Clark missed time during the summer of 2009, earning a call up to the United States for the 2009 FIFA Confederations Cup. He scored his only goal of the season following his return to from South Africa, a strike on August 9 in a 3–2 victory over Chicago. Thanks in part to his international duties, Clark only made 22 appearances in league play. He also saw his playing time in the CONCACAF Champions League decrease, appearing in two of the Dynamo's six games in the competition. Clark did play every minute in the MLS Cup Playoffs, including going 120 minutes against LA Galaxy in the conference finals on November 13. Houston was defeated 2–0 after extra time, and with Clark's contract expiring at the end of the season it would mark his final match of his first stint with the club. He announced following the season that he would pursue opportunities abroad, departing Houston with eight goals in 129 appearances across four seasons with the Dynamo.