Colin KaepernickThe athletic and versatile playmaker began his second season with the 49ers getting occasional bit cameo roles within the offense during the first half of the year. He ended the season as one of the NFL's new sensations and rising forces at the position after taking the 49ers within five yards of winning the Super Bowl. Kaepernick displayed his athleticism and ability to make plays mostly by running the football when he got on the field for sporadic snaps throughout the season's first eight games – three of which he did not play in at all – including a 7-yard touchdown run against the Jets in Week 4, the first of his career and first of several to come later in the season. Kaepernick's big break came in Week 10 after the 49ers returned from their bye week and he took over behind center after Alex Smith sustained a concussion midway through the first half against the Rams. After a slow start as the every-down QB, Kaepernick directed a comeback that salvaged a tie against St. Louis, then his big breakout came the next week on the Monday night stage against Chicago, when in his first NFL start Kaepernick stunned the Bears for 243 yards and two TDs passing. Kaepernick rushed for a touchdown and passed for another the next week to lead a comeback victory over New Orleans, and he was on his way to securing his role as the starter. Kaepernick threw a career-high four touchdown passes to spark a pivotal 41-34 victory at New England in Week 15, then threw for a career-high 276 yards in the season finale against Arizona. But Kaepernick truly saved his best for the playoffs, when he passed for 263 yards and two TDs and rushed for 181 yards – a NFL record for a quarterback – and two more scores to spark a 45-31 divisional victory over Green Bay. He then led the 49ers back from a 17-0 deficit to beat Atlanta in the NFC Championship Game, then almost led the Niners all the way back from a 22-point deficit against Baltimore in the Super Bowl, where Kaepernick threw for 302 yards and rushed for 62 more. Kaepernick finished the season with a 98.3 passer rating and 415 yards rushing – fourth among NFL quarterbacks – and with his totals projected over a full 16-game season, Kap would have finished with more than 3,800 yards passing, 800 yards rushing and 30 combined touchdowns.
Final season grade: A
Alex SmithWho would ever have thought the eighth-year veteran would be leading the NFL in completion percentage and rank among the league leaders in passer rating at midseason only to lose his starting job … without doing anything to lose it besides sustaining a concussion that forced him to the sidelines for two games? That was that fate that befell Smith in what was developing as a season that truly established him as a legitimate winning NFL quarterback. Smith built on his breakout 2011 season and was putting together a Pro Bowl-season resume before he went scrambling out of the pocket on a first-down play late in the first quarter of a Week 10 game against St. Louis after the 49ers returned from their bye week. As he went sliding to the ground after a 4-yard gain, Smith was hit in the back of the helmet by Rams linebacker Jo-Lonn Dunbar. Smith remained in the game for 11 more plays and completed a 78-yard touchdown drive with a 14-yard scoring pass to Michael Crabtree before being pulled with concussion-like symptoms. It would be the last significant snap Smith would take the remainder of the season. The 49ers kept him out as a precaution the next two weeks, then he officially lost his job when Kaepernick was named the starter going forward in December. But Smith did nothing to lose the job besides play the best football of his career. In his nine starts, Smith had a passer rating of 100 or better in five of them and 125.6 or better in four, and he had a 156.2 rating to go along with 303 yards passing and 49 yards rushing as the 49ers became the first team in NFL history to record both 300 yards passing and 300 yards rushing in a Week 5 blowout of Buffalo. Smith also set a NFL record for highest completion percentage in a game for a QB with a minimum of 15 attempts, completing 18 of 19 passes for 232 yards and three TDs in a Week 8 rout over Arizona, after which Smith received the first NFC Offensive Player of the Week award of his career. Smith completed 7 of 8 passes for 72 yards and a 143.8 passer rating the next game before being hurt against St. Louis, then lost his starting job, perhaps forever. With Kaepernick apparently entrenched now as the team's QB, Smith's future with the team is cloudy and he could be traded or released within the next month. His 2012 season, however, was clearly the best of his career before it was ended prematurely.
Final season grade: A
Scott TolzienThe second-year veteran played well enough in the exhibition season to beat out free-agent veteran newcomer Josh Johnson and retain his job as San Francisco's No. 3 quarterback, though his 41.9 passer rating during the preseason was the worst of San Francisco's four QBs. That low rating was mostly a product of Tolzien's two interceptions – the only picks thrown by San Francisco QBs during the preseason – as he displayed some ability to lead the offense and produce from the pocket while completing 18 of 34 passes for 165 yards. For the second consecutive year, Tolzien did not play in a game during the regular season or playoffs, but he was active for games in Week 2, 11 and 15. Tolzien continued to perform as a capable practice player during the season and gave San Francisco's defense strong looks running the scout offense. Whether he is ready to take the quantum leap from that to backup status behind Kaepernick will be determined by his progress in the upcoming months.
Final season grade: B