Examining the 49ers Quarterback Controversy

Alex Smith is losing his starting spot to challenger Colin Kaepernick, and he may never get it back.

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Dan Anderson / ZUMAPRESS.com

Colin Kaepernick of the San Francisco 49ers walks through the field after playing the New Orleans Saints in New Orleans on Nov. 25, 2012.

On paper, the San Francisco 49ers quarterback battle that incumbent Alex Smith and challenger Colin Kaepernick have been waging since Smith sustained a concussion two weeks ago is almost entirely incomprehensible.

Smith is a seven-year veteran and former No. 1 overall pick who ranked third in the NFL in passer rating (104.1) and led the league in completion percentage (70%) at the time of his injury. Only three other quarterbacks in the last 30 years have finished the regular season with a completion percentage above 70%: Joe Montana, Steve Young and Drew Brees. The first two are 49ers legends who have already been enshrined in Canton, and the third is headed there as soon as his remarkable career ends.

Plus, Smith has won 20 of his last 25 starts and led the Niners to the NFC championship game last season. In that game, he threw two touchdowns, no interceptions and came within a pair of Kyle Williams fumbles of reaching Super Bowl XLVI. This is not the resume of someone who seems in jeopardy of losing his job.

Especially when his backup is a sophomore quarterback who was drafted in the middle of the second round and was better known for making plays with his legs than with his arm at Nevada.

And yet somehow, Smith’s concussion opened the door for Kaepernick. It’s largely because, in spite of his recent success and impressive numbers this season, Smith has always been seen as a competent game-manager at best. Though a No. 1 overall pick in 2005, Smith was never considered dynamic and has always had to fight—on more than one occasion, unsuccessfully—to hold on to his starting job.

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As recently as this past summer, 49ers head coach Jim Harbaugh was wooing Peyton Manning and Smith seemed primed to receive little more than a ‘thank you’ on his way out of the Bay Area. Of course, Manning opted to sign with Denver and Smith returned to San Francisco, the only franchise he’s ever known. More importantly, he returned to the only system—which Harbaugh implemented upon his arrival last season—that has enabled Smith to achieve any level of sustained success.

After falling short against the Giants in the NFC Championship game last January, however, Harbaugh and offensive coordinator Greg Roman began to search for more dynamic offensive weapons. Despite losing out in the Manning Sweepstakes, Harbaugh still signed Giants castoff Mario Manningham and future Hall-of-Famer Randy Moss. Over the course of the nine games that Smith started, however, the pair combined for just 552 yards on 51 catches. In fact, their largest impact was stretching the field to open up the running game and short-to-mid-range passes.

Though the offensive had not reached the level of explosiveness that Harbaugh and Roman had sought, San Francisco—with a couple notable exceptions—was winning and Smith was improving upon his impressive 2011 campaign. And yet, Kaepernick was just too alluring for Harbaugh. In addition to being a gifted scrambler, Kaepernick’s arm is a cannon. So if Harbaugh and Roman wanted to feed opposing defenses a steady diet of long passing plays, Kaepernick was well-suited for the task.

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On October 14, the Niners were struggling against the Giants. Down 10-3 and with Alex Smith already having been intercepted once, Harbaugh brought in Kaepernick in the final minute of the first half. The second-year quarterback—who up to this point had only attempted two passes all season—promptly fired a 36-yard strike to Manningham on his first throw. With Smith struggling (he would finish with no touchdowns and three picks), Harbaugh went back to Kaepernick several times in the second half. The Nevada grad finished the game four of seven for 82 yards.

Kaepernick didn’t make a throw the next week against the Seahawks, but when the Rams knocked Smith out of the game on November 11, Kaepernick came on and finished with 117 yards in the air and 66 more on the ground. Then, with Smith still suffering from concussion symptoms, Kaepernick led a 32-7 dismantling of the vaunted Bears defense on November 19, completing nearly 70% of his passes and throwing for two touchdown and no interceptions. When asked after the game who would start against the Saints six days later, Harbaugh said the Niners “usually tend to go with the guy with the hot hand.” And that’s how you start a quarterback controversy.

There’s really no precedent in the NFL—at least in recent memory—for what’s happening right now in San Francisco.  A successful quarterback, coming off a 13-3 campaign and having the best season of his career, being so rapidly and thoroughly supplanted by a largely unheralded backup. Even though Drew Bledsoe had compiled some impressive stats before a similarly unproven Tom Brady replaced him in New England, Bledsoe was coming off a 5-11 season in 2000, and a 0-2 start in 2001, before he got hurt and lost his job.

Much of Harbaugh’s approach could be explained by one simple fact: he wants Kaepernick to be QB1. In spite of Smith’s impressive campaign, it’s an understandable desire. Harbaugh understands recent football history: under center for every Super Bowl champion team for the last nine years, there’s been a so-called ‘elite’ quarterback. Tom Brady, Ben Roethlisberger, Peyton Manning, Eli Manning, Drew Brees and Aaron Rodgers. Even accounting for his recent success, Alex Smith just doesn’t quite fit into that group.

Of course, Colin Kaepernick doesn’t either. Not yet anyway. But someday—perhaps very soon—he might. At the least, Kaepernick gives Harbaugh the opportunity to run the offense he’s been yearning to run since leaving Stanford and Next Big Thing Andrew Luck—an offense he seems to believe is necessary for the 49ers to realize their full potential.

Harbaugh is hoping that Kaepernick can push San Francisco over the edge and into the Super Bowl. So far, the gamble looks pretty good.