He moved to the Miami Fusion for the 2001 season, where he scored three goals and eight assists on a team that went on to win the MLS Supporters' Shield in their final year. Upon Fusion's contraction, Henderson was reacquired by the Rapids in the 2002 MLS Dispersal Draft. Henderson continued to be a threat on the right for the Rapids, scoring 11 goals and seven assists in his first season back. Although he began to show his age in the next two seasons, Henderson continued to be dangerous on the flank. He is the Rapids' all-time leader with 178 games played, 53 assists, and 120 points. Henderson was traded to the Columbus Crew in May 2005 in a three-team deal. After the season, he was dealt again, to the MetroStars — soon renamed New York Red Bulls — for Tim Ward. Henderson played every match of the 2006 season, and by its end he was the league's all-time leader in games played, though he has since lost the title. At the end of the season, however, Henderson was waived. He went on to announce his retirement from professional soccer on December 22, 2006.
