Is 49ers’ Smith the new Captain Comeback?

SAN FRANCISCO — Alex Smith was stuck in San Francisco. Not a bad place to be for a summer, but after six miserable seasons as the 49ers’ quarterback, it was time to get out.

Smith, the first overall pick of the 2005 draft, was considered a bust, especially compared to the other celebrated first-round pick of that draft, Green Bay’s Aaron Rodgers, the 24th selection, who had just led the Packers to a Super Bowl championship.

Unfortunately for Smith, an unrestricted free agent, the NFL lockout froze player movement. It turned out the labor strife saved his career.

Smith met with new head coach Jim Harbaugh during the one day the lockout was temporarily lifted and picked up the club’s new playbook. Smith organized his teammates for workouts known as Camp Alex at San Jose State and decided to sign a one-year deal with San Francisco when the lockout ended.

He made a real connection with Harbaugh, who was a former quarterback and first-round draft pick himself. Smith was comfortable in Harbaugh’s West Coast offense, and the two took off together.

Smith threw for a career-best 3,144 yards and 17 touchdowns with only five interceptions — breaking the club record of seven by Hall of Famer Steve Young for the fewest in 49ers history. And Harbaugh directed the 49ers to a 13-3 record, a playoff win over New Orleans and a spot in today’s NFC championship game against the New York Giants.

Until this season, Smith had yet to play for a 49ers team with a winning record, and he threw 51 touchdown passes and 53 interceptions in six frustrating seasons.

It would have been easy for Smith to want to say “I told you so” to his two previous 49ers head coaches, five offensive coordinators and all those fans who wanted to run him out of town because he wasn’t the next Young or Joe Montana.

“I think if we win this game and go to the Super Bowl it will say it in itself,” Smith said. “I’m not thinking about that right now. I really feel like winning games as a quarterback this time of year speaks for itself. That’s how you do your talking.

“I had a great season up to this point, but like I said, it just got us a ticket to the dance like everybody else.”

Smith was at his best in the 49ers’ stirring 36-32 win over New Orleans. He threw for 299 yards and three touchdowns and shocked the Saints with his 28-yard bootleg for a go-ahead touchdown with 2:11 to play. When the Saints regained the lead 44 seconds later, Smith cooly drove the 49ers downfield for the game-winning touchdown, a14-yard laser to tight end Vernon Davis with 9 seconds left.

It was Smith’s sixth fourth-quarter comeback of the season, replicating the reputation of Harbaugh, who was known as Captain Comeback during his playing career.

And it was a defining performance for Smith, 27, who has taken the 49ers to their first NFC championship game since the days of Hall of Famers Young and Montana.

“Hopefully, he’s got his game-manager label or whatever that label is off of him,” said defensive lineman Justin Smith, a former Mizzou star.

49ers general manager Trent Baalke, who will have to negotiate a new contract with Smith after this season, said: “I don’t know if I’ve ever been happier for an individual than I was for Alex to come through in those moments like he did and to have the type of game he had.

“And to just see the joy on his face … if anyone deserved it, Alex deserved it.”

Much of Smith’s mastery of the 49ers’offense can be traced to those summer workouts. He asked his uncle and former Michigan State coach John L. Smith for tips about running a practice, so when the lockout ended, the players were ready to go despite a late start for the coaching staff.

“We were there all offseason, obviously working out and conditioning and running and doing that,” Smith said. “There was a little bit of familiarity there with the guys on what kind of language we’d be speaking, the verbiage, what some things meant. So, it was like the first coat of paint I guess, the primer, just kind of the first taste of it and then obviously the bulk of it came in camp and during the season.”

Harbaugh gets plenty of credit for the revival of Smith’s career as well.

“The biggest thing Jim did was give this kid a belief that he could be a good player, and he could win and he was wanted,” said Hall of Fame quarterback and Fox NFL analyst Troy Aikman. “I don’t know he had really felt that he was wanted within that organization.

“You look at the talent they’ve had there for now a few years … they run the ball well, they play good defense, they’ve got good special teams, they give the ball back to their offense in favorable situations and Harbaugh was able to impress upon him how they were going to win. As the season has progressed, he’s gotten more and more confident in his abilities and he’s continued to play better.”

It was that confidence that enabled Smith to take execute the bootleg for the touchdown run. And to thread the game-winning pass to Davis between two defenders rather than check down to a running back and settle for a game-tying field goal.

“For me the quarterback’s job is obviously to distribute the football, but there’s so many of those plays in the game … you don’t know when they’re coming, but you’ve got to make the play,” Smith said. “Sometimes you’ve got to do the little things to help give your team a chance to win.

“You talk about that winning edge, whatever it is with the quarterback, those are the things I look to. Some guys do it with their legs. Some guys just do it distributing the football and making accurate throws. Over the course of the game, over those 60, 70, 80 plays … you have no idea which handful it’s going to come down to that are really going to change the game. But the fact that you do it each play, you’re doing those little things and really kind of giving you that edge.”