In a new interview with The Daily Beast, the "The X-Files" alum revealed he was attending a friend's wedding at the the Church's Celebrity Centre in Los Angeles when the controversial organization had him try out a few "auditing" procedures.
"They made a play for me," he explained. "I did squeeze the cans and I did a session on the E-meter, and I realized immediately, because they're asking very personal questions, that they were gathering information that I didn't want to give out to a stranger."
"So, the session didn't go well. I didn't play by the rule, and I never went back."
Duchovny went on to say the friend who was getting married -- fellow actor and former "Melrose Place" star Jason Beghe -- was a Scientologist at the time, but wasn't pushing for him to sign up.
"He only 'recruited' me in the sense of saying, 'This is great, and I think you should try it,' not anything harder than that."
Although Beghe would eventually leave Scientology and brand it a "cult," Duchovny said his time in the Church caused them to "drift apart" because "Scientology hangs with their own when they’re doing it." They would still see each other periodically, but Duchovny noticed a change in his childhood pal.
"The way he described the world and his experiences, particularly his psychological experiences, was not cult-ish and had changed completely."
Duchovny even questioned if he should have intervened, saying, "either I didn't have the balls to slap him and snap him out of it, or he said it was working for him."