Through a series of events that began with Arsenio Hall stepping down from his late-night talk show and the acquisition of Paramount Communications by Viacom, the parent company of MTV at the time, The Jon Stewart Show was retooled and launched in daily syndication for the 1994–1995 season as a 60-minute program with the first episode airing on September 12, 1994.

Celebrity guests who made appearances on the show included Howard Stern, David Letterman, Quentin Tarantino, Jonathan Brandis, Courteney Cox, Sherry Stringfield, Lorenzo Lamas, Bronson Pinchot, Conan O'Brien, Alicia Silverstone and William Shatner.

The show was also popular for showcasing the type of musical guests that usually were not seen on other talk shows, such as Sinéad O'Connor, The Breeders, King's X, Quicksand, Blind Melon, Killing Joke, Buffalo Tom, The Figgs, Diamanda Galás, Megadeth, Van Halen, Peter Murphy, Sunny Day Real Estate, Bad Religion, Naughty by Nature, White Zombie, Marilyn Manson, Redd Kross, Gin Blossoms, Dom Pachino, Faith No More, Rocket from the Crypt, Ol' Dirty Bastard, Belly, American Music Club, Fossil, Letters to Cleo, the Crash Test Dummies, "Weird Al" Yankovic, The Afghan Whigs, The Notorious B.I.G., Guided by Voices, Samiam, Warren Zevon, Mike Watt, Body Count, Danzig, Face to Face, Helmet, and Pop Will Eat Itself, as well as fringe sub-culture guests such as Rev.

The episode sparked nationwide controversy after their front man, Marilyn Manson, set a Bible ablaze onstage (which later was revealed to be a lunchbox), which elicited public outcry of blasphemy.

The band finished their set by throwing instruments around the stage, and ended with a piggyback ride offstage on Jon Stewart.