After Quantrill became a free agent, Mota became the setup man for Gagné in 2004. He started the season with eight straight scoreless games. From June 27 to July 16, he did not allow a run in 10 straight games. On July 29, he started a career-high five-game winning streak when he got a win by pitching two scoreless innings in a 2–1 victory over the San Francisco Giants. He was the winning pitcher when he pitched two scoreless innings in an 8–5 victory over the Anaheim Angels on July 3 in a game notable for Gagné getting the final save of his 84 straight converted save chances. On July 30, a day before the trade deadline, Mota had a 2.14 ERA in 52 games. That day, he was traded to the Florida Marlins with Juan Encarnación and Paul Lo Duca for Hee-seop Choi, Brad Penny, and Bill Murphy.