Colin Kaepernick's Future Rests with Risk Tolerance of New 49ers Head Coach

The future feels fragile for the San Francisco 49ers and their marriage to quarterback Colin Kaepernick. But for the more optimistic among us it could be filled with hope and glowing rainbows if (another) pioneering offensive mind is brought in to whisper sweet quarterback nothings into Kaepernick’s ear.

There’s a split between those two extremes, which leads to something even more troubling when it involves the quarterback: uncertainty.

Parting ways with Jim Harbaugh will become increasingly confusing over time, and it is a move that reflects misaligned organizational priorities. But it’s also done and in the past now, with Harbaugh likely set to take up residence in Ann Arbor and the 49ers already moving on to the business of finding a new leader.

Kaepernick’s future is linked to that mystery coach, and the fluctuating levels of risk tolerance both in the front office and on the field. How long will a new coach be comfortable tying himself to a quarterback who’s wildly inconsistent as a passer? And how long will Kaepernick’s contract remain financially justifiable?

The second question can be answered. The first one? Well, it depends on the hiring direction.

Kaepernick halted his regression when games became meaningless over the final two weeks this season. Of his 639 total rushing yards, 214 yards (more than a third) came during that two-game span.

But if a regression resumes next season it’s not difficult to anticipate a new head coach wanting to sever the connection between his employment status and Kaepernick. That end will be dictated by performance, but also by money and Kaepernick’s steadily rising paycheck.

We can’t have separate conversations about Kaepernick and his future under a new coach, one focusing on his play and the other his compensation. The two are bound together, with the latter arguably more important than the former in this case.

Regardless of who’s hired, there would be more patience without a sharp and steady rise in Kaepernick’s cap hit. But as we see from his salary structure below (via Spotrac), whoever inherits the 49ers’ sideline has at best a two-year window to decide if the quarterback should be jettisoned.

Year	Base Salary	Cap hit
2014	$645,000	$3,767,444
2015	$12.4 million	$17.266 million
2016	$13.9 million	$18.766 million
2017	$16.5 million	$21.366 million

That’s a portion of the cleverly designed contract extension Kaepernick signed last June. It’s an agreement filled with more fluffy stuff than your average county fair food court, and one that keeps Kaepernick under team control for seven seasons while allowing the 49ers to cut him at any time with only a minimal dead money sacrifice.

Valued at a total of $126 million, the contract contains only $13 million in truly guaranteed money. Most of the contract functions under a pay-as-you-go structure, with his base salary for each season between 2014 and 2017 becoming guaranteed as of April 1.

None of this is fresh or shocking information, and you’ll recall the full breakdown from ProFootballTalk shortly after Kaepernick signed his shiny new deal. I’m rehashing it here because a new head coach comes with a new direction. And if he doesn’t want that direction to include Kaepernick, there’s an exit sign hanging over 2017.

A change at quarterback won’t be immediate. The 2015 quarterback draft class takes a steep plunge after Jameis Winston and Marcus Mariota, and free agency at the position is an annual cesspool of suck.

So possibly by default the Kaepernick experiment will continue for one more season at minimum. And then likely another in 2016, too, because his cap hit increase is minimal. But in 2017 the contract pain train accelerates.

That's when Kaepernick’s cap hit takes a right-angled turn upwards, finally finishing at $21.4 million. Kaepernick will have a higher cap value than Green Bay Packers quarterback Aaron Rodgers, and he’ll be only slightly behind the Cowboys’ Tony Romo and the Lions’ Matthew Stafford (all per Spotrac).

Overall Kaepernick is currently scheduled to be the fifth-highest-valued quarterback against the cap in 2017. Maybe at that point questions about his future will subside, and we’ll all be able to have a hearty chuckle about those strange times in late 2014.

That’s the hope, of course, but an emergency exit still exists for a new head coach who may not have any previous ties to Kaepernick or the organization.

Immediately after Harbaugh’s move onward there was talk of an internal promotion. That’s still a possibility, and both current defensive line coach Jim Tomsula and defensive coordinator Vic Fangio will receive consideration.

Externally Browns offensive coordinator Kyle Shanahan will be among those considered, according to a report from Mary Kay Cabot of the Cleveland Plain Dealer. He’s familiar with the riddle of the running quarterback after working with Robert Griffin III in Washington (which included Griffin's 2012 Offensive Rookie of the Year season).

But what if the 49ers go against expectations and once again favor a well-established head coach with a history of not only winning, but winning championships? Even if that history came in the far distant past when we were all busy learning how to raise the roof.

That head coach could be Kyle’s father, which would be a curious relationship for all involved, including Kaepernick. Bleacher Report’s Jason Cole has heard from multiple sources there’s interest in Mike Shanahan.

The mere interest in Shanahan—who last won a playoff game in 1998—shows hiring a first-time head coach who will bow to authority isn’t guaranteed.

The fallout from Harbaugh’s exit and his lost battle for control to general manager Trent Baalke and CEO Jed York leads to the assumption a more puppet-like coach will be the 49ers’ next target. And that may still be the case, with ESPN.com’s Josina Anderson reporting interviews have also been requested with Arizona Cardinals defensive coordinator Todd Bowles and Seattle Seahawks defensive coordinator Dan Quinn.

But a seasoned head coach would have a better feel for the quarterback who best suits his approach and management style. He could also have even less patience with Kaepernick, who’s still often more athlete than quarterback, and more runner than passer.

The drain-swirling conclusion of the Kaepernick experience isn’t difficult to see by the end of that two-year salary window regardless of who’s hired. It just might be accelerated with a veteran coach who’s more stubborn and knows he’s likely been given his last opportunity in the top job.

A quarterback who often lacks touch and the required vision to work through his reads is difficult to tolerate. That challenge grows when the quarterback is limited primarily to one offensive approach (read-option, and plenty of movement) during times of success.

That’s the fundamental nature of Kaepernick as a quarterback. He may still improve over time, but he’ll likely never be at ease when asked to become a conventional pocket passer. His future will be determined by whether a new coach can do more than just accept that reality.

The entire Kaepernick package needs to be embraced. If it’s not then change and a reboot looms in the not-so-distant future.