San Jose State finished 1–12 in 2010 and 5–7 in 2011 under MacIntyre. In MacIntyre's third season, the 2012 San Jose State Spartans football team finished 11–2 including a win over Bowling Green in the 2012 Military Bowl. The 2012 team earned top-25 post-season rankings in the Associated Press (AP), Coaches and BCS polls. Kent Baer served as interim head coach for the Military Bowl because MacIntyre resigned to accept the head coach position at Colorado.
