After moving around the Hurricanes system as a scout, and even as an assistant coach, Stefan returned to Plymouth in December 2007 to become the head coach of the club, taking over for Mike Vellucci, who would solely focus on his general manager duties.
The Whalers posted a record of 16–20–3 under Stefan, after starting the season with an 18–8–3 record under Vellucci, however, the team would make the playoffs as the eighth seed in the Western Conference. In the first round of the post-season, the Whalers were quickly eliminated by the Kitchener Rangers in four games. Stefan came back to Plymouth for a second season in 2008–09, however, after a start of 6–11–2, he resigned from the position to return to the Carolina Hurricanes organization as a scout. In 2006, Stefan won the Stanley Cup as Goalie Coach/Scout with the Carolina Hurricanes.
