Before Mota ever played for the Red Sox, however, he was traded again to the Cleveland Indians. He struggled in his time with the Indians in 2006 and was designated for assignment by them in August. The New York Mets acquired him, and Mota improved mightily upon joining them. Following the season, he became a free agent, but he again signed with the Mets. After struggling in 2007, he was traded to the Milwaukee Brewers. He got off to a poor start with Milwaukee in 2008 but improved in the second half. Following the season, Mota became a free agent and signed with the Dodgers again. He had his best year since 2004 and became a free agent again after the season. For the first time in his career, in 2010 he signed a minor league contract with the San Francisco Giants. After making the team out of spring training, Mota won his first career World Series despite struggling at times during the season. Following the season, he signed another minor league contract with the Giants and made the team out of spring training again. During the 2012 season, Mota became one of three players in league history to fail a drug test twice when it was shown he tested positive for Clenbuterol, a performance-enhancing drug.