Mortensen redshirted his first season at BYU, served a church mission in Venezuela for two years and then battled stiff competition for playing time at BYU for the next three years. He backed up Brandon Doman for a season, then spent the next two seasons competing with Brett Engemann, Matt Berry, Ben Olsen, Lance Pendleton and John Beck. He played in 14 games, but never more than a half. The results were not good. He completed 27 of 77 passes for 217 yards, 1 TD and 4 interceptions.
"To prepare and know the offense, there's no substitute for getting reps in practice," he says. "As a backup I didn't get as many as the starter, or I probably would have done better."
He had planned to finish his final season of football eligibility and his master's degree in Spanish linguistics at BYU, but then his father, a coach at Mesa City Community College at the time, learned that San Diego was hiring Harbaugh and was returning virtually its entire offense — except quarterback. It was a difficult decision. Mortensen was one class and a thesis away from finishing his master's degree and, despite his spotty playing time, he liked his coaches and teammates and the school itself. A transfer would also cost him money — San Diego offers no scholarships.
"But I had a strong desire to be a starter and play every week and see what I could do," he says.
He made the leap and thrived under Harbaugh. "He loved to game plan, and I loved that kind of thing," says Mortensen. "Studying under Jim was as good of a situation as I could hope for."
They lost two of their first four games, but they won six of their last seven. Mortensen, who completed 234 of 389 passes for 2,874 yards, 25 TDs and 6 interceptions, was named co-Offensive Player of the Year in the Pioneer Conference and All-American.
"It was very fulfilling," he says. "That's what I was hoping for in a college experience. Having played quarterback helps Coach Harbaugh. It's easy for him to understand his quarterback's mind. What made him great for me is that he made my decision-making very clear and very easy to move through quickly. He called three plays at a time. I picked the play at the line of scrimmage based on simple keys — if the safety's in the box, check to the pass, if they show blitz, check to the blitz, if the safety's back, check to the run. Then after the snap I looked for another key — if he does this, then do this; if not open, check down. It was easy to go through the progressions quickly."
Mortensen signed a free-agent contract with the Detroit Lions, who released him after training camp. He signed with the New England Patriots the following season; the Patriots sent him to NFL Europe, where he won a starting job. He rejoined the Patriots a year later and was cut. He signed with the B.C. Lions of the Canadian Football League and was active for a couple of games. He closed out his career in 2007 playing in the Arena League.
He resumed his schooling in 2008 after being accepted by the prestigious Wharton School of Business. He is pursing a combination law/MBA degree with plans to work as either an investor or an advisor for troubled companies.
"My favorite thing to do as a quarterback is to run the two-minute drill," he says. "You have to make quick decisions under pressure and put all your knowledge of the opponent to work. This is similar. When a company is struggling, there is pressure. Everyone is watching and you've got to think fast and make good decisions fast."
He continues to follow Harbaugh's career. He and his San Diego teammates used to speculate about the coach's future; they saw big things ahead for their rookie coach. "It's been fun watching Harbaugh with Stanford and the 49ers," he says. "I get jealous. If I had another year with Harbaugh, how good would I have been? I played against Alex Smith in college. It's been neat to see Jim bring Alex back and have a successful season. I can understand what he was going through — the frustration early in his career and then finding a good fit with a great coach and a system and a game plan that fit his strengths."
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