San Francisco 49ers quarterback Colin Kaepernick (7) runs for a...

San Francisco 49ers quarterback Colin Kaepernick (7) runs for a 20-yard touchdown during the first quarter of an NFC divisional playoff game against the Green Bay Packers. (Jan. 12, 2013) Credit: AP

This is a story about a quarterback and an offense. They have become inseparable. One cannot be written about without the other.

It is a story about Colin Kaepernick, the barely recruited kid from California whose high school career consisted of just over 400 rushing yards but last Saturday had the greatest rushing game any NFL quarterback has ever had.

It is a story about the pistol offense, a gamble that the coaching staff at the University of Nevada took almost a decade ago that now is the most dangerous scheme at the sport's highest level.

Together they have brought the 49ers to the precipice of football glory.

"The marriage here was a great marriage because the scheme was unique and fresh, and when you add a player like Kap to it, it freshens it all the way through," former Nevada coach Chris Ault, sculptor of both player and philosophy, said this past week. "It makes that rose smell pretty doggone good."

Kaepernick could be The Messiah of the Modern Quarterback, the prophet of pistols to come. And he's doing it with a system that he didn't quite create but helped define.

"I don't know if you can say it's funny or what," the 25-year-old Kaepernick said of bringing a "college-style" offense with him to the pros, "but it's another asset to our offense to help us move the ball."

The 49ers are moving it to the NFC Championship Game, where they'll face the top-seeded Falcons Sunday at the Georgia Dome. It will be the most high-profile appearance for the quarterback and the system to date. The only way the stage could be bigger is if the 49ers win.

"Oh, boy," Ault said of his two projects possibly moving on to the Super Bowl in two weeks. "Wouldn't that be something?"


The Pistol

Ault remembers walking into a coaches' meeting in early 2005 with a radical new idea. It was a few weeks before the start of spring workouts for the team and Ault was looking for something to, as he said, "get on the map." What he came up with was an offense that set the quarterback about 4 yards behind the center, not quite where a traditional shotgun setup would be at 6 yards, and added a running back behind him, not beside him. It took the best parts of the spread offense with the best parts of the power game and melded them into a hybrid.

"These guys looked at me, and I'm sure when they left that meeting, they were all getting their resumes ready," Ault said of the initial meeting.

The scheme wasn't frowned upon only in Nevada circles, either.

"When I talked to some of my buddies in football, they said, 'You're doing what?' " Ault said. "So I quit talking to them."

Nevada did not take a single snap under center that spring. Slowly the offense developed, and at first it was very close to a traditional system. Nevada ran traps and dives and counters and bootlegs out of it, just as a team would in a standard setup.

After two years of employing the system in its most nascent form, it was time for Nevada to expand the scheme. Broaden it. Diversify it.

They introduced a read-option element to it in the fall of 2007, but for that to be successful, they needed the right quarterback. And they found one in one of the most unlikely settings: a basketball game.


The Pistoleer

Ault was always very meticulous when it came to recruiting quarterbacks, and in the summer of 2005 -- just a few months after he introduced the pistol philosophy -- Kaepernick was at his passing camp for star high school players.

He was impressive, Ault remembers, a decent athlete with a strong arm. But Ault wasn't sold and Nevada never sent a coach to watch Kaepernick play football during his senior season at John H. Pitman High School in Turlock, Calif.

That winter, though, Nevada assistant coach and lead recruiter Barry Sacks saw Kaepernick play basketball.

"For those young men who do that, basketball can be a great dictator of competitiveness, grittiness, all the intangibles along with his athleticism," Sacks said. "I was watching a lot of basketball games with football players."

The night he saw him play, Kaepernick was sick. Had a fever. Chills. But he played. Played the entire game. And dominated.

"The young man was captivating, to say the least," Sacks said. "I called up coach Ault and I said, 'We're crazy if we don't take this guy. He will lead us into the futureland.' "

He did. When he finally got on the field midway through his redshirt freshman season, Kaepernick replaced an injured quarterback with 8:23 left in the second quarter against Fresno State. Although Nevada lost, Kaepernick wound up with 384 yards passing, four touchdown passes and 60 yards rushing.

"That's when Kap started and never looked back," Ault said. "There was no question he was a unique breed for us. We're developing the pistol and he comes along and helps us develop it with all his great athleticism. It's really led us to where we are right now in the pistol, which is a pretty diverse offense."


The Marriage

There are few things more exciting in football -- and more difficult to defend -- than a running quarterback.

"A quarterback that can get out of the pocket, run, pick up first downs; that's a threat that the defense has to account for," 49ers coach Jim Harbaugh said. "There are some quarterback-driven runs that have been added [to our offense] because our quarterbacks are very good at those, and Colin especially."

But at first no one recognized it. Kaepernick ran a wing-T offense in high school, so he hardly ever carried the ball. When he went to Ault's passing camp, he was quick and agile, tall and athletic, but there was no sense that he had blazing speed. He wasn't even timed in a 40-yard dash at the event.

"There wasn't anything that said this guy can just flat run," Ault said. "When you see him run now, you say, 'Boy, did they have a good one!' But he was an enigma at that time . . . I really don't think Kap knew he could run the ball that well."

Pretty quickly, everyone found out. Sacks and Andy Buh, who both coach at the University of California now but were defensive coaches at Nevada, were among the first to learn.

"We used to have a saying that the guy ran squares around our defense," Sacks said. "Andy Buh used to say that. 'How can he run squares around us? This is impossible!' Not circles, not semi-circles. Not anything bending. Just out 90 degrees, make a 90-degree cut and hit the end zone."

Soon the pistol offense under Kaepernick's command was creating headlines and putting Nevada on the map, just as Ault designed. Kaepernick finished his career with 10,098 passing yards and 4,112 rushing yards and is the only player in Football Bowl Subdivision history to pass for more than 2,000 yards and rush for more than 1,000 yards in a single season three times in a career.

Other teams came to Reno to learn about the system, and Ault happily would show them the basics as well as the possibilities.

One of those teams that showed an interest was Stanford. Coach Jim Harbaugh, now with the 49ers. Offensive coordinator Greg Roman, now with the 49ers.

"They wanted to look at it and see what it was about," Ault recalled. "They were here a day and a half [in the summer of 2010]. We opened up and had a great visit with them."

Stanford didn't use much of the system the next season with Andrew Luck as the quarterback, but the following year, the two coaches moved to the NFL and one of their first draft picks was . . . Kaepernick.

Coincidence? Ault, slow to take credit, thinks it might be. But it's certainly curious that the offensive system and the player that could return the 49ers to the Super Bowl were both in place during that seemingly innocuous and unproductive meeting in 2010.

"From Stanford, they had some notes and film of it," Ault said. "I know Kap has probably passed along quite a bit of information."

Since he took over as the starting quarterback on Nov. 19, the 49ers are 6-2. Against the Packers last week, the first time Kaepernick used the pistol and read-option extensively, the second-year pro ran for an NFL-record 181 yards with two touchdowns. He also threw for 263 yards and two touchdowns.

Kaepernick's development as a quarterback corresponds with the development of an offensive system that is his perfect match. The two elements, the quarterback and the offense, simply needed each other to reach their potential heights.

The 49ers, after all, were in the NFC title game a year ago and had a pretty good thing going with Alex Smith as their quarterback (they were 6-2-1 with Smith this season). But Smith got hurt, Kaepernick stepped in with a new system and, just as he did in college, has not looked back.

"There is so much more to the pistol and you can run anything you like [out of it]," Ault said. "With a quarterback being in a position where he can carry the ball . . . I think that adds a dimension that I know in the NFL they haven't had before.

"It's pretty interesting to see, isn't it?"


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