in spring training before the 2000 season, peña was projected for the fifth starting rotation spot. he was 2-2 with a 1.64 era in 16⅔ innings, but was hit in the elbow by a line drive and then experienced pain in the elbow during a warmup. an exam confirmed a torn medial collateral ligament in his elbow that required surgery, causing him to miss the season. by 2002, peña had worked his way back to triple-a, but he went just 4-11 with a 5.33 era, after which the red sox let him go. he spent the 2003 season in the toronto blue jays organization, then spent two seasons pitching in the independent leagues and the mexican league before retiring in 2005 at the age of 28.