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Associated Press
Todd Mortensen

SALT LAKE CITY — Before Jim Harbaugh revived the career of Alex Smith, before he honed the talents of Andrew Luck, before he put Josh Johnson on the NFL radar, there was Todd Mortensen, the kid from BYU — aka Harbaugh's First Quarterback.

Remember Mortensen? Probably not.

He played quarterback at BYU on and off for four forgettable years. After seeing spotty action in a few games each season, he reluctantly bolted in 2004 to the University of San Diego, a Division I-AA school that had a new football coach — Harbaugh, a former Michigan and NFL quarterback who was making his debut as a head coach.

Under Harbaugh's guidance in their one and only season together, Mortensen transformed from a clipboard holder at BYU to a professional prospect and turned the Toreros into winners. Harbaugh has worked the same magic ever since then, with San Diego, Stanford and the San Francisco 49ers. This weekend Harbaugh's 49ers will meet the New York Giants in the NFC championship game.

"I'm not surprised at what he's done," says Mortensen. "Enthusiasm and sound game planning in Xs and Os is a good combination."

Harbaugh is on a hot streak. He concluded his three years at San Diego by winning 27 of his last 29 games. He concluded his four seasons at Stanford with a 12-1 season, transforming a losing program into a national title contender. In his first year with the 49ers, a team that was 6-10 last season and in complete disarray, he has won 14 of 17 games and is one win away from the Super Bowl.

Each step of the way, the hallmark of Harbaugh's teams has been the development of the quarterback. He transformed Smith from NFL bust into one of the league's steadiest quarterbacks, one who led two stunning touchdown drives in the last four minutes of Saturday's playoff win over the New Orleans Saints. Harbaugh helped Andrew Luck become college football's best quarterback and likely the first choice in this spring's NFL draft. He coached the unknown Johnson at San Diego into a fifth-round draft pick and a backup for the Tampa Bay Buccaneers.

Before that, he turned Mortensen, who languished at BYU, into an NFL free-agent signee.

Not that Mortensen didn't bring something to the table for Harbaugh to work with. Mortensen could be the poster boy for the NCAA's student-athlete concept. Motivated and intelligent, he won the Gordon B. Hinckley Presidential Scholarship — the most prestigious scholarship awarded to a BYU student. The requirements for the scholarship are a minimum composite ACT score of 33, a minimum combined SAT score of 1460 and a minimum 3.85 GPA — and then selection gets really difficult, based on academic qualifications, leadership, service, and recommendations.

Mortensen received the award for four years.

He was valedictorian at Tempe (Ariz.) High School, with a 4.0 GPA. He was valedictorian in the humanities college at BYU, with a 4.0 GPA. He earned his undergrad degree at BYU in three years and worked on his master's degree while playing a fourth year of football.

He was also a serious musician. He began playing the piano at 5, then took up the trumpet in junior high. He played in jazz and symphonic bands. He composed music, as well. He once presented his band teacher a box filled with 50 pages of his compositions, which the band performed. He continued to play in jazz combos in college and cut a CD of his piano music.

If that weren't enough, Mortensen was an all-state quarterback at Tempe High. At 6-foot-4, 225 pounds, he threw for 4,950 yards and 60 touchdowns and led his team to the state championship. His coach was his father, Fred, a former star quarterback at Arizona State who played in the NFL and USFL.

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."