Colorado Rockies
Thomson pitched in the Rockies minor league system for the Arizona Rockies of the Arizona Rookie League in 1993, the Asheville Tourists of the low single-A South Atlantic League (1994), the Central Valley Rockies of the advanced single-A California League (1994), the New Haven Ravens of the double-A Eastern League (1995–1996) and the Colorado Springs Sky Sox of the triple-A Pacific Coast League (1996–1997).
In his major league debut May 11, 1997, Thomson gave up three runs (only one earned) on five hits in 7⅔ innings with 7 strikeouts and 4 walks in a 3-1 loss to the Philadelphia Phillies. He earned his first major league win in a complete game against the Florida Marlins June 1. He remained in the Rockies starting rotation for the rest of 1997, posting seven wins and nine losses with a 4.71 ERA and 106 strikeouts in 166⅓ innings pitched.
Thomson made 26 starts for the Rockies in 1998 and led their starting pitchers with a 4.81 ERA. He missed a month of the season with a blister on his right middle finger that would become a recurring problem for him over the ensuing years.
The 1999 season was a poor one for Thomson. After six appearances (five starts), he was 0-5 with an 11.84 ERA and the Rockies sent him down to triple-A Colorado Springs where he didn't fare much better (0-2, 9.45 ERA in five starts). He returned to the Rockies August 14 and was credited with his first win since September 8, 1998, but failed to win another game the rest of the season. He finished 1999 at 1-10 with an 8.04 ERA. After the season, it was discovered that Thomson had a torn labrum (another injury that would recur later in his career). He had shoulder surgery October 12 and a second surgery the following day to repair his blister-prone right middle finger. With the exception of four rehabilitation appearances with the Rockies' Arizona Rookie League team and the Portland Rockies of the short-season, single-A Northwest League in August and September, he missed the entire 2000 season.
Thomson began 2000 on the disabled list (DL) as he continued rehabilitation of his surgically repaired shoulder. After five rehabilitation starts at Colorado Springs, he was activated May 12 and made three starts for Colorado before returning to the DL just two weeks later on May 26. This time, he made seven rehabilitation starts for the Sky Sox and returned to the Rockies August 2. He got his first win in more than two years August 19 against Florida. Over his final eight starts, he was 4-0 with a 3.36 ERA and for the season, he was 4-5 with a 4.05 ERA.
2002 would be Thomson's final season with the Rockies and he returned to his pre-injury form. In his first 11 starts for Colorado, he was 6-3 with a 3.86 ERA. With the Rockies unlikely to compete for a National League playoff spot and Thomson a free agent at the end of the season, he became a target of trade talks as the July 31 non-waiver deadline approached. After his final start for Colorado July 23, he was 7-8 with a 4.88 ERA in 21 starts.
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