He maintained his secret for years, and it was the final weeks that were the most difficult.

Chris Ault had an idea and a few notes. He had been athletic director at the University of Nevada, and in 2005 he was resuming his job as the football team’s head coach, a position he had previously held twice. Now it was time to bring life to a new offense that had been bouncing around his mind.

The shotgun offense scattered the ball around the field. But what if the primary threat in Nevada’s new base formation came from one player, a mobile quarterback who could also pass? Ault didn’t know exactly how it would look, but whenever he resumed coaching, at least he had a name.

“With the ‘Pistol,’ ” Ault said, “it’s one bullet.”

Nearly eight years after its creation, the Pistol offense has swept through college football and become popular among NFL teams. The Washington Redskins won the NFC East using rookie quarterback Robert Griffin III as their primary bullet, and they’re not alone in adopting Ault’s invention. The Carolina Panthers have used it with Cam Newton, and even the Pittsburgh Steelers tinkered with it. Now, the San Francisco 49ers and second-year quarterback Colin Kaepernick — Ault’s former protege at Nevada — have ridden Ault’s creation to the Super Bowl.

In the early days, the coach kept it secret. He summoned his running backs coach into a room, putting white adhesive tape on the floor to represent positions and movements. Ault didn’t bother telling his offensive coordinator — or many others, for that matter.

“I never let anybody see us,” Ault said, “because I thought they’d have me committed.”

Slowly, his idea began to make sense. In the traditional shotgun, the running back lines up to the left or right of the quarterback, restricting the direction the back is likely to go — and giving the defense a hint. By “hiding” the back — moving him a few yards behind the quarterback — defenses were left to guess. Who could tell which direction a player would run or, to complicate things further, who would even have the ball?

Ault began introducing wrinkles, including pre-snap movement and the zone-read option. His other assistant coaches were let in on the secret, and after the skepticism faded, hope took its place.

“I just loved it,” Ault said, “because there are so many things you can do.”

That season, the Wolf Pack went 9-3, averaged 449.3 yards in total offense, and went to a bowl game for the first time in nearly a decade. Ault was named the Western Athletic Conference’s coach of the year, but his proudest moment came when an opposing coach told a reporter that, indeed, it sure was difficult to see the running back in that Nevada offense.

In February 2006, Ault signed a skinny kid named Kaepernick to a football scholarship. No other school took the same risk. Kaepernick ran the Wing-T in high school, threw with a sidearm motion, and as Ault recalled last week, the youngster wasn’t exactly an athletic specimen. But Ault figured that, if nothing else, he could move the youngster to free safety or wide receiver.

“Just an okay athlete,” Ault said of Kaepernick, who had attended Nevada’s football camp.

Even when Kaepernick enrolled, there were few signs that he had much of a future.

“Nothing there that told me: ‘Man, this guy is our future,’ ” Ault said.

When Nevada’s starting quarterback was injured in 2007, Ault pointed at the thin redshirt freshman rather than a more experienced quarterback. Ault’s offensive vision had paid off; now another gamble would reveal his soulmate. In Kaepernick’s first game as the Wolf Pack’s starter, Nevada finished with 702 yards of total offense. Kaepernick took to the Pistol, rushing for at least 1,000 yards in his final three seasons at Nevada. He threw nearly four times as many touchdown passes as interceptions, and by the time the 2010 season finished, Kaepernick was responsible for 142 total touchdowns.

He was the 49ers’ second-round draft pick in 2011, and again, another injury led to Kaepernick’s rise. Starting quarterback Alex Smith suffered a concussion in November, and San Francisco Coach Jim Harbaugh named Kaepernick his permanent starter.

Ault said perhaps no team runs his innovation as well as the Redskins, whose offensive coordinator, Kyle Shanahan, took advantage of the Pistol’s creative possibilities.

The 49ers, though, have rekindled a marriage that began as an unlikely match in Reno, and Ault said he believes the Pistol and Kaepernick can win the Super Bowl together.

Ault stepped down from Nevada after the 2012 season, but he said he’d like to coach again. Perhaps his next job will be in the NFL. Ault knows new Philadelphia Eagles Coach Chip Kelly, though last week he said he hadn’t heard from Kelly and had carried on only casual dialogue about joining any NFL team.

Years later, sometimes he thinks back to those earliest months, when he believed most everyone was going home and telling their families about the wild-eyed coach with the strange idea.

“I can tell you, we went through that spring, and there were days that it looked ugly,” Ault said.

But “in my mind,” he added, “it made a lot of sense.”