Gray was once again named the starting quarterback for the Golden Gophers for the 2012 season. Shortell was listed as the backup following spring camp, and served that role for the first three games of the season. During the week 3 game against Western Michigan, Gray left the game with an injury, and Shortell led the Gophers back from an early deficit to defeat the Broncos throwing three touchdowns. Shortell would start the next three weeks, leading the Gophers to a 1–2 record during that time. A surprise came during the Gopher's week 7 game at Wisconsin, when true freshman, Philip Nelson was named the starting quarterback. Gray moved to wide receiver, and Nelson started every game for the rest of the season. Shortell was limited to the backup role for the rest of the season. Following the end of the Minnesota semester, Shortell announced his intentions to transfer. On May 9, 2013, Shortell announced via Twitter, that he was transferring to Jacksonville State. Through the end of the 2012 season, Shortell's statistics are as follows: Shortell has a 1–3 win/loss ratio for his career as the starting quarterback at Minnesota. In 2018, Shortell signed for the Birmingham Iron of the Alliance of American Football (AAF). However, he was not selected in the 2019 AAF QB Draft.