San Francisco 49ers

Ron Agostini on 49ers: Kaepernick will miss the coach who always had his back

San Francisco 49ers head coach Jim Harbaugh, left, stands next to quarterback Colin Kaepernick (7) against the Arizona Cardinals during the fourth quarter of an NFL football game in Santa Clara, Calif., Sunday, Dec. 28, 2014.
San Francisco 49ers head coach Jim Harbaugh, left, stands next to quarterback Colin Kaepernick (7) against the Arizona Cardinals during the fourth quarter of an NFL football game in Santa Clara, Calif., Sunday, Dec. 28, 2014. AP

SANTA CLARA – No one will miss Jim Harbaugh more than Colin Kaepernick.

Frank Gore might place a respectable second, but Kaepernick never will enjoy a better coach-to-quarterback relationship.

Harbaugh, he of the “mutual parting” Sunday from the 49ers, caught Kaepernick’s pregame warmup passes, pounded on his man’s shoulder pads and praised him as “great with a capital G” when such fluff was unwarranted. If he ever criticized the man from Turlock, it’s not been recorded.

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

Talk about “mutual decision”: Harbaugh and Kaepernick were virtually attached at the hip. Harbaugh traveled to Nevada and personally worked out the prospect, then sweet-talked the front office into drafting him in the second round.

Harbaugh promoted Kaepernick over the injured Alex Smith during the 2012 season. Simply, the coach pushed his chips to the middle of the table for the uber-athlete from Pitman High. For better or worse, Kaepernick was Harbaugh’s man.

For his part, Kaepernick came within one completed pass of winning a Super Bowl for the black-shirt-and-khakis leader who bet on him. Whether or not the QB was ready for that moment in New Orleans, he’ll be forever appreciative of the chance Harbaugh gave him. Kaepernick delivered four playoff victories and 29 of Harbaugh’s 49 overall wins which, by the way, is one perfect stat.

I suspect they’ll be friends for life.

See, Harbaugh, a former quarterback himself, understood what worked for him. He loved Bo Schembechler, his coach at Michigan, no doubt his next address. Both believed in the importance of a tight end, a fullback and a happy quarterback.

As Kaepernick, Gore and the 49ers reached the never-never land of 8-8 with a 20-17 win over the Arizona Cardinals, I pondered Kaepernick’s football world after Sunday. I suspect it will change a lot.

Everything – his progress, mood and M.O. on the field – will be affected by Harbaugh’s successor. Can Kaepernick lean on his next boss like he trusted Harbaugh? Or will the new coach dress him down in public like Mike Nolan did with Smith?

Who’s to say the future coach will hang his future win-loss record on a so-called “running quarterback” who mixes pocket-presence problems with dazzling physical skills?

It’s become trendy to say Kaepernick has regressed through this rocky season, and at least part of that argument is fair. Also true is the fact that everything around him – line, receivers, scheme, etc. – failed. He was sacked 52 times, the most for any NFL quarterback. That the defense downsized to a MASH unit cannot be blamed on the quarterback.

Still, Kaepernick’s six-year, $126 million contract is structured in a way that the 49ers, in any given year, can move on from him. Think about it: Could Kaepernick be leaving through the same door still swinging via Harbaugh’s departure? Two words – Blaine Gabbert – should end such conjecture. But all things are possible in the NFL. Kaepernick may have been auditioning for his next boss against the Cardinals, for all we know.

“(Harbaugh) has been a huge part, but I’m playing football regardless,” Kaepernick said. “I’m the quarterback for the San Francisco 49ers until they tell me something different. So I’m going to keep trucking on.”

That we expected Harbaugh’s farewell doesn’t make it any less of a gaffe. The 49ers just chased a guy who gave them three NFC Championship Games and a Super Bowl in four seasons. Mutual or not, it’s incredibly foolhardy in such a dog-eat-dog league.

Harbaugh may have been a pain to CEO Jed York and General Manager Trent Baalke. I doubt they’ll find a better coach. Perhaps the front office will be more at peace with a yes man who goes 6-10.

As for Kaepernick, he’s considering the hiring of a quarterback guru during the offseason. Tom Brady, among others, have benefited from such a move. If Kaepernick’s flaws were exposed in 2014, his work rate – which is manic – remained the same.

I’m not sure he’ll again have in his corner someone like Harbaugh, who was the first to defend him during that unsavory episode earlier this year in Miami. Harbaugh had Kaepernick’s back on the field, off the field and everywhere in between.

Surely as the 49ers watch the upcoming playoffs on TV, they won’t forget the coach who revived the franchise. Bank on it: Kaepernick will repay Harbaugh down the road. He’ll go anywhere for him.

Well, almost.

“I’ll always be a fan of coach Harbaugh,” Kaepernick said. “Not too sure about (rooting for) Michigan, though.”

Bee staff writer Ron Agostini can be reached at ragostini@modbee.com or (209) 578-2302. Follow him on Twitter @ModBeeSports.

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