Before the 1999–2000 season, the Lobos and seven other teams left the WAC to form the Mountain West Conference (MWC). Fraschilla inherited three returning starters, but the team was clearly heading into a rebuilding period after losing Thomas. The inconsistent squad started 5–5 but then stunned 21-point favorite, #2 Arizona in Tucson, the highest ranked opponent the Lobos had beaten on the road since 1966. The team meandered to a 13–11 record but then won four straight, including over #21 Utah. They went to the NIT and beat South Florida before losing at eventual champion Wake Forest, finishing 18–14. Lamont Long averaged 18.7 points a game to lead the league and earn All-MWC honors, finishing his career as the third leading scorer in Lobo history, three points ahead of former teammate Shields.