Judaism, and so forth.
Agent Comer told Scully that the cult leader Josepho believed the craft he and his followers found in Alberta (or, rather the letters on it) to be the physical manifestation of God (TXF: "Providence")
In 1993, Verla McLennen told FBI Special Agents Fox Mulder and Dana Scully that - even though she had initially been upset by her husband's odd behavior - "when you're the wife of a test pilot, you thank God just to have him home alive." (TXF: "Deep Throat")
The term "God" is also occasionally used as an exclamation. While Scully and Mulder were questioning Theresa Nemman in March 1992, Scully exclaimed, "Oh, God!", when Theresa's nose suddenly started to bleed. (TXF: "Pilot") Shortly thereafter, the same phrase - "Oh, God!" - was used by Detective Miles, upon seeing his son, Billy Miles, apparently make a sudden and complete recovery from a "waking coma", and by Anita Budahas, when she came home to discover that her house was surrounded by Military Police who wanted her husband, who was inside, as they believed he had violated base security procedure, commandeered a military vehicle and was armed. (TXF: "Pilot", "Deep Throat")
A similar phrase - "Oh, my God!" - was used by Agent Scully after she and Mulder observed two lights as they danced in the sky over Ellens Air Base before rising through the clouds and disappearing. (TXF: "Deep Throat") Scully used this same phrase upon telling Mulder that she thought a substance, used in the construction of a nest made by Eugene Victor Tooms, was bile, and upon discovering that sheets of binary data written by young Kevin Morris represented, when seen from a distance, a picture of his abducted sister, Ruby Morris. (TXF: "Squeeze", "Conduit")
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