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The season continues to follow the cases of FBI special agents Fox Mulder and Dana Scully, portrayed by David Duchovny and Gillian Anderson respectively, who investigate paranormal or supernatural cases, known as X-Files by the FBI.

The season features the conclusion of several plot-lines introduced in season two, while also introducing several new plot elements. Major plot arcs include an elaborate conspiracy being discovered when a fake alien autopsy video is acquired by Mulder, Scully's search for the killer of her sister, and the mystery surrounding X (Steven Williams). Pivotal characters such as the First Elder (Don S. Williams) and the alien virus black oil were first introduced in this season. In addition, the season features a wide variety of "Monster-of-the-Week" episodes, which feature stand-alone stories not of influence to the wider mythology of the series.

The season attained higher ratings than season two, receiving the highest viewing audience the series had yet achieved. Season premiere "The Blessing Way" debuted with a Nielsen household rating of 19.94, which more than doubled the premiere of the last season. The ratings consistently stayed above 15.0, making it one of the most watched series of the 1995–96 television line-up. The season received generally positive reviews from television critics, winning five Primetime Emmy Awards. Many of the episodes written by writer Darin Morgan received critical acclaim, including the episodes "Clyde Bruckman's Final Repose" and "Jose Chung's From Outer Space" which are often cited as some of the best of the series. Morgan left the series following this season, due to an inability to keep up with the fast paced nature of the show.