2003-04: Stoner was second in points from a defenseman for the Tri-City Americans (WHL) with 31 on seven goals and 24 assists. He also led the team in plus/minus rating at +21. Named team playoff Co-MVP. Drafted by the Wild in the third round, 79th overall.
2004-05: Set WHL career-high marks and led Tri-City defensemen in goals with 12 and assists with 34 in 60 games. Was second-leading scorer on team and ninth in the WHL for defensemen. Named to Second WHL All-Star Team.
2005-06: In his AHL rookie season with the Houston Aeros, had 24 points on 6 goals and 18 assists in 73 games, which led the team for rookie defensemen and was third overall on the team in scoring for defensemen.
2006-07: Like many players on the Aeros, Stoner took a step back, and was one of the Wild prospects singled out by GM Doug Risebrough for his disappointing play at the end of the season. Missed Wild training with a separated shoulder sustained in the final game of the Traverse City prospects tournament. With Houston, scored one goal and had six assists in 65 games and had a plus/minus rating of -9.
2007-08: Struggled with injuries and played a career-low 56 games. Suffered a concussion early in the season and missed a few weeks. Like the Aeros however, got his game back on track with three goals and 12 assists and a +7 plus/minus rating.