Unfortunately Mullee was forced to undergo Tommy John Surgery in June 2011 after experiencing elbow pain, he pitched five innings for the Staten Island Yankees before requiring surgery after suffering an avulsion fracture in which his repaired Ligament tore off the bone. This time a screw had to be used to hold the Ligament in place.[3] Mullee was forced to undergo surgery a third time in February, 2013 after his bone failed to properly heal around the screw.[4] Having thrown only five innings from 2011 to 2013 due to the elbow issues, he returned in 2014 and pitched well for the Staten Island Yankees and the Charleston RiverDogs and moved up the minor league ladder to the Yankees' Triple–A affiliate, the Scranton/Wilkes-Barre RailRiders, in 2015.[5]
Mullee was called up to the majors for the first time on May 14, 2016.[6] Mullee pitched in three games, giving up one run in three innings pitched before he was placed on the 15-day DL with nerve issue in his hand on July 3. The Yankees announced he would miss the rest of the season and subsequently put him on the 60 day disabled list on August 13.[7]
Chicago Cubs
Mullee was claimed off waivers by the Chicago Cubs on November 2, 2016,[8] On December 2, he was non–rendered by the Cubs and became a free agent.[9]
On December 12, 2016, Mullee re–signed with the Cubs organization on a minor league contract that included an invitation to spring training.[10][11] In 13 games for the Triple–A Iowa Cubs, he struggled to a 7.36 ERA with 13 strikeouts across 18+1⁄3 innings pitched. Mullee was released by Chicago on July 5, 2017.