MLS
After the CISL folded at the end of 1997, Dougherty began pursuing full-time employment in an outdoor league. On February 3, 1998, the MetroStars of Major League Soccer (MLS) signed Dougherty. He played sixteen games that season, before the MetroStars traded him to the Tampa Bay Mutiny for Mike Duhaney in July. Dougherty began the 1999 season with the Mutiny but was traded on August 2, 1999 with Sam George and a draft pick to the Chicago Fire for Ritchie Kotschau and Manny Lagos. When Dougherty failed to produce with Chicago, they sent him on loan to the Charleston Battery of the USL First Division. In March 2000, Dougherty was able to add another team to his resume, having been a member of it for only a few hours. The Fire released Dougherty on March 15, 2000. He was then selected by the New England Revolution the next day in the Waiver Draft. The Revs then turned around and traded Dougherty to the Colorado Rapids in exchange for a fifth round pick in the upcoming Super Draft. Dougherty spent the 2000 season with the Rapids, but failed to score in twenty-four games and on October 31, 2000 he announced his retirement.
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