Ailene Voisin

Opinion: Harbaugh will be fine, but what about Kaepernick?

What will become of the 49ers’ Colin Kaepernick if coach and mentor Jim Harbaugh leaves? Kaepernick’s decision-making and ability to become a pocket passer have been questioned.
What will become of the 49ers’ Colin Kaepernick if coach and mentor Jim Harbaugh leaves? Kaepernick’s decision-making and ability to become a pocket passer have been questioned. Sacramento Bee file

If the dysfunction and discord in the 49ers’ organization is beyond repair – as reasonably can be assumed, given the recent tweets by the team CEO, even more recent tweets by the general manager’s daughter and the chronic communication breakdowns that have gnawed at Levi’s Stadium throughout its inaugural season, coupled with the team’s tenuous playoff prospects – the Jim Harbaugh Era is soon to become history.

But don’t feel too bad for Harbaugh. He will take his leave amid three exceptional seasons and a cloud of dust. NFL and college suitors will knock on his door before he can toss his khakis, baseball caps and 49ers sweaters into the washing machine for a final time.

Colin Kaepernick is the one to worry about, because while Harbaugh has a history of developing quarterbacks Josh Johnson (University of San Diego) and Andrew Luck (Stanford), reviving the death-rattling career of former No. 1 overall draft pick Alex Smith, and unleashing a once-electrifying standout from the University of Nevada, the coach’s presumed departure will be like abandoning the groom at the altar.

Brady-Belichick, Rodgers-McCarthy, Brees-Payton, etc., Harbaugh-Kaepernick is not. But if not exactly love at first sight, theirs was an instant infatuation and one helluva short romance. In mostly happier times, Harbaugh spoke often of his original Wolf Pack scouting mission, of being impressed with the quarterback’s size (6-foot-4) and length, his fastball of an arm and sprinter’s speed, along with an almost freaky escapability and playmaking ability. His effusive praise of Kaepernick’s work ethic and competitive nature came a little later, or right about the time he ditched Smith – who had been sidelined with a concussion nine games into Kaepernick’s second season – and never looked back.

And now? In the what-have-you-done-for-me-lately chapter? Well, let’s see. Harbaugh selected the tuxedo, wrote Kaepernick’s lines, escorted him down the aisle and guided him to three NFC Championship Games and one Super Bowl appearance, yet seems poised to depart while his fourth-year quarterback stands up there, dazed and confused, confronting the first mini-crisis of his professional career.

The reasons the 49ers haven’t evolved into this season’s darlings – they instead take a 7-5 record into Sunday’s meeting against the Raiders – extend far beyond Kaepernick’s individual struggles, of course. They include injuries to key players; legal issues and suspensions; simmering workplace tension between Harbaugh and the front office; and a philosophical, at times confusing, shift away from the power running game anchored by Frank Gore and toward multiple wide receiver sets. Complicating the shift, possession receivers Michael Crabtree and Anquan Boldin have had trouble gaining separation and dropped an inordinate number of catchable passes, while tight end Vernon Davis, once Kaepernick’s favorite deep target, has been ailing or invisible.

All of which sort of suggests 2014 isn’t the 49ers’ year. But there’s more. While players heal, rosters are bolstered by trades and drafts, and even some of the most accomplished coaches change ZIP codes, none of this solves the Kaepernick conundrum.

The 49ers have taken away his shoes – clearly discouraged him from those daring, read-option, yard-devouring scrambles so common in his first few years – though perhaps not without reason. Kaepernick, who signed a hefty multiyear contract during the offseason, revealed earlier this season that he played part of last season with a foot injury; the 49ers need him healthy, emotionally and physically.

But repeatedly in recent weeks, NFL experts including former 49ers Steve Young and Trent Dilfer have questioned Kaepernick’s decision-making and ability to become more of a pocket passer, and loudly intimated that he has regressed. Last week, onetime Raiders standout Rich Gannon offered these thoughts to the San Francisco Chronicle: “The quarterback has been really inconsistent. He’s missing too many throws. The accuracy is not there. He just has to be better in the pocket, better at decision-making, all those things.”

An attitude adjustment is also advisable, and not all that painful, either. Kaepernick’s increasingly surly, almost rude demeanor during his one mandatory midweek news conference is unseemly, though not unprecedented. Marshawn Lynch is no interview prize, either, and for that matter, virtually every pro sports league has tried – and often failed – to coax cooperation out of certain recalcitrant players. (Christian Laettner, Kevin Brown and Moses Malone rank near the top of my list.)

Conversely, the Giants’ clubhouse presided over by Bruce Bochy consistently earns positive reviews. And note the reference to Bochy. Legacies and leadership entail a multitude of elements. Should Harbaugh in fact walk out the door when the season ends, he should first pull Kaepernick aside and suggest the young quarterback skip the interview clips featuring Barry Bonds and instead study those featuring Peyton Manning, Aaron Rodgers, Drew Brees, Tony Romo and the oft-maligned Smith.

What was that not-so-old 49ers line? Who has it better than us? Well, who had it worse than Smith? Yet few athletes could have handled adversity and painfully awkward situations with more grace and dignity. Grace. Dignity. Class. Once, not so long ago, those were the 49ers.

Call The Bee’s Ailene Voisin, (916) 321-1208.