In January 2004, Looper signed with the New York Mets as a free agent and had his best season to date going 2-5 with 29 saves and a 2.70 ERA. However, Looper had many crucial blown saves during the 2005 season, including blown saves on Opening Day, in a game that would have clinched a Met sweep at Yankee Stadium and as part of an eight-run collapse by the Mets pen against the Nationals. These performances still fresh in fans' minds, he was greeted with loud boos and "Looper sucks!" chants upon his returns to Shea with the Cardinals, most prominently during the 2006 NLCS.