49ers at crossroads after Jim Harbaugh tenure ends

SANTA CLARA, Calif. -- While coach Jim Harbaugh leaving the San Francisco 49ers was not unexpected, what it means for the franchise is more of a mystery.

The team must hire a head coach after four star-crossed seasons under the sometimes maniacal Harbaugh, a tenure that began with three straight NFC title games and a Super Bowl appearance but ended with an 8-8 season and missing the playoffs. The team and Harbaugh mutually agreed to part ways, the 49ers said in a statement released after the victory against Arizona on Sunday.

The player Harbaugh’s departure affects most is his hand-picked quarterback, Colin Kaepernick, who initially thrived under Harbaugh’s guidance but regressed this past season as the Niners moved from a power-running attack to more of a spread offense.

“Coach Harbaugh’s the coach that drafted me," Kaepernick said. "He’s the coach that chose to start me. He’s the coach that stood behind me through everything.

“He has been a huge part (of my career), but I’m playing football regardless. I’m the quarterback for the San Francisco 49ers, until they tell me different. So, I’m going to keep truckin’ on, be looking forward to finding out who they’re going to bring in and what we’re going to be working on…I’m going to continue to work.”

Whoever is hired as the next coach will assuredly have to either be an offensive-minded coach or bring in an offensive coordinator that will tailor the offense around Kaepernick's unique skills.

Yes, defensive line coach Jim Tomsula appears to be the clubhouse leader for the job, winning one game as an interim coach in 2010. He is a players’ coach, a familiar face and voice to the Niners’ front office. But he would have to hire an offensive coordinator familiar with the intricacies of the pistol offense to better use Kaepernick, who called Tomsula “a great guy.”

Other, more established offensive-minded coaches to keep an eye on, then, would be Cincinnati Bengals offensive coordinator Hue Jackson, who said he was interested in drafting Kaepernick when he was coach of the Oakland Raiders; Stanford coach David Shaw, who has said he’s content with his current gig and might not want to follow Harbaugh’s coaching footprints again; and a pair of old-school offensive 60-something minds in Mike Shanahan and Mike Holmgren.

The 49ers need to move on from the turbulent and, until this past season, wildly successful Harbaugh era, yet need as much continuity as possible to reclaim said success.

Moving on from the combative Harbaugh, who was far from the only heavy in the Silicon Valley soap opera, the 49ers in general -- and general manager Trent Baalke and CEO Jed York in particular -- need peace as they search for sustained success in their new $1.2 billion football palace in Levi’s Stadium. Sure, you could say it’s the house that Harbaugh built, but it’s one from which many stalwart 49ers players might quickly depart.

Consider that six key players are scheduled to become unrestricted free agents in running back Frank Gore, receiver Michael Crabtree, left guard Mike Iupati, linebacker Dan Skuta and cornerbacks Perrish Cox and Chris Culliver. Defensive end Justin Smith has hinted at retirement and the Niners will have to find a replacement for defensive end Ray McDonald, who was cut after being accused of sexual assault.

The departure of Harbaugh, who was 49-22-1 overall with the Niners, might affect free agents’ decisions about whether to re-sign.

This much is sure, though: The Niners will have a hard time finding someone like Harbaugh, who led the team out of mediocrity and back to the playoffs while becoming the face of the franchise.