Starter in season opener: Alex Smith
Starter in season finale (Super Bowl): Colin Kaepernick
Unit MVP: Colin Kaepernick
Top newcomer: None
Most improved: Colin Kaepernick
Biggest disappointment: None
Biggest surprise: Colin Kaepernick
On the rise: Colin Kaepernick
On the slide: None
Overachiever: Alex Smith
Final unit season grade: A
It was a year of change for the 49ers at quarterback – the kind of good change that the Niners haven't seen since the team had Joe Montana and Steve Young vying against each other at the position a quarter-century ago. This time it was Colin Kaepernick and Alex Smith who would give the 49ers two effective, productive signal-callers to lead the way and ultimately create a mini-controversy that was swift in its decisive conclusion as Kaepernick wowed the NFL in general and the team and its fans in particular with a stunning emergence near midseason to overtake Smith for the job. Until that point, Smith was on course toward a career season, leading the NFL with a 70.0 completion percentage and ranking among the NFL leaders with a 104.1 passer rating when he sustained a concussion midway through the first half of San Francisco's Nov. 11 game against St. Louis. Though he practiced each day the following week, Smith was not cleared to play for the team's Monday night showcase game against Chicago on Nov. 19, giving Kaepernick an opportunity he literally ran with to gain a stranglehold as the starter and develop rapidly into one of the league's most exciting young QBs. Smith never played another significant snap as Kaepernick went 5-2 down the stretch, including decisive road victories at New Orleans and New England, while establishing himself as a unique dual threat at the position with his rocket arm and breakaway running ability. Kaepernick's aura and legend grew in the playoffs with his record-setting performance against Green Bay in the divisional round and his comeback-leading efforts that erased a 17-0 deficit at Atlanta in the NFC Championship Game and almost erased a 22-point deficit against Baltimore in the Super Bowl. It made a lot of people forget that Smith was seemingly gaining momentum toward his first Pro Bowl appearance had he not taken that fateful hit to the back of his helmet while sliding to the ground 12 weeks earlier against the Rams.
Top individual performance
There were several noteworthy performances here, including Smith's record-setting night in an Oct. 29 victory at Arizona, when he completed 18 of 19 passes for 232 yards and three TDs in a 24-3 victory, setting a new NFL record for highest completion percentage in a game for a quarterback with a minimum of 15 attempts. That was one of four times in his nine 2012 starts that Smith finished with a passer rating of 125.6 or better. But for sheer impact on a significant stage, nothing could touch Kaepernick's breakout performance in his playoff debut against Green Bay, when the second-year QB set a NFL playoff record for most rushing yards by a quarterback – Kaepernick's 181 yards rushing actually were the most ever by a QB in any NFL game – and also threw for 263 yards to spark a 45-31 rout of the Packers. In setting a new franchise single-game playoff rushing record, Kaepernick became just the third QB in NFL history to both rush and throw for two touchdowns in a playoff game, and his scintillating 56-yard scoring sprint in the third quarter – the longest run ever by a 49ers quarterback – broke a 24-24 tie and put the 49ers ahead to stay. Kaepernick's 437 net yards of total offense accounted for 75.5 percent of San Francisco's 579 total yards, a new franchise playoff record.
The switch to Kaepernick at quarterback transformed San Francisco's offense into a varied attack that featured the constant threat of a running quarterback out of a Pistol formation that featured a stacked backfield with Kaepernick and gave the young QB a read/option alternative out of several alignments. After taking over as the starter, Kaepernick had at least six carries in eight of his final 11 games including the postseason, and he rushed for 27 or more yards in a game 10 times during the season and 50 or more six times. Despite starting just seven games, Kaepernick finished fourth in the NFL in rushing among quarterbacks with 415 yards behind full-season starters Robert Griffin III, Cam Newton and Russell Wilson.
Don't expect this one to play out like Montana/Young, where it took Young several seasons after emerging as a viable threat to overtake the accomplished veteran as the regular starter and finally push him out of San Francisco. Kaepernick appears to have done that to Smith in just half a season. At age 25, Kaepernick figures to only get better, and his physical ability and potential became vividly evident as he led the 49ers down the stretch and got them within five yards of winning the Super Bowl. The 49ers will owe Smith a guaranteed $7.5 million if he still is on the roster on April 1, so a trade or release of the 2005 No. 1 overall draft pick could soon be coming. That would leave the 49ers needing to establish a legitimate backup behind Kaepernick, which could by Tolzien, though the team would figure to bring in an experienced veteran to compete for that job. Though the 49ers could afford it because Kaepernick still is working on his rookie contract, the prospect of having Smith on the bench as Kaepernick's backup – after what Smith has accomplished with the team over the past two seasons – is unlikely to sit well with many on the team, Smith included.