Anatomy of the 49ers' quarterback switch
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NEW ORLEANS -- The day the 49ers traded up nine spots to select Colin Kaepernick with the No. 36 overall pick in the 2011 draft, the youngster was eager for the next stage of his life to begin.

Instead of waiting until the next morning to visit the 49ers' training facility in Santa Clara, Kaepernick and several family members made the 90-mile drive from Turlock that evening.

An excited and talkative -- yes, talkative -- Kaepernick met with the media. He was clearly the future of the 49ers. After all, the 49ers traded their second-, fourth-, and fifth-round selections to move up in the draft to select him. And Kaepernick did not even attempt to hide his enthusiasm.

"I think I'm going to come and work as hard as I can and compete for that starting spot," Kaepernick said. "When it comes down to it, that'll be coach (Jim) Harbaugh's decision, whether he feels I'm ready and whether he feels I'm the best quarterback for that. For me, I'm going to try to do my part and work hard."

Nineteen months later, Harbaugh made the controversial decision to elevate Kaepernick into the starting lineup ahead of veteran Alex Smith, who was playing the best football of his career. it was a risky call. But, ultimately, it appeared to be the correct decision.

After all, Kaepernick has made nine NFL starts. His 10th starting assignment will come Sunday against the Baltimore Ravens in Super Bowl XLVII.

Harbaugh anticipated making the call to Kaepernick at some point. It was only a matter of timing. Harbaugh seemingly had in his mind the kind of quarterback he wanted to lead his team upon agreeing on a five-year contract, $25 million contract in January 2011.

[RELATED: Ray Ratto -- Another gut-punch coming for Alex Smith?]

Two months later, Harbaugh spoke of the potential of eventual No. 1 overall pick Cam Newton, whom he described as "plutonium-grade raw material."

Harbaugh also had a high opinion of Kaepernick, a record-setting passer and runner at Nevada. Kaepernick was in the same mold of Newton. And in the same draft. But he was considered even more raw.

About a month before the draft, Harbaugh and general manager Trent Baalke made the drive to Reno from the 49ers' annual fund-raising event at Squaw Valley to hold a private session with Kaepernick.

While there, Harbaugh paced Kaepernick through a workout in which he made all the throws in the route tree. Afterward, Harbaugh challenged Kaepernick to some passing competitions. The former NFL quarterback and the future NFL quarterback hit it off immediately.

"I think the first thing that came to mind, No. 1, was the energy he brought," Kaepernick said. "He was running all over the place and throwing the football around. It was a competition to see who could throw the most perfect spirals to each other, to see who could be the most accurate throwing through the goal posts from different spots."

Harbaugh also scheduled Kaepernick to visit the 49ers practice facility for an official visit. But Harbaugh later deemed it unnecessary. He already knew he wanted to draft Kaepernick, if given the opportunity. And Harbaugh did not want to take the risk of telegraphing his move if word got out that the 49ers were bringing in Kaepernick for a visit. Offensive coordinator Greg Roman did not attend the workout in Reno. But Harbaugh returned with positive reports.

"We felt really good about him going in, and I think that just sealed the deal," Roman said.

In the early months of Harbaugh's tenure with the 49ers, he often spoke of what he believes are the main qualities of a success NFL quarterback.

"The No. 1 thing for a quarterback is athletic instincts," Harbaugh said.

With the lockout looming, Harbaugh developed a rapport with Smith, who would be a free agent after the lockout. Harbaugh often cited Smith's athletic instincts.

"The most touchdown passes are off of quarterbacks moving," Harbaugh said in September 2011, "whether they're scrambling (or) buying time in the pocket."

It's the same quality -- a quality that Bill Walsh cherished, as well -- that Harbaugh saw in Kaepernick, who combined a powerfully built 6-foot-3 frame with a strong throwing arm and exceptional speed.

[RELATED: Would 49ers be in Super Bowl with Alex Smith?]

Kaepernick was the first quarterback that Harbaugh added after coming to the 49ers as head coach. Smith assured Harbaugh that he would sign with the 49ers, but that would have to wait until the lockout ended in the summer. Smith would remain with the 49ers for his first year under Harbaugh on a one-year contract.

And Kaepernick immediately recognized the 49ers would be a "perfect situation."

"I fit coach Harbaugh's offense well, their style of play," Kaepernick said. "Just watching a little bit of Stanford and knowing Andrew Luck a little bit, a lot of things they do follow my skill set. They like a mobile quarterback. They like a quarterback who can do a lot of different things."

Kaepernick saw no significant playing time as a rookie. At practices, receivers and defensive backs privately said he lacked touch on his throws. He often unleashed difficult-to-handle fastballs on routes that demanded a little more finesse.

Even during training camp before this season, Kaepernick appeared raw and not ready to become a starter. At one point, several defensive starters playfully mocked him on the practice field for never throwing the ball. He appeared too eager to use his running ability to escape the pocket.

Smith, who was having the best season of his career, went down on Nov. 11 with a concussion. There was no telling how Kaepernick would perform in his first NFL start a week later against the Chicago Bears.

[RELATED: Alex Smith: 'I have my best football ahead of me']

"In practice, it's kind of hard to tell, especially in the game of football because everybody is not going full speed," 49ers receiver Michael Crabtree said. "It just happens in the game. He is a gamer. It's not something you can read. There is not body language that you can read at practice to know until you get to the field on Sunday."

It might not have been plutonium grade, but Kaepernick played exceptionally well and demonstrated boundless potential in leading the 49ers to victories over the Bears and the New Orleans Saints in his first road start.

And Harbaugh had a decision to make after Smith was medically cleared to return to action.

Team CEO Jed York had a brief exchange with Harbaugh the next week, he told Dave Feldman on "49ers Central."

"Just popping in to see how he's doing," York said, "and asking him, 'What's your gut?' And he said, 'My gut's Kap.' OK. You could argue it either way. He's the head coach. He has to live with the decisions he makes and I have to support him. And if you don't support your head coach, you should go find another one. I support Jim 100 percent."

Smith, who led the NFL in completion percentage and ranked among the leaders in passer rating, was crushed to find out he lost his starting job. After all, Smith was the quarterback on a team that went 13-3 the previous season and reached the NFC Championship Game. The 49ers were considered a strong contender for the Super Bowl with Smith at the controls.

"You state your case with your play," Smith said. "I feel like I've done that. I feel like the only thing I did to lose my job was get a concussion."

[RELATED: Kaepernick -- 'Pressure comes from lack of preparation']

Two months later, Smith is still the backup. And Kaepernick is the quarterback who has led the 49ers through the Green Bay Packers and Atlanta Falcons and into Super Bowl XLVII. And, in the process, Kaepernick has played so well that Harbaugh is no longer second-guessed.

Harbaugh said it was not part of the master plan to make the transition from Smith to Kaepernick this season. But when Kaepernick was given a chance to perform due to Smith's injury, his production could not be ignored.

Smith pointed out that he got his chance to become a starter at Utah when the incumbent, Brett Elliott, went down in 2003 with a broken wrist. So he knew it was possible he would not get his old job back.

"I knew there was an opportunity there (for Kaepernick), no question," Smith said. "You're letting the next guy step in and get an opportunity. I fully knew what Colin was potentially capable of. He came in and made the most of it. It's the nature of sports."

When training camp opened, Kaepernick was just trying to hold off veteran free-agent Josh Johnson for the backup job. Johnson was a notable signing because he appeared to have the advantage of playing for Harbaugh at the University of San Diego.

"It was hard work, and it was a competition," Kaepernick said. "I was trying to do everything I could to prove that I needed to be at least No. 2, and that I could go out and play."

And when there was an opportunity to move up the depth chart, Kaepernick was determined to never return to the role of the backup.

"It's a competitive situation," he said. "The NFL is a business and you have to take advantage of the opportunity when you have it. Alex is a great guy. I have nothing but great things to say about him, but at the same time you have to try and do what's best for you at the same time."

In his final full game, Smith completed 18 of 19 passes against the Arizona Cardinals and was named NFC Offensive Player of the Week. Smith was riding the hottest streak of his eight-year career when he was injured.

But after two starts, Harbaugh declared Kaepernick as the "hot hand" at quarterback. And, ultimately, Harbaugh made the call on which quarterback he believed had the greater chance of leading the 49ers to the Super Bowl.

"(We had) two quarterbacks that were playing extremely well," Harbaugh said. "We did what we thought was best for the team. We did what we thought would give us the best chance to win games."