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Originally published Saturday, January 19, 2013 at 8:29 PM

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College offense sparks Niners

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...

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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 a little more than 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 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 on 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"

Ault remembers walking into a coaches' meeting in early 2005 with a radical new idea. Ault was looking for something to "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.

There are few things more exciting — 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."

Since Kaepernick took over as the starting quarterback 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."

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