John Nephew began freelancing for TSR as a Dungeons & Dragons author in 1986 while he was still in high school, first writing material for Dragon and Dungeon magazines.:252 As Nephew continued to write for the magazines, he was invited to contribute to projects such as Kara-Tur: The Eastern Realms (1988), Castle Greyhawk (1988), and his first solo book, Tall Tales of the Wee Folk (1989).:252 Nephew went to Carleton College in Minnesota, where he met the Lion Rampant crew.:252 Jonathan Tweet and Mark Rein Hagen founded Lion Rampant in 1987 while they were attending St. Olaf College, and Nephew was one of the Minnesota locals who joined the company later; Carleton College was the traditional rival of St. Olaf.:232 Nephew joined the company in 1988, and variously acted as acquisitions director, editor, and briefly president during his tenure.:252
Nephew left Lion Rampant in 1990 when the company moved to Georgia as he did not want to leave Minnesota.:235 He had purchased a photocopier for Lion Rampant to use, and struck a deal with the company that allowed them to keep the photocopier, while they gave Nephew a license which allowed him to publish supplements for Ars Magica; using this license, Nephew founded Atlas Games with help from friends from Lion Rampant such as Nicole Lindroos and Darin Eblom.:252 In addition to supplements for Ars Magica, Underground, and Cyberpunk, Nephew published Tweet's Over the Edge and supplements, including Wildest Dreams which first brought together Robin Laws, Greg Stolze, and John Tynes near the beginnings of their careers in the RPG industry.
Nephew and Jonathan Tweet designed On the Edge (1994), a collectible card game based on Tweet's Over the Edge RPG.:253 When the CCG industry crashed in 1996, Atlas was forced to lay off all the staff other than Nephew and Jeff Tidball to pay the final printing bills for On the Edge.:254 After Wizards of the Coast shut down its RPG lines in 1995, they put their existing games lines up for bid, so Atlas Games made an offer for Everway and Ars Magica; on February 12, 1996, Nephew withdrew the bid for Everway and on March 6, Wizards announced that Atlas Games had acquired Ars Magica.:254 In addition to his major roles, managing Atlas Games and editing its publications, Nephew wrote supplements for Ars Magica, Over the Edge, and d20 over the next few years.